Contacts of the helix formed by residues 3165 - 3186 (chain A) in PDB entry 3CMT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY3165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2199A ILE* 4.2 6.0 - - - +
3163A HIS 3.2 2.2 + - - -
3164A MET* 1.3 69.7 - - - +
3166A LEU* 1.3 57.8 - - - +
3167A ALA 3.5 2.5 - - - -
3168A ALA* 3.6 7.2 - - - +
3169A ARG* 2.9 38.6 + - - +
1009B C 4.3 13.2 + - - -
1010B T 4.3 24.3 + - - -
1011B T 4.9 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3123A GLU* 4.7 8.1 - - - +
3151A PRO* 3.8 29.8 - - + -
3153A ALA* 3.8 25.4 - - + -
3163A HIS* 3.1 35.6 + - + +
3164A MET 2.9 2.8 + - - -
3165A GLY* 1.3 73.4 - - - +
3167A ALA* 1.3 61.5 - - - +
3169A ARG* 3.2 24.6 + - + +
3170A MET* 2.8 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3149A LEU 4.8 2.9 - - - +
3151A PRO* 3.8 26.8 - - + +
3163A HIS 4.9 0.2 + - - -
3166A LEU* 1.3 79.2 - - - +
3168A ALA* 1.3 58.3 + - - +
3170A MET* 3.3 10.7 + - + +
3171A MET* 2.9 34.7 + - + +
3210A THR* 6.5 0.9 - - + -
3211A GLY* 4.8 7.4 - - - -
4176A ARG* 4.9 10.8 - - - +
1011B T 3.9 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3165A GLY 3.5 7.4 + - - +
3166A LEU 3.2 0.4 - - - -
3167A ALA* 1.3 80.0 - - - +
3169A ARG* 1.3 56.5 + - - +
3171A MET* 3.3 3.1 + - - +
3172A SER* 2.9 29.5 + - - -
3211A GLY 4.0 11.5 - - - +
3212A GLY* 3.8 6.9 - - - -
3214A ALA* 5.1 1.2 - - - +
1009B C 3.4 23.7 - - - +
1010B T 3.6 33.1 + - - +
1011B T 3.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3164A MET 3.4 5.9 + - - -
3165A GLY 2.9 30.4 + - - +
3166A LEU* 3.6 31.1 - - + +
3168A ALA* 1.3 77.4 - - - +
3170A MET* 1.3 57.6 + - - +
3172A SER* 3.4 7.1 + - - -
3173A GLN* 3.0 27.4 + - - +
3176A ARG* 5.9 0.4 - - - +
1008B C 3.3 38.1 + - - +
1009B C 2.4 49.1 + - - +
2007C G 3.3 16.5 - - - +
2008C G 3.8 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2159A ILE* 4.5 6.4 - - + +
2160A GLY* 5.9 0.7 - - - -
3122A GLY* 4.1 2.5 - - - -
3123A GLU* 3.7 44.2 - - + +
3126A LEU* 3.9 18.4 - - + -
3149A LEU* 3.7 24.9 - - + +
3151A PRO* 4.4 9.2 - - - -
3166A LEU* 2.8 20.9 + - + +
3167A ALA* 3.5 15.7 - - + +
3169A ARG* 1.3 75.6 - - - +
3171A MET* 1.3 87.3 + - + +
3173A GLN* 3.3 11.9 + - - +
3174A ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3126A LEU* 3.5 33.9 - - + -
3146A VAL* 4.5 17.7 - - + -
3149A LEU* 3.4 30.5 - - + -
3167A ALA* 2.9 20.3 + - + +
3168A ALA 3.5 2.5 - - - +
3170A MET* 1.3 81.9 - - + +
3172A SER* 1.3 65.7 + - - +
3174A ALA* 3.2 3.3 + - + +
3175A MET* 3.0 44.9 + - + +
3191A PHE* 4.8 4.3 - - + -
3211A GLY* 3.4 30.7 - - - +
3214A ALA* 4.2 6.5 - - + -
3215A LEU* 5.6 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2196A ARG* 3.3 31.4 + - - -
2210A THR* 6.0 0.2 - - - +
3168A ALA 2.9 17.3 + - - -
3169A ARG 3.5 6.5 - - - -
3170A MET 3.2 0.2 - - - -
