Contacts of the helix formed by residues 55 - 65 (chain B) in PDB entry 1GV3
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 ASP 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.8 12.3 - - - +
54B ILE* 1.3 77.2 - - - +
56B ALA* 1.3 65.9 + - - +
57B GLU* 3.8 10.5 - - + +
58B THR* 2.7 45.0 + - - +
59B MET* 3.1 19.5 + - - +
206B TYR* 6.0 1.0 - - - -
208B LEU* 3.9 9.2 - - - +
209B ARG* 3.5 36.9 + - + +
210B TYR* 5.6 0.2 - - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 3.3 27.5 - - + +
48B ASP* 3.9 13.7 - - + -
51B GLU* 2.9 22.2 + - - +
55B ASP* 1.3 72.4 - - - +
57B GLU* 1.3 62.5 + - - +
59B MET* 3.2 2.9 + - - +
60B LYS* 3.0 33.1 + - - +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 3.2 11.7 - - + +
56B ALA* 1.3 76.9 - - - +
58B THR* 1.3 57.7 + - - +
60B LYS* 3.3 23.2 + - - +
61B LEU* 3.0 44.6 + - + +
208B LEU* 4.0 17.3 - - + -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 5.8 0.6 - - + +
54B ILE* 4.0 10.8 - - + -
55B ASP* 2.7 35.5 + - - +
57B GLU* 1.3 74.3 - - - +
59B MET* 1.3 58.5 + - - +
61B LEU* 4.5 5.6 - - + +
62B HIS* 2.7 45.9 + - + +
204B HIS 3.7 23.0 + - - +
205B ALA* 3.8 19.1 - - - +
206B TYR* 5.4 1.5 + - - -
208B LEU* 3.6 22.8 + - - +
209B ARG 5.0 0.2 + - - -
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Residues in contact with MET 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.0 18.6 - - + -
45B TYR* 4.1 6.3 - - + -
47B TYR* 3.3 37.7 - - + +
50B LEU* 3.8 31.2 - - + -
54B ILE* 3.9 29.4 - - + +
55B ASP 3.1 16.9 + - - +
56B ALA 3.2 4.5 + - - +
58B THR* 1.3 74.5 - - - +
60B LYS* 1.3 62.3 + - - +
62B HIS* 4.0 4.9 - - - +
63B HIS* 3.0 28.6 + - - +
120B PHE* 6.1 0.2 - - - -
121B TRP* 3.8 33.2 - - + -
124B MET* 4.6 0.7 - - + -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 3.6 38.4 - - + -
56B ALA* 3.0 21.5 + - - +
57B GLU* 3.4 26.8 + - - +
58B THR 3.2 0.2 - - - -
59B MET* 1.3 76.4 - - - +
61B LEU* 1.3 54.7 + - - +
64B ASP* 2.7 48.4 + - - +
65B LYS* 5.4 0.2 - - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TYR* 3.9 17.9 - - + +
211A GLN* 3.8 28.3 - - + +
212A ASN* 4.0 20.2 - - - +
213A ARG* 5.8 1.3 - - - +
57B GLU* 3.0 35.8 + - + +
58B THR* 3.8 3.8 - - - +
60B LYS* 1.3 74.8 - - + +
62B HIS* 1.3 60.4 + - - +
65B LYS* 2.9 39.7 + - + +
66B HIS* 3.0 13.2 + - + -
208B LEU* 3.7 27.4 - - + -
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TYR* 5.1 0.4 + - - -
58B THR* 2.7 31.6 + - + +
59B MET* 4.0 4.7 - - - +
61B LEU* 1.3 73.7 - - - +
63B HIS* 1.3 56.2 + - - +
66B HIS* 3.3 12.2 - - + +
67B HIS* 2.9 27.2 + - - +
117B HIS* 3.0 16.6 + + - -
120B PHE* 3.9 17.8 - + - -
121B TRP* 3.6 16.7 - + + -
200B ASP* 3.1 9.6 - - - -
204B HIS* 3.2 14.6 + + + +
205B ALA* 3.9 22.5 - - + +
1238B MN 2.2 36.3 + - - -
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 3.8 27.8 - - + +
41B PRO 2.6 28.0 + - - -
42B PRO* 4.2 4.7 - - + -
43B LEU* 3.8 33.3 + - + -
47B TYR* 3.7 9.1 + - + -
59B MET 3.0 18.0 + - - +
62B HIS* 1.3 77.2 - - - +
64B ASP* 1.3 86.6 + - - +
67B HIS* 3.3 18.5 - - - +
68B ALA 3.4 6.8 + - - -
121B TRP* 3.5 36.6 - + + -
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.0 3.0 - - - +
47B TYR* 2.7 36.1 + - - -
60B LYS* 2.7 32.3 + - + +
63B HIS* 1.3 93.4 + - - +
65B LYS* 1.3 70.7 + - + +
68B ALA* 3.1 19.4 - - - +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASN* 3.8 40.8 + - + +
61B LEU* 2.9 32.9 + - + +
64B ASP* 1.3 91.3 + - + +
66B HIS* 1.3 59.0 + - - +
68B ALA* 3.9 1.7 - - - +
69B ALA* 3.1 30.0 + - - +
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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
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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