Contacts of the helix formed by residues 58 - 65 (chain G) in PDB entry 3S4S
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 ARG 58 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU* 4.3 12.6 + - - +
13G GLU* 4.6 7.2 + - - -
57G SER* 1.3 82.1 + - - +
59G ARG* 1.3 65.0 + - - +
60G SER* 3.2 25.1 + - - +
61G LEU* 2.9 32.2 + - + +
62G TRP* 3.5 10.7 - - - -
66G ASN 4.5 0.3 - - - +
68G PRO* 3.8 17.9 - - + +
70G ILE* 4.2 16.6 - - + +
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Residues in contact with ARG 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU* 3.4 29.5 + - + +
89A VAL 5.2 3.6 + - - -
90A THR* 3.6 35.9 + - - +
42G SER* 2.5 35.5 + - - +
43G PHE* 4.8 0.8 - - - +
44G LEU* 4.2 29.1 - - + +
56G ASP* 5.9 1.8 - - - +
57G SER 3.9 2.0 - - - +
58G ARG* 1.3 71.3 - - - +
60G SER* 1.3 65.9 + - - +
62G TRP* 2.8 53.5 + - + +
63G ASP 4.3 0.5 + - - -
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PRO 5.9 1.1 - - - -
88A GLU* 3.9 22.7 + - - +
58G ARG* 3.2 30.4 + - - +
59G ARG* 1.3 77.9 - - - +
61G LEU* 1.3 71.6 + - - +
62G TRP 3.2 0.9 + - - -
63G ASP* 3.7 6.2 + - - +
64G GLN* 3.4 16.0 + - - +
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Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLU* 4.4 9.2 - - - +
58G ARG* 2.9 38.2 + - + +
60G SER* 1.3 84.3 - - - +
62G TRP* 1.3 63.7 + - - +
63G ASP 3.2 0.7 - - - -
64G GLN* 3.1 29.4 + - + +
66G ASN* 3.1 45.9 + - + +
68G PRO* 4.2 11.9 - - + -
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Residues in contact with TRP 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G SER* 3.2 35.2 + - - +
26G PHE* 3.5 22.6 - + - -
39G ASN* 3.3 41.1 - - + -
41G GLY 4.6 1.6 - - - -
42G SER* 4.0 19.1 - - - -
43G PHE 4.3 0.2 - - - -
44G LEU* 4.1 24.7 - - + -
57G SER* 2.6 32.1 + - - -
58G ARG 3.5 11.4 + - - -
59G ARG* 2.8 40.9 + - + +
61G LEU* 1.3 75.7 - - - +
63G ASP* 1.3 63.2 + - - +
65G GLY 3.5 6.6 + - - -
66G ASN 3.3 17.9 - - - -
67G PHE* 3.7 13.7 - + + +
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Residues in contact with ASP 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.5 12.5 - - + +
175A LEU 5.1 3.6 - - - +
176A LYS* 3.4 27.9 + - - -
21G LYS 2.9 26.0 - - - +
22G LYS* 3.0 4.4 + - - -
23G SER* 4.1 16.4 + - - +
59G ARG 4.3 0.6 + - - -
60G SER 3.7 5.5 + - - +
61G LEU 3.2 0.8 - - - -
62G TRP* 1.3 80.3 - - - +
64G GLN* 1.3 68.7 + - - +
65G GLY 3.4 0.2 - - - -
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Residues in contact with GLN 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G THR* 5.3 1.0 - - - +
21G LYS* 3.5 45.5 - - + +
60G SER 3.4 16.4 + - - +
61G LEU* 3.1 38.1 + - + +
63G ASP* 1.3 84.9 - - - +
65G GLY* 1.3 59.8 + - - +
66G ASN* 3.3 17.7 + - - +
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Residues in contact with GLY 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G THR* 3.2 4.5 - - - +
18G ALA* 2.9 30.8 + - - -
20G GLN 4.1 15.3 - - - -
21G LYS* 3.6 3.2 - - - +
22G LYS 3.7 1.5 - - - +
62G TRP 3.5 3.0 + - - -
63G ASP 3.4 5.7 + - - -
64G GLN* 1.3 72.5 - - - +
66G ASN* 1.3 69.6 + - - +
67G PHE* 3.3 22.3 - - - -
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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