Contacts of the strand formed by residues 86 - 94 (chain B) in PDB entry 5J13
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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.7 29.2 - - + -
40B GLN 3.3 17.3 - - - +
41B LYS* 3.9 7.9 - - + +
42B PRO* 5.1 3.4 - - - -
84B ASP 3.1 8.7 + - - +
85B GLU* 1.3 76.2 - - - +
87B ASP* 1.3 64.5 + - - +
88B TYR* 3.4 9.0 - - + -
107B LYS* 3.8 1.9 - - - +
108B LEU 2.9 29.3 + - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR 3.7 0.9 - - - +
39B GLN* 3.6 2.9 - - - -
40B GLN* 2.8 45.6 + - + +
86B ALA* 1.3 72.4 - - - +
88B TYR* 1.3 60.8 + - - +
89B TYR* 3.9 29.4 + - + +
105B GLY 6.1 0.4 - - - -
106B THR 3.4 5.6 - - - +
107B LYS* 3.3 37.5 - - - +
42C GLN* 5.6 0.7 + - - -
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 2.9 9.9 + - - -
23B ILE* 3.8 27.1 - - + -
37B TRP* 4.7 4.5 - - + -
38B TYR 3.3 14.4 - - - +
39B GLN* 3.0 40.7 + - + -
49B VAL* 4.9 2.2 - - + -
64B PHE* 3.7 16.8 - + - -
75B LEU* 3.5 29.4 - - + -
77B ILE* 3.7 8.8 - - + +
84B ASP* 2.7 30.8 + - - -
86B ALA 3.4 20.6 - - - -
87B ASP* 1.3 73.9 - - - +
89B TYR* 1.3 62.8 + - - +
105B GLY* 3.4 0.5 - - - -
106B THR 2.8 38.9 + - - +
108B LEU* 3.6 13.9 - - + -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.6 2.0 - - - -
37B TRP* 3.3 7.7 - - - -
38B TYR* 2.8 46.0 + - + +
40B GLN* 3.6 22.7 + - + -
46B PRO* 6.0 0.2 - - + -
87B ASP* 3.9 31.8 + - + -
88B TYR* 1.3 75.4 - - - +
90B CYS* 1.3 65.8 + - - +
102B PHE* 4.5 7.2 - - + -
103B GLY 3.6 13.2 - - - -
104B GLY 3.5 20.4 + - - -
105B GLY* 3.5 14.8 - - - -
42C GLN* 3.3 19.3 + - - -
46C LYS 3.6 2.9 + - - -
47C GLY* 3.5 9.8 - - - -
48C LEU* 3.6 45.5 - - + -
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Residues in contact with CYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.0 2.9 - - - -
9B GLN* 3.1 31.3 + - - -
25B CYS* 2.0 52.0 - - + -
35B VAL* 4.3 4.0 - - + -
36B HIS 3.3 7.2 - - - +
37B TRP* 3.8 19.2 - - + -
89B TYR* 1.3 73.4 - - - +
91B GLN* 1.3 64.0 + - - +
102B PHE* 3.5 2.6 - - - +
103B GLY* 2.8 31.9 + - - -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 2.4 - - - +
34B SER 3.8 0.7 - - - +
35B VAL* 3.6 1.3 - - - +
36B HIS* 2.9 47.8 + - - -
38B TYR* 2.7 42.2 + - + -
90B CYS* 1.3 78.1 - - - +
92B VAL* 1.3 97.3 + - - +
93B TRP* 3.8 3.4 - - - +
100B VAL* 3.7 22.6 - - + +
101B VAL 3.3 13.7 - - - +
102B PHE* 3.7 21.5 - - + -
109C HIS 5.2 1.4 + - - -
110C GLU 5.1 4.0 + - - -
111C ALA* 4.7 0.9 - - - -
112C PHE* 4.3 6.8 - - - -
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Residues in contact with VAL 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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5B TYR* 4.0 24.5 - - + -
7B LEU* 3.9 17.7 - - + -
30B LEU* 3.8 26.2 - - + -
33B LYS* 4.1 17.0 - - + -
34B SER 3.7 17.7 - - - +
35B VAL* 3.8 9.0 - - + -
36B HIS* 5.0 0.7 - - - -
91B GLN* 1.3 93.2 + - - +
93B TRP* 1.3 62.0 + - - +
94B ASP 4.5 1.1 - - - +
100B VAL* 3.6 0.5 - - - -
101B VAL* 2.9 36.1 + - + +
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Residues in contact with TRP 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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33B LYS* 4.5 11.8 + - - +
34B SER 4.7 2.8 + - - -
36B HIS* 5.5 2.0 + - - +
91B GLN* 3.8 3.9 - - - +
92B VAL* 1.3 74.1 - - - +
94B ASP* 1.3 62.3 + - - +
95B SER* 3.4 20.5 + - - +
98B ASP* 3.3 43.1 - - + -
99B HIS* 3.5 30.7 - - - -
100B VAL* 3.6 18.6 - - + -
50C TRP* 4.9 7.4 - + - -
53C VAL* 5.6 1.1 - - + -
62C HIS* 4.8 5.4 - + + -
107C LEU* 3.3 25.8 + - + +
108C VAL* 3.9 26.8 - - + +
109C HIS* 3.5 50.0 - + + +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.3 36.6 + - + +
33B LYS* 3.0 26.1 + - - +
92B VAL* 3.9 2.7 - - + -
93B TRP* 1.3 72.6 - - - +
95B SER* 1.3 53.7 + - - +
96B SER* 3.1 25.2 + - - -
97B SER* 2.5 27.4 + - - +
98B ASP* 2.7 35.0 + - - -
99B HIS 2.9 17.1 + - - +
101B VAL* 4.4 5.8 - - + -
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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