Contacts of the helix formed by residues 4165 - 4186 (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 GLY4165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3199A ILE* 4.2 2.3 - - - +
4164A MET* 1.3 76.2 - - - +
4166A LEU* 1.3 62.6 + - - +
4167A ALA 3.4 2.2 - - - -
4168A ALA* 3.6 11.7 + - - +
4169A ARG* 3.5 26.8 + - - +
1012B T 4.5 5.7 - - - +
1013B T 4.5 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4123A GLU* 5.3 3.1 - - - +
4151A PRO* 3.8 27.0 - - + +
4153A ALA* 4.6 20.9 - - + -
4154A GLU* 5.8 5.6 - - + +
4164A MET 3.6 6.0 - - - +
4165A GLY* 1.3 76.2 - - - +
4167A ALA* 1.3 63.6 + - - +
4169A ARG* 3.8 25.7 + - - +
4170A MET* 3.5 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4149A LEU 4.7 3.4 - - - +
4151A PRO* 3.9 24.6 - - + +
4154A GLU* 5.7 0.9 - - - +
4166A LEU* 1.3 77.4 - - - +
4168A ALA* 1.3 61.2 + - - +
4170A MET* 3.2 11.8 + - + +
4171A MET* 2.9 34.4 + - + +
4210A THR* 6.3 1.3 - - + -
4211A GLY* 4.7 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4165A GLY* 3.6 13.1 + - - +
4166A LEU 3.3 0.2 - - - -
4167A ALA* 1.3 79.7 - - - +
4169A ARG* 1.3 57.0 + - - +
4171A MET* 3.4 3.1 + - - +
4172A SER* 2.9 29.6 + - - -
4211A GLY* 4.0 13.0 - - - +
4212A GLY* 3.8 19.5 - - - +
4214A ALA* 5.1 1.2 - - - +
1012B T 3.3 24.1 - - + +
1013B T 4.0 15.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4164A MET 4.3 5.7 + - - -
4165A GLY 3.5 24.3 + - - +
4166A LEU* 3.9 31.5 - - - +
4167A ALA 3.3 0.2 - - - -
4168A ALA* 1.3 79.2 - - - +
4170A MET* 1.3 57.9 + - - +
4172A SER* 3.5 2.3 + - - -
4173A GLN* 3.0 27.0 + - - +
4176A ARG* 4.5 1.2 + - - +
1011B T 3.8 43.0 + - - +
1012B T 3.7 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET4170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3159A ILE* 4.4 11.4 - - + +
3160A GLY* 5.6 1.3 - - - +
4122A GLY* 4.1 2.2 - - - -
4123A GLU* 3.6 44.2 - - + +
4126A LEU* 3.9 12.6 - - + -
4149A LEU* 3.6 26.9 - - + +
4151A PRO* 4.3 9.0 - - + -
4166A LEU* 3.5 12.3 + - + +
4167A ALA* 3.2 19.4 + - + +
4169A ARG* 1.3 77.3 - - - +
4171A MET* 1.3 87.3 + - + +
4173A GLN* 3.3 12.0 + - - +
4174A ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET4171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4126A LEU* 3.5 33.9 - - + -
4146A VAL* 4.5 18.6 - - + -
4149A LEU* 3.4 30.5 - - + -
4167A ALA* 2.9 17.2 + - + +
4168A ALA 3.5 2.2 - - - +
4170A MET* 1.3 82.1 - - + +
4172A SER* 1.3 65.5 + - - +
4174A ALA* 3.2 3.8 + - + +
4175A MET* 3.0 43.2 + - + +
4191A PHE* 4.8 4.5 - - + -
4211A GLY* 3.4 34.5 - - - +
4214A ALA* 4.2 7.0 - - + -
4215A LEU* 5.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER4172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3196A ARG* 3.2 29.4 + - - -
3210A THR* 5.9 0.5 - - - +
4168A ALA 2.9 17.7 + - - -
4169A ARG 3.6 2.0 - - - -
4170A MET 3.3 0.2 - - - -
4171A MET* 1.3 77.0 - - - +
4173A GLN* 1.3 60.9 + - - +
4175A MET* 3.6 3.5 + - - +
4176A ARG* 3.4 27.1 + - - +
