Contacts of the helix formed by residues 3121 - 3136 (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 THR3121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3119A PRO* 3.9 4.1 - - - +
3120A ASP* 1.3 86.1 - - + +
3122A GLY* 1.3 64.1 + - - +
3123A GLU* 3.7 15.5 + - - +
3124A GLN* 3.1 28.6 + - - +
3125A ALA* 3.1 19.9 + - - +
3150A THR 3.5 6.7 - - - -
3152A LYS* 3.9 32.6 - - + +
3155A ILE* 3.8 18.6 - - + -
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Residues in contact with GLY3122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3121A THR* 1.3 68.9 - - - +
3123A GLU* 1.3 65.4 + - - +
3125A ALA* 3.2 5.4 + - - +
3126A LEU* 3.0 27.8 + - - +
3149A LEU* 3.9 29.8 - - - -
3150A THR 2.7 23.4 + - - +
3170A MET* 4.1 8.7 - - - -
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Residues in contact with GLU3123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2159A ILE* 3.6 31.1 - - - +
2160A GLY* 4.1 13.9 - - - -
3121A THR* 3.8 4.9 - - - +
3122A GLY* 1.3 76.6 - - - +
3124A GLN* 1.3 49.9 - - - +
3126A LEU* 3.3 1.9 + - - +
3127A GLU* 2.8 40.2 + - + +
3151A PRO* 3.5 11.3 - - - +
3152A LYS* 2.7 45.7 + - + +
3153A ALA 5.3 0.2 + - - -
3166A LEU* 4.7 6.2 - - - +
3170A MET* 3.7 24.2 - - + +
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Residues in contact with GLN3124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3118A GLN 4.9 0.3 - - - +
3119A PRO* 3.4 9.6 - - + +
3120A ASP* 3.4 48.5 + - - +
3121A THR* 3.1 20.8 + - - +
3122A GLY 3.3 0.2 - - - -
3123A GLU* 1.3 78.3 - - - +
3125A ALA* 1.3 63.8 + - - +
3127A GLU* 3.2 2.0 + - - +
3128A ILE* 2.9 37.7 + - + +
4021A PHE* 3.4 53.2 + - + +
4025A SER* 4.4 8.0 - - - -
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Residues in contact with ALA3125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3093A ILE* 4.0 13.1 - - + +
3119A PRO* 3.6 30.0 - - + +
3121A THR 3.1 7.2 + - - +
3122A GLY 3.2 9.8 + - - +
3124A GLN* 1.3 78.4 - - - +
3126A LEU* 1.3 58.2 + - + +
3128A ILE* 3.4 7.1 + - - +
3129A CYS* 3.2 28.8 + - - -
3143A VAL* 5.5 1.8 - - + -
3149A LEU* 3.8 24.0 - - + -
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Residues in contact with LEU3126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2159A ILE* 3.7 22.9 - - + +
3122A GLY 3.0 20.0 + - - +
3123A GLU 3.9 2.0 - - - +
3125A ALA* 1.3 75.5 - - + +
3127A GLU* 1.3 60.4 + - - +
3128A ILE 3.2 0.4 - - - -
3129A CYS* 3.3 9.9 + - - +
3130A ASP* 3.0 27.0 + - - +
3143A VAL* 5.6 1.1 - - + -
3149A LEU* 4.2 7.9 - - + -
3170A MET* 3.9 22.9 - - + -
3171A MET* 3.5 35.4 - - + -
3174A ALA* 3.8 21.1 - - + -
3178A LEU* 4.5 6.5 - - + +
3191A PHE* 4.1 24.5 - - + -
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Residues in contact with GLU3127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2158A GLU* 3.3 31.4 - - - +
2159A ILE* 3.1 41.0 + - + +
3123A GLU* 2.8 19.4 + - + +
3124A GLN 3.7 0.7 - - - +
3126A LEU* 1.3 74.7 - - - +
3128A ILE* 1.3 63.2 + - - +
3130A ASP* 3.4 7.7 + - - +
3131A ALA* 3.0 23.7 + - - +
3134A ARG* 5.1 8.0 + - - -
3177A LYS* 3.5 15.8 + - - -
4020A GLN* 4.4 6.4 - - - +
4021A PHE* 3.6 24.1 - - + -
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Residues in contact with ILE3128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3093A ILE* 3.9 23.6 - - + -
3117A SER* 3.5 22.4 - - - +
3119A PRO* 4.7 1.6 - - + -
3124A GLN* 2.9 41.6 + - + +
3125A ALA* 3.6 8.3 - - - +
3127A GLU* 1.3 74.3 - - - +
3129A CYS* 1.3 65.7 + - - +
3131A ALA* 3.2 7.0 + - - +
3132A LEU* 3.0 35.0 + - + +
4017A ILE* 3.9 32.3 - - + -
4021A PHE* 4.1 11.4 - - + -
4025A SER* 4.5 4.3 - - - +
4026A ILE* 4.5 7.9 - - + -
