Contacts of the helix formed by residues 86 - 94 (chain B) in PDB entry 3G65
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 LEU 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.3 22.7 - - + +
34B ILE* 3.7 26.7 - - + +
35B HIS* 3.5 28.3 - - + -
37B ARG 4.1 4.7 - - - +
38B GLU 2.8 15.2 + - - +
39B HIS 4.3 0.4 - - - -
40B ALA* 4.1 17.0 - - + -
51B VAL* 4.9 2.9 - - + -
53B VAL* 3.8 16.6 - - + -
84B ILE* 3.4 5.8 + - + -
85B ASN* 1.3 70.3 - - - +
87B THR* 1.3 59.2 + - - +
89B LEU* 3.2 23.0 + - + +
90B LEU* 2.9 40.5 + - + +
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B HIS* 2.8 31.9 + - + +
38B GLU* 3.0 33.0 + - - +
85B ASN* 2.8 9.2 + - - -
86B LEU* 1.3 79.4 - - - +
88B VAL* 1.3 65.0 - - + +
90B LEU* 3.3 2.8 + - - +
91B ASP* 3.0 38.2 + - - +
175C ASN* 6.2 0.7 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 5.1 0.7 - - - +
85B ASN* 2.9 40.1 + - + +
87B THR* 1.3 75.0 - - + +
89B LEU* 1.3 64.0 + - - +
91B ASP* 3.2 7.6 + - - +
92B CYS* 2.9 25.1 + - - -
134B ILE* 4.0 13.5 - - + -
175C ASN 5.9 0.9 - - - +
176C ILE* 4.0 20.9 - - + -
198C LEU* 5.6 2.2 - - + -
199C VAL* 3.6 43.1 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 6.1 0.2 - - + -
31B LEU* 4.0 23.6 - - + -
42B CYS* 5.5 6.7 - - - -
51B VAL* 6.2 1.6 - - + -
84B ILE* 4.7 16.4 - - + -
85B ASN 3.2 16.2 + - - +
86B LEU* 3.5 15.9 - - + +
87B THR 3.2 0.4 - - - -
88B VAL* 1.3 79.5 - - - +
90B LEU* 1.3 62.2 + - - +
92B CYS* 3.1 4.3 + - - +
93B LEU* 3.0 38.3 + - + +
110B MET* 5.0 7.6 - - + -
119B LEU* 4.3 11.7 - - + -
121B LEU* 3.5 35.7 - - + -
134B ILE* 3.8 14.6 - - + +
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Residues in contact with LEU 90 (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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28B SER* 3.4 34.7 - - - +
31B LEU* 3.7 18.4 - - + -
32B LYS* 3.7 18.4 - - + +
35B HIS* 3.4 48.9 - - + +
86B LEU* 2.9 23.9 + - + +
87B THR* 3.7 3.6 - - - +
89B LEU* 1.3 75.6 - - - +
91B ASP* 1.3 64.1 + - - +
93B LEU* 3.4 4.9 + - + +
94B SER* 2.9 30.7 + - - -
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Residues in contact with ASP 91 (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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87B THR* 3.0 30.9 + - - +
88B VAL* 3.5 11.2 - - - +
90B LEU* 1.3 77.2 - - - +
92B CYS* 1.3 62.8 + - - +
94B SER* 3.6 5.4 + - - -
95B ILE* 3.3 21.0 + - - +
172C LYS* 3.7 32.7 + - + +
175C ASN* 3.4 37.9 + - - +
176C ILE* 4.9 8.3 - - + +
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Residues in contact with CYS 92 (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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88B VAL* 2.9 35.7 + - - -
89B LEU 3.5 8.1 - - - +
91B ASP* 1.3 76.2 - - - +
93B LEU* 1.3 65.3 + - - +
95B ILE* 3.1 20.7 - - - +
121B LEU* 3.9 11.9 - - + -
123B LEU* 2.9 17.4 - - - +
132B CYS* 3.5 37.3 - - - -
134B ILE* 4.1 6.1 - - - -
176C ILE* 5.2 4.0 - - - -
199C VAL* 4.7 0.2 - - - -
201C VAL* 4.1 13.9 - - - -
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Residues in contact with LEU 93 (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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24B VAL* 3.8 30.9 - - + +
27B LEU* 4.2 9.2 - - + -
28B SER* 3.6 34.5 - - - +
31B LEU* 4.2 17.9 - - + -
89B LEU* 3.0 29.1 + - + +
90B LEU* 3.8 8.3 - - + +
92B CYS* 1.3 79.3 - - - +
94B SER* 1.3 57.6 + - - +
95B ILE* 3.2 5.4 + - - +
96B PHE* 4.7 3.5 + - - -
106B THR* 4.9 5.0 + - - +
108B LEU* 4.0 25.8 - - + -
121B LEU* 4.4 14.8 - - + -
123B LEU* 3.7 14.0 - - + +
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Residues in contact with SER 94 (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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28B SER* 5.6 6.7 - - - -
90B LEU* 2.9 17.1 + - - +
91B ASP* 3.6 3.2 + - - -
93B LEU* 1.3 75.5 - - - +
95B ILE* 1.3 61.7 + - - +
96B PHE 3.4 2.0 - - - -
97B GLY* 3.5 13.6 + - - -
98B SER* 3.2 23.5 + - - -
172C LYS* 3.1 30.3 + - - -
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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