4214A ALA* 3.5 14.3 - - - +
4218A TYR* 5.1 1.2 + - - -
1012B T 3.0 33.4 + - - -
1013B T 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN4173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3154A GLU* 3.0 36.7 - - + +
3158A GLU 4.1 4.8 - - - +
3159A ILE* 3.9 11.0 - - - +
3160A GLY* 2.9 35.0 - - - +
3161A ASP 3.0 21.9 + - - +
3163A HIS* 3.9 2.1 - - - -
4169A ARG 3.0 12.6 + - - +
4170A MET* 3.6 11.7 + - - +
4172A SER* 1.3 74.6 - - - +
4174A ALA* 1.3 65.1 + - - +
4176A ARG* 3.2 21.9 + - - +
4177A LYS* 3.2 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3159A ILE* 4.2 17.9 - - + +
4126A LEU* 3.8 30.1 - - + -
4170A MET 2.9 13.6 + - - +
4171A MET* 3.2 9.6 + - - +
4173A GLN* 1.3 75.6 - - - +
4175A MET* 1.3 65.7 + - + +
4177A LYS* 3.2 3.3 + - - +
4178A LEU* 2.7 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET4175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4061A ILE* 4.1 17.5 - - - -
4171A MET* 3.0 31.8 + - - +
4172A SER 3.9 2.9 - - - +
4173A GLN 3.3 0.4 - - - -
4174A ALA* 1.3 86.9 - - + +
4176A ARG* 1.3 63.1 + - - +
4178A LEU* 4.4 6.5 - - + +
4179A ALA* 2.9 30.3 + - - +
4191A PHE* 3.8 28.3 - - + -
4214A ALA* 3.8 13.9 - - + -
4215A LEU* 3.9 24.5 - - + +
4218A TYR* 3.4 41.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3147A ALA 3.2 28.7 - - - +
3148A ALA* 4.3 4.4 - - - +
3149A LEU 5.2 1.6 - - - -
3150A THR* 3.1 36.8 + - + +
3151A PRO* 4.9 0.6 - - - +
3154A GLU* 2.8 33.2 + - - +
3155A ILE* 5.5 1.2 - - - +
3167A ALA* 4.9 14.3 - - - +
3210A THR* 6.1 4.5 - - - +
4169A ARG* 4.5 1.8 + - - +
4172A SER* 3.4 12.3 + - - +
4173A GLN* 3.2 35.3 + - - +
4174A ALA 3.3 0.2 - - - -
4175A MET* 1.3 79.9 - - - +
4177A LYS* 1.3 60.4 + - - +
4179A ALA* 4.2 7.1 + - - +
4180A GLY* 4.5 3.5 + - - -
4218A TYR* 3.6 11.9 - - - +
1011B T 5.0 8.7 + - - -
1012B T 3.7 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS4177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3150A THR* 4.4 14.6 - - + -
3154A GLU* 3.3 31.4 - - + +
3155A ILE* 3.3 25.4 + - + +
3157A GLY 2.7 23.4 + - - -
3158A GLU 4.0 4.8 - - - +
3159A ILE* 3.9 18.6 - - + +
4127A GLU* 3.5 16.6 + - - -
4130A ASP* 3.4 27.5 + - - +
4134A ARG* 5.1 0.8 - - - +
4173A GLN* 3.2 13.7 + - + +
4174A ALA 3.2 7.0 + - - +
4176A ARG* 1.3 79.5 - - - +
4178A LEU* 1.3 63.5 + - - +
4180A GLY* 4.2 1.0 + - - -
4181A ASN* 3.7 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3159A ILE* 5.0 3.4 - - + -
4061A ILE* 4.9 2.5 - - + -
4126A LEU* 4.5 9.2 - - + +
4129A CYS* 4.1 11.2 - - + +
4130A ASP* 3.6 43.7 - - + +
4133A ALA* 4.8 4.3 - - + -
4174A ALA* 2.7 38.7 + - + +
4175A MET* 4.1 6.5 - - + +
4177A LYS* 1.3 72.6 - - - +
4179A ALA* 1.3 67.3 + - - +
4181A ASN* 2.9 4.0 + - - -
4182A LEU* 2.9 38.9 + - + +
4189A LEU* 3.8 24.2 - - + -
4191A PHE* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3095A ALA 5.0 2.0 - - - +
3096A GLU 4.2 15.0 - - - +
3097A HIS* 4.0 10.1 - - + +
3148A ALA* 5.9 0.7 - - + -
4059A GLY 4.6 1.9 - - - +