3171A MET* 1.3 75.8 - - - +
3173A GLN* 1.3 62.7 + - - +
3175A MET* 3.6 3.6 + - - +
3176A ARG* 3.4 27.1 + - - +
3214A ALA* 3.5 15.4 - - - +
3218A TYR* 5.1 1.4 + - - -
1009B C 3.4 26.4 + - - -
1010B T 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2154A GLU* 3.3 30.4 - - + +
2158A GLU 3.9 6.0 - - - +
2159A ILE* 3.7 10.7 - - - +
2160A GLY* 2.8 36.8 + - - +
2161A ASP 3.0 20.9 + - - +
2163A HIS* 4.1 3.8 - - - -
3169A ARG 3.0 12.0 + - - +
3170A MET* 3.5 11.9 + - - +
3171A MET 3.2 0.2 - - - -
3172A SER* 1.3 75.6 - - - +
3174A ALA* 1.3 63.7 + - - +
3176A ARG* 3.2 20.5 + - - +
3177A LYS* 3.2 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2159A ILE* 4.1 19.2 - - + +
3126A LEU* 3.8 29.8 - - + -
3170A MET 2.9 13.6 + - - +
3171A MET* 3.2 9.6 + - - +
3173A GLN* 1.3 75.4 - - - +
3175A MET* 1.3 65.4 + - + +
3177A LYS* 3.2 3.1 + - - +
3178A LEU* 2.7 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3061A ILE* 4.1 18.6 - - - +
3171A MET* 3.0 32.1 + - - +
3172A SER 3.9 2.7 - - - +
3173A GLN 3.3 0.2 - - - -
3174A ALA* 1.3 86.1 - - + +
3176A ARG* 1.3 64.6 + - - +
3178A LEU* 4.4 6.3 - - + -
3179A ALA* 3.0 30.5 + - - +
3191A PHE* 3.8 28.5 - - + -
3214A ALA* 3.8 14.8 - - + -
3215A LEU* 4.0 24.2 - - + +
3218A TYR* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2147A ALA 3.4 25.8 - - - +
2148A ALA* 4.5 3.2 - - - +
2149A LEU 5.4 1.3 - - - -
2150A THR* 3.2 37.3 + - + +
2151A PRO* 5.0 3.2 - - - +
2154A GLU* 2.7 39.0 + - - +
2155A ILE* 5.4 1.7 - - - +
2167A ALA* 5.0 9.9 - - - +
2210A THR* 6.3 3.9 - - - +
3169A ARG* 4.5 1.2 + - - +
3172A SER* 3.4 12.9 + - - +
3173A GLN* 3.2 33.6 + - - +
3174A ALA 3.3 0.2 - - - -
3175A MET* 1.3 80.5 - - - +
3177A LYS* 1.3 60.5 + - - +
3179A ALA* 4.2 7.1 + - - +
3180A GLY* 4.5 3.5 + - - -
3218A TYR* 3.6 13.2 + - - +
1008B C 6.0 3.6 - - - -
1009B C 3.3 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2150A THR* 4.8 2.2 - - + -
2154A GLU* 3.5 24.5 - - + +
2155A ILE* 3.4 35.4 + - - +
2157A GLY 2.8 23.7 + - - +
2158A GLU* 3.9 3.9 - - - +
2159A ILE* 3.7 23.7 - - + +
3127A GLU* 3.5 17.8 + - - -
3130A ASP* 3.4 27.4 + - - +
3134A ARG* 5.1 1.2 - - - +
3173A GLN* 3.2 14.8 + - + +
3174A ALA 3.2 7.1 + - - +
3176A ARG* 1.3 80.2 - - - +
3178A LEU* 1.3 63.4 + - - +
3180A GLY* 4.2 0.9 + - - -
3181A ASN* 3.7 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2159A ILE* 5.0 3.8 - - + -
3061A ILE* 4.9 2.5 - - + -
3126A LEU* 4.5 9.6 - - + +
3129A CYS* 4.1 11.7 - - + +
3130A ASP* 3.6 42.6 - - + +
3133A ALA* 4.8 4.3 - - + -
3174A ALA* 2.7 37.6 + - + +
3175A MET* 4.1 6.3 - - + +
3177A LYS* 1.3 73.0 - - - +
3179A ALA* 1.3 66.3 + - - +
3181A ASN* 2.9 4.2 + - - -
3182A LEU* 2.9 38.5 + - + +
3189A LEU* 3.8 25.1 - - + -
3191A PHE* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2095A ALA 5.3 1.6 - - - +
