Contacts of the strand formed by residues 95 - 104 (chain B) in PDB entry 3GAX
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 ALA 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B TYR* 5.5 5.8 - - - +
66B VAL 4.6 0.2 - - - -
67B GLU* 3.2 14.2 - - - -
68B LEU* 2.9 37.8 + - + +
93B ARG 3.3 3.6 + - - +
94B LYS* 1.3 77.2 - - - +
97B CYS* 3.8 34.9 + - - -
117B CYS* 4.5 4.3 - - + -
118B GLN 3.3 29.2 - - - +
119B ASP* 3.7 14.6 - - - +
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Residues in contact with CYS 97 (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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64B LEU 3.7 0.5 - - - +
65B ASP* 3.4 3.8 - - - +
66B VAL* 2.8 49.5 + - + +
68B LEU* 3.7 25.4 - - - -
95B ALA* 3.8 25.8 + - - -
98B SER* 1.3 62.7 + - - +
99B PHE* 3.6 17.9 - - + -
116B THR 3.1 9.9 - - - +
117B CYS* 2.1 50.5 - - - +
118B GLN* 4.9 3.4 + - - +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU 3.2 5.2 - - - -
65B ASP* 2.9 21.8 + - - +
97B CYS* 1.3 73.8 + - - +
99B PHE* 1.3 63.1 + - - +
114B LYS* 4.1 1.2 - - - +
115B SER* 3.4 3.5 + - - -
116B THR* 2.9 46.0 + - - +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.9 2.7 - - + -
30B ALA* 3.5 43.3 - - + -
31B VAL* 4.4 13.5 - - + -
34B TYR* 5.0 4.7 - - + -
62B TYR 3.5 0.9 - - - +
63B PHE* 3.4 5.0 - - - +
64B LEU* 2.8 47.1 + - + +
66B VAL* 3.6 26.0 - - + -
68B LEU* 4.1 15.3 - - + -
97B CYS* 3.6 24.7 - - + -
98B SER* 1.3 75.9 - - - +
100B GLN* 1.3 60.7 + - - +
101B ILE* 3.8 9.0 - - + -
112B LEU* 4.4 1.8 - - + -
114B LYS 3.4 4.3 - - - +
115B SER* 3.2 29.8 - - - -
117B CYS* 4.1 5.2 - - - -
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Residues in contact with GLN 100 (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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61B ASN* 4.2 18.8 + - + +
62B TYR 3.2 3.8 - - - +
63B PHE* 3.5 36.7 - - + -
99B PHE* 1.3 73.5 - - - +
101B ILE* 1.3 65.0 + - - +
112B LEU* 3.5 4.5 - - - +
113B SER* 2.9 44.8 + - - +
114B LYS* 2.9 48.9 + - + +
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Residues in contact with ILE 101 (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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26B ALA* 3.8 28.5 - - + +
29B PHE* 4.1 4.7 - - + -
30B ALA* 4.0 8.5 - - + -
60B VAL 3.5 1.9 - - - +
61B ASN* 3.3 6.5 - - - -
62B TYR* 2.9 43.2 + - + +
64B LEU* 3.8 24.9 - - + -
99B PHE* 3.8 25.4 - - + -
100B GLN* 1.3 77.1 - - - +
102B TYR* 1.3 64.9 - - - +
103B ALA 3.8 1.1 + - - +
110B MET* 3.3 38.6 - - + -
111B THR 3.5 7.6 - - - +
112B LEU* 4.1 6.5 - - + -
113B SER* 4.5 0.2 - - - -
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Residues in contact with TYR 102 (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 VAL* 3.8 15.7 - - + -
58B ALA* 2.4 34.0 + - - +
59B GLY* 4.2 0.2 - - - -
60B VAL 3.7 4.7 - - - -
61B ASN* 3.4 22.4 - - - +
101B ILE* 1.3 71.7 - - - +
103B ALA* 1.3 66.6 + - - +
104B VAL* 3.3 23.4 + - + +
109B THR* 4.5 2.4 - - - -
110B MET* 3.3 2.4 - - - -
111B THR* 2.9 52.1 + - + +
113B SER* 3.8 15.5 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY* 3.4 3.1 - - - -
60B VAL* 2.8 39.4 + - + +
62B TYR* 4.1 21.3 - - + -
101B ILE* 3.8 0.8 + - + -
102B TYR* 1.3 75.5 - - - +
104B VAL* 1.3 62.7 + - - +
105B PRO* 3.5 14.9 - - + +
109B THR 3.4 9.9 - - - +
110B MET* 4.2 15.3 - - + +
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Residues in contact with VAL 104 (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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58B ALA 3.9 4.9 - - - +
59B GLY* 4.3 1.1 - - - -
102B TYR* 3.3 42.6 - - + +
103B ALA* 1.3 73.1 - - - +
105B PRO* 1.3 61.3 - - - +
106B TRP* 3.4 33.7 - - + +
107B GLN* 2.9 47.6 + - + +
108B GLY 3.0 8.8 + - - -
109B THR* 3.0 28.0 + - - +
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Residues in contact with PRO 105 (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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60B VAL* 4.5 10.8 - - + -
62B TYR* 5.4 5.2 - - - +
103B ALA* 3.5 17.7 - - + +
104B VAL* 1.3 88.4 - - - +
106B TRP* 1.3 81.3 + - + +
108B GLY* 3.0 20.4 + - - +
109B THR 4.9 2.5 - - - +
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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