4061A ILE* 4.4 13.1 - - + +
4175A MET 2.9 18.6 + - - +
4176A ARG 4.5 3.4 - - - +
4177A LYS 3.6 0.4 - - - -
4178A LEU* 1.3 76.2 - - - +
4180A GLY* 1.3 61.2 + - - +
4182A LEU* 3.5 4.5 + - - +
4183A LYS* 3.2 22.2 + - - +
4218A TYR* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3097A HIS* 3.6 27.5 - - - -
3120A ASP* 6.1 1.8 - - - -
4176A ARG 4.5 4.2 + - - -
4177A LYS 4.2 3.5 + - - -
4178A LEU 3.2 0.4 - - - -
4179A ALA* 1.3 75.9 - - - +
4181A ASN* 1.3 66.3 + - - +
4183A LYS* 3.4 3.5 + - - +
4184A GLN* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3155A ILE* 6.0 4.1 - - - +
4130A ASP* 2.9 26.1 - - - +
4133A ALA* 4.0 18.6 - - + +
4134A ARG* 3.3 31.8 + - + +
4177A LYS* 3.7 8.8 + - - +
4178A LEU 2.9 7.6 + - - +
4180A GLY* 1.3 77.5 - - - +
4182A LEU* 1.3 60.4 - - - +
4184A GLN* 3.7 6.9 + - - +
4185A SER* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4059A GLY* 3.3 11.3 - - - +
4060A ARG 4.9 0.9 - - - +
4061A ILE* 3.7 23.6 - - + -
4133A ALA* 4.0 15.9 - - + -
4141A ILE* 4.8 3.4 - - + -
4178A LEU* 2.9 30.1 + - + +
4179A ALA 3.8 3.6 - - - +
4181A ASN* 1.3 74.8 - - - +
4183A LYS* 1.3 60.3 + - - +
4185A SER 3.5 0.3 + - - -
4186A ASN 3.0 7.4 + - - -
4187A THR* 2.9 66.5 + - + +
4189A LEU* 3.7 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS4183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3097A HIS* 3.5 33.2 + - + +
3098A ALA* 4.7 0.6 - - - +
3099A LEU 4.8 5.3 + - - -
3118A GLN* 3.6 29.2 - - - +
4034A SER* 3.8 26.1 + - - +
4035A MET* 5.0 7.1 + - - +
4058A MET 4.6 4.9 - - - -
4059A GLY* 3.5 19.0 + - - +
4060A ARG* 3.5 32.9 - - - +
4179A ALA 3.2 15.2 + - - +
4180A GLY 3.4 0.6 + - - +
4182A LEU* 1.3 78.6 - - - +
4184A GLN* 1.3 63.2 + - + +
4186A ASN* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN4184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3097A HIS* 3.7 27.7 - - - -
3118A GLN* 3.9 11.9 + - - +
3119A PRO 5.0 0.2 + - - -
3120A ASP* 3.1 27.6 + - - +
4180A GLY* 3.1 17.8 + - - +
4181A ASN* 3.7 7.7 + - - +
4183A LYS* 1.3 78.4 - - + +
4185A SER* 1.3 58.5 + - - +
4186A ASN* 3.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER4185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4133A ALA 2.5 29.2 + - - -
4134A ARG* 4.2 5.4 + - - -
4136A GLY* 3.9 21.5 + - - +
4138A VAL 4.9 2.1 - - - +
4139A ASP* 5.6 1.2 - - - +
4181A ASN 3.0 15.3 + - - -
4182A LEU 4.1 0.2 - - - -
4183A LYS 3.1 0.4 - - - -
4184A GLN* 1.3 77.8 - - - +
4186A ASN* 1.3 70.6 + - - +
4187A THR* 3.1 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4034A SER 5.6 1.6 - - - +
4036A ASP 5.5 3.1 - - - +
4038A GLU* 3.2 28.8 + - - +
4058A MET* 3.3 49.9 - - - +
4059A GLY* 3.6 7.4 + - - -
4139A ASP* 4.1 3.5 - - - +
4182A LEU 3.0 6.8 + - - -
4183A LYS* 3.1 14.5 + - - +
4184A GLN 3.4 0.4 - - - -
4185A SER* 1.3 81.0 - - - +
4187A THR* 1.3 58.6 + - - +
----------------------------------------------------------
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