Contacts of the helix formed by residues 52 - 61 (chain B) in PDB entry 3GA1
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 SER 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LEU* 2.9 14.5 + - - +
49B ALA 3.8 0.9 + - - +
50B ALA 3.7 1.0 - - - -
51B SER* 1.3 78.5 - - - +
53B SER* 1.3 58.4 + - - +
54B TYR* 3.6 0.5 - - - +
55B PHE* 3.0 36.1 + - - +
56B ARG* 3.0 33.1 + - - +
85B CYS* 5.5 1.3 - - - -
107B LEU 2.6 25.5 + - - -
108B GLN 3.9 0.7 - - - -
109B ILE* 3.6 13.0 - - - -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER 4.1 0.4 - - - -
52B SER* 1.3 70.6 - - - +
54B TYR* 1.3 64.7 + - - +
56B ARG* 3.6 30.5 + - - +
57B ASP* 3.3 22.2 + - - +
108B GLN* 3.3 36.2 + - - -
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Residues in contact with TYR 54 (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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52B SER* 3.2 1.5 + - - +
53B SER* 1.3 78.9 - - - +
55B PHE* 1.3 64.9 + + - +
57B ASP* 3.2 7.2 + - - +
58B LEU* 2.9 54.8 + - + +
68B GLU 5.5 0.3 + - - -
69B LEU* 4.0 15.0 - - + +
70B PRO* 3.5 27.2 - - - +
106B PHE* 3.4 35.9 - + - +
107B LEU* 3.4 38.6 + - + +
108B GLN* 3.9 16.8 - - + +
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Residues in contact with PHE 55 (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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34B VAL* 4.2 27.4 - - + -
48B LEU* 4.1 27.1 - - + -
52B SER* 3.0 34.9 + - - +
54B TYR* 1.3 78.5 - + - +
56B ARG* 1.3 66.6 + - - +
58B LEU* 3.0 24.4 + - + +
59B PHE* 2.9 58.4 + + + -
67B VAL* 4.4 1.6 - - + -
69B LEU* 4.3 14.4 - - + -
78B PHE* 4.0 29.4 - + - -
81B ILE* 6.1 0.7 - - + -
107B LEU* 4.2 16.6 - - + -
109B ILE* 5.9 0.7 - - + -
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Residues in contact with ARG 56 (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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29A TYR* 3.6 20.4 - - - +
49B ALA* 2.6 54.0 + - + +
50B ALA 4.3 6.7 + - - -
51B SER 4.7 0.8 - - - -
52B SER 3.0 22.8 + - - +
53B SER* 3.7 31.8 + - - +
55B PHE* 1.3 77.4 - - - +
57B ASP* 1.3 61.6 + - - +
59B PHE* 3.4 3.5 + - - +
60B ASN* 2.9 31.6 - - - +
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Residues in contact with ASP 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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53B SER 3.3 9.9 + - - +
54B TYR* 3.2 11.6 + - + +
55B PHE 3.1 0.4 - - - -
56B ARG* 1.3 77.6 - - - +
58B LEU* 1.3 68.5 + - - +
60B ASN* 3.2 8.7 + - - +
61B ASN* 3.1 40.1 + - - +
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Residues in contact with LEU 58 (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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54B TYR* 2.9 44.5 + - + +
55B PHE* 3.0 26.2 + - + +
57B ASP* 1.3 79.2 - - - +
59B PHE* 1.3 62.7 + - + +
60B ASN 3.5 0.5 + - - -
61B ASN* 3.7 5.2 + - + +
62B SER* 3.5 25.3 + - - -
67B VAL* 4.1 30.0 - - + +
68B GLU 5.6 2.5 - - - +
69B LEU* 4.3 6.5 - - + -
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Residues in contact with PHE 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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29A TYR* 4.4 11.8 - + + -
32B VAL* 4.1 7.2 - - + -
45B ARG* 3.7 62.6 - - + -
48B LEU* 4.0 14.1 - - + -
49B ALA* 4.6 5.2 - - + -
55B PHE* 2.9 55.3 + + + +
56B ARG* 3.9 3.6 - - - +
58B LEU* 1.3 80.7 - - + +
60B ASN* 1.3 67.6 + - - +
62B SER* 3.2 21.3 - - - +
64B SER 5.9 0.4 - - - -
67B VAL* 4.1 26.5 - - + -
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Residues in contact with ASN 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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28A LEU* 5.6 5.0 - - - +
29A TYR* 3.5 26.8 + - - -
56B ARG* 2.9 22.6 + - - +
57B ASP* 3.2 6.6 + - - +
59B PHE* 1.3 79.6 - - - +
61B ASN* 1.3 64.9 + - - +
62B SER 3.2 8.7 + - - +
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Residues in contact with ASN 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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57B ASP* 3.1 33.9 + - - +
58B LEU* 3.7 5.1 + - + +
60B ASN* 1.3 85.5 + - - +
62B SER* 1.3 60.1 + - - +
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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