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Residues in contact with CYS3129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3093A ILE* 4.1 5.2 - - - -
3125A ALA 3.2 17.2 + - - -
3126A LEU* 3.4 15.7 - - - +
3128A ILE* 1.3 79.3 - - - +
3130A ASP* 1.3 51.3 + - - +
3132A LEU* 3.3 4.0 + - - +
3133A ALA* 2.7 36.4 + - - +
3141A ILE* 3.9 28.4 - - + +
3143A VAL* 3.7 29.8 - - - -
3178A LEU* 4.1 17.3 - - + -
3189A LEU* 4.7 8.5 - - + -
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Residues in contact with ASP3130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2159A ILE* 4.6 2.5 - - + -
3126A LEU 3.0 16.3 + - - +
3127A GLU* 3.7 13.0 - - - +
3129A CYS* 1.3 76.0 - - - +
3131A ALA* 1.3 58.0 + - - +
3133A ALA* 3.3 2.1 + - - +
3134A ARG* 2.5 59.5 + - - +
3177A LYS* 3.4 37.1 + - - +
3178A LEU* 3.6 20.8 - - + +
3181A ASN* 2.8 23.4 - - - +
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Residues in contact with ALA3131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3127A GLU 3.0 13.7 + - - +
3128A ILE 3.2 8.5 + - - +
3130A ASP* 1.3 77.5 - - - +
3132A LEU* 1.3 57.9 + - - +
3134A ARG* 3.4 21.9 + - - +
3135A SER* 3.0 28.6 + - - -
4013A ALA* 4.5 6.9 - - + +
4016A GLN* 5.2 10.5 - - + +
4017A ILE* 4.0 24.2 - - + -
4020A GLN* 6.1 0.9 - - - +
4021A PHE* 6.3 0.4 - - + -
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Residues in contact with LEU3132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3091A ALA* 3.7 29.2 - - + -
3093A ILE* 4.7 5.4 - - + -
3115A LEU* 4.7 1.3 - - + -
3128A ILE* 3.0 35.1 + - + +
3129A CYS 3.7 2.9 - - - +
3131A ALA* 1.3 72.4 - - - +
3133A ALA* 1.3 67.2 + - - +
3135A SER* 2.7 24.0 + - - +
3136A GLY 3.6 1.7 + - - -
3138A VAL* 3.8 29.7 + - + +
3141A ILE* 3.9 17.0 - - + -
4010A LEU* 5.7 0.2 - - + -
4013A ALA* 5.0 3.8 - - + -
4014A LEU* 4.7 13.5 - - + -
4017A ILE* 3.8 21.8 - - + -
4026A ILE* 4.2 12.1 - - + -
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Residues in contact with ALA3133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3129A CYS 2.7 21.8 + - - +
3130A ASP* 3.5 7.4 - - - +
3132A LEU* 1.3 76.1 - - - +
3134A ARG* 1.3 57.4 + - - +
3136A GLY 3.2 2.4 + - - -
3141A ILE* 4.2 4.4 - - + +
3178A LEU* 4.8 2.0 - - + -
3181A ASN* 4.0 21.1 - - + +
3182A LEU* 4.0 26.5 - - + -
3185A SER* 2.5 31.0 + - - -
3187A THR* 4.1 8.9 + - - -
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Residues in contact with ARG3134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2155A ILE 5.9 1.0 + - - -
3127A GLU* 5.1 7.7 + - - -
3130A ASP* 2.5 53.9 + - - +
3131A ALA* 3.6 24.6 - - - +
3133A ALA* 1.3 73.6 - - - +
3135A SER* 1.3 62.7 + - - +
3136A GLY* 3.2 1.7 + - - -
3177A LYS* 5.1 1.4 - - - +
3181A ASN* 3.2 33.4 + - - +
3185A SER* 4.3 4.9 + - - -
4016A GLN* 5.0 10.5 - - - +
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Residues in contact with SER3135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3131A ALA 3.0 15.6 + - - -
3132A LEU* 2.7 22.0 + - - +
3134A ARG* 1.3 76.4 - - - +
3136A GLY* 1.3 60.1 + - - +
3137A ALA* 3.1 18.0 + - - +
3138A VAL* 4.1 3.3 + - - +
4009A ALA* 3.9 28.4 - - - +
4010A LEU* 5.3 0.3 - - - +
4013A ALA* 3.7 25.4 - - - +
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Residues in contact with GLY3136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3132A LEU 3.6 0.8 + - - -
3133A ALA 3.2 12.4 + - - -
3134A ARG 3.2 4.9 - - - -
3135A SER* 1.3 77.1 + - - +
3137A ALA* 1.3 58.5 + - - +
3138A VAL 3.6 5.5 - - - +
3139A ASP* 5.8 0.5 - - - +
3185A SER* 4.0 22.1 - - - +
4006A LYS* 4.2 13.9 - - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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