Contacts of the strand formed by residues 88 - 94 (chain B) in PDB entry 1AXS
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 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LYS* 3.8 17.0 - - + -
39B GLN 3.2 19.3 - - - +
40B ARG* 3.5 15.9 - - + +
41B PRO* 5.1 3.6 - - - -
86B ASP 3.1 7.1 + - - +
87B SER* 1.3 77.7 - - - +
89B VAL* 1.3 66.0 + - - +
90B TYR* 3.5 9.7 - - + -
108B SER* 4.5 0.9 - - - -
109B VAL 2.9 27.6 + - - -
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Residues in contact with VAL 89 (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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37B VAL 3.9 0.5 - - - +
38B LYS* 3.8 0.3 - - - -
39B GLN* 3.0 40.9 + - - +
88B ALA* 1.3 78.1 - - - +
90B TYR* 1.3 65.2 + - - +
91B TYR* 3.5 36.4 - - + +
105B GLN 5.1 0.4 - - - +
106B GLY* 3.8 4.0 - - - -
107B THR 3.5 19.1 - - - +
108B SER* 4.2 19.1 - - - +
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Residues in contact with TYR 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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6B GLU* 2.7 21.7 - - - +
20B ILE* 3.7 22.7 - - + -
36B TRP* 5.1 1.1 - - + -
37B VAL 3.6 2.0 - - - -
38B LYS* 3.6 32.2 - - + -
48B ILE* 3.7 32.8 - - + -
63B PHE* 5.6 1.0 - + - -
80B MET* 3.8 11.7 - - + -
82B LEU* 3.6 27.6 - - + +
86B ASP* 2.5 37.1 + - - +
88B ALA* 3.5 18.6 - - + -
89B VAL* 1.3 73.7 - - - +
91B TYR* 1.3 56.9 + - - +
106B GLY* 3.1 1.0 - - - -
107B THR* 2.9 23.9 + - - +
109B VAL* 3.8 19.1 - - + -
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Residues in contact with TYR 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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38A GLN* 3.7 7.3 + - - -
42A LYS 4.1 3.3 + - - -
43A SER* 3.2 32.6 - - - -
44A PRO* 3.7 14.8 - - + -
6B GLU* 3.3 6.1 - - - +
36B TRP* 3.3 11.0 - - - -
37B VAL* 2.9 50.2 + - + +
39B GLN* 3.0 38.0 + - + -
45B LEU* 4.6 1.1 - - + -
89B VAL* 3.5 21.8 - - + +
90B TYR* 1.3 75.1 - - - +
92B CYS* 1.3 61.9 - - - +
103B TRP* 3.9 22.4 - + + -
104B GLY 3.9 5.2 - - - +
105B GLN 3.5 13.4 + - - -
106B GLY* 3.4 16.4 - - - -
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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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4B LEU* 3.8 8.0 - - - +
6B GLU* 3.3 21.7 + - - -
22B CYS* 2.0 48.2 - - - -
34B ILE* 4.2 2.0 - - + -
35B GLU 3.1 9.6 - - - +
36B TRP* 3.6 24.7 - - + -
37B VAL* 5.8 0.4 - - - -
91B TYR* 1.3 75.6 - - - +
93B ALA* 1.3 63.2 + - - +
103B TRP* 3.8 0.2 - - - -
104B GLY 2.9 25.5 + - - -
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Residues in contact with ALA 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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4B LEU* 3.7 4.0 - - - -
34B ILE* 3.5 4.8 - - - +
35B GLU* 2.7 41.9 + - + +
37B VAL* 5.4 1.3 - - + -
92B CYS* 1.3 77.9 - - - +
94B ARG* 1.3 63.4 + - - +
101B ASP* 4.7 0.4 - - + -
102B TYR 3.0 16.4 - - - +
103B TRP* 3.9 27.1 - - + -
1004B HOP 4.2 18.4 - - + -
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Residues in contact with ARG 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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2B VAL* 3.4 19.8 - - + +
4B LEU* 3.5 12.0 - - + +
27B TYR* 3.3 60.1 - - + +
32B PHE* 3.6 48.2 - - + -
33B TRP 3.7 4.7 - - - +
34B ILE* 4.5 2.9 - - + -
35B GLU* 4.9 0.4 - - - -
93B ALA* 1.3 71.8 - - - +
95B GLY* 1.3 66.8 + - - +
100B PHE* 4.2 17.4 - - - -
101B ASP* 3.0 31.9 - - - +
102B TYR* 2.8 47.2 + - + +
1001B TYR* 5.8 1.0 - - - +
1002B ASP* 4.5 1.8 + - - +
1003B GLY 4.2 4.1 + - - +
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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