2096A GLU 4.4 14.1 - - - +
2097A HIS* 4.2 10.9 - - + +
2148A ALA* 6.1 0.2 - - + -
3059A GLY 4.6 1.9 - - - +
3061A ILE* 4.4 13.2 - - + +
3175A MET 3.0 18.4 + - - +
3176A ARG 4.5 3.1 - - - +
3177A LYS 3.6 0.2 - - - -
3178A LEU* 1.3 76.0 - - - +
3180A GLY* 1.3 62.1 + - - +
3182A LEU* 3.5 4.0 + - - +
3183A LYS* 3.2 22.7 + - - +
3218A TYR* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2097A HIS* 3.9 26.2 - - - -
3176A ARG 4.5 4.0 + - - -
3177A LYS 4.2 3.9 + - - -
3178A LEU 3.2 0.4 - - - -
3179A ALA* 1.3 76.3 - - - +
3181A ASN* 1.3 67.3 + - - +
3183A LYS* 3.3 3.5 + - - +
3184A GLN* 3.1 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2155A ILE* 6.0 3.6 - - - +
3130A ASP* 2.8 26.2 - - - +
3133A ALA* 4.0 19.0 - - + +
3134A ARG* 3.2 31.8 - - + +
3177A LYS* 3.7 9.0 + - - +
3178A LEU 2.9 7.6 + - - +
3180A GLY* 1.3 76.4 - - - +
3182A LEU* 1.3 60.5 + - - +
3184A GLN* 3.7 7.0 + - - +
3185A SER* 2.9 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3059A GLY* 3.4 10.7 - - - +
3060A ARG 4.9 0.4 - - - +
3061A ILE* 3.7 23.6 - - + -
3133A ALA* 4.0 15.0 - - + -
3141A ILE* 4.8 2.9 - - + -
3178A LEU* 2.9 30.4 + - + +
3179A ALA* 3.8 4.0 - - - +
3181A ASN* 1.3 74.7 - - - +
3183A LYS* 1.3 61.9 + - - +
3185A SER 3.5 0.3 + - - -
3186A ASN 3.0 7.3 + - - -
3187A THR* 2.9 66.9 + - + +
3189A LEU* 3.7 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2097A HIS* 3.7 36.3 + - + +
2098A ALA 4.9 0.2 - - - +
2099A LEU 5.1 3.8 + - - -
2118A GLN* 3.9 20.8 - - - +
3034A SER* 3.9 24.6 + - - +
3035A MET* 5.1 8.9 + - - +
3058A MET 4.6 5.2 - - - -
3059A GLY* 3.6 19.5 + - - +
3060A ARG* 3.6 33.7 - - - +
3179A ALA 3.2 15.1 + - - +
3180A GLY 3.8 4.0 - - - +
3182A LEU* 1.3 79.8 - - - +
3184A GLN* 1.3 63.7 + - + +
3186A ASN* 3.1 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2097A HIS* 4.0 24.0 - - - -
2118A GLN* 4.4 7.7 + - - +
2120A ASP* 3.4 26.6 + - - +
3180A GLY* 3.1 19.2 + - - +
3181A ASN* 4.4 7.6 + - - +
3182A LEU 3.4 0.2 - - - -
3183A LYS* 1.3 78.6 - - + +
3185A SER* 1.3 58.5 + - - +
3186A ASN* 3.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3133A ALA 2.5 25.2 + - - -
3134A ARG* 4.3 5.2 + - - -
3136A GLY* 4.0 22.2 - - - +
3138A VAL 4.9 1.9 - - - +
3139A ASP* 5.6 1.2 - - - +
3181A ASN 2.9 15.0 + - - -
3182A LEU 4.1 0.2 - - - -
3183A LYS 3.1 0.4 - - - -
3184A GLN* 1.3 77.6 - - - +
3186A ASN* 1.3 70.2 + - - +
3187A THR* 3.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3034A SER 5.7 0.5 - - - +
3036A ASP 5.6 2.1 - - - +
3038A GLU* 3.2 29.4 + - - +
3058A MET* 3.4 48.0 - - - +
3059A GLY* 3.6 8.3 + - - -
3138A VAL 5.4 0.2 - - - -
3139A ASP* 4.1 3.5 - - - +
3182A LEU 3.0 6.3 + - - -
3183A LYS* 3.1 14.8 + - - +
3184A GLN 3.4 0.2 - - - -
3185A SER* 1.3 81.4 - - - +
3187A THR* 1.3 58.3 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il