Contacts of the strand formed by residues 81 - 95 (chain A) in PDB entry 2ARV
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 CYS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A CYS* 2.1 52.5 - - + -
12A CYS 3.8 1.6 - - - -
40A CYS* 3.8 14.3 - - - +
41A GLU* 3.5 25.6 - - - -
42A GLY 3.3 24.5 + - - +
44A CYS* 3.5 5.1 - - - -
80A CYS* 1.3 71.3 - - - +
82A VAL* 1.3 63.6 + - - +
114A GLY 3.5 4.5 - - - -
77B LEU* 6.1 0.9 - - - +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A CYS* 3.7 5.8 - - - -
80A CYS* 3.6 21.5 - - + +
81A CYS* 1.3 81.4 - - - +
83A PRO* 1.3 82.6 - - + +
84A THR* 3.8 6.9 - - + +
113A CYS* 3.4 1.7 - - - -
114A GLY 2.8 35.3 + - - +
116A SER* 4.4 7.9 - - - +
123A GOL 5.3 3.4 - - - +
82B VAL* 3.9 34.5 - - + -
83B PRO* 6.2 0.2 - - + -
116B SER* 3.8 25.4 - - - +
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Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A CYS* 3.6 13.6 - - + +
82A VAL* 1.3 97.0 - - + +
84A THR* 1.3 62.2 + - - +
86A LEU* 3.8 33.6 - - + +
110A VAL* 3.7 25.8 - - + -
112A GLU 3.5 9.9 - - - +
59B HIS* 4.8 9.0 - - + +
82B VAL* 5.9 0.3 - - - +
83B PRO 5.7 1.4 - - - +
116B SER* 5.4 8.1 - - - +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A SER* 2.8 24.8 + - - +
82A VAL* 3.5 7.2 + - + +
83A PRO* 1.3 77.9 - - - +
85A LYS* 1.3 62.0 + - - +
86A LEU* 5.0 2.9 - - - -
112A GLU* 2.9 14.0 + - - +
113A CYS 3.7 4.7 - - - -
114A GLY* 3.5 28.9 - - - +
123A GOL 3.6 28.0 - - - +
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO 3.6 0.2 - - - -
84A THR* 1.3 80.4 + - - +
86A LEU* 1.3 73.4 + - - +
110A VAL* 3.8 0.5 - - - -
111A GLU* 2.8 53.2 + - + +
112A GLU* 3.1 45.6 + - + +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO* 3.8 27.6 - - + +
84A THR 5.0 1.3 - - - -
85A LYS* 1.3 86.1 - - - +
87A ARG* 1.3 65.6 + - - +
88A PRO* 4.7 1.2 - - - +
107A ASN* 3.7 51.1 + - + +
109A ILE 3.1 10.3 - - - +
110A VAL* 4.0 17.3 - - + -
111A GLU* 4.1 1.1 - - - +
57B SER* 5.0 3.6 - - - +
59B HIS* 4.0 18.6 - - + +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.0 9.7 - - - +
38A ASN* 4.5 3.0 - - - +
86A LEU* 1.3 75.8 - - - +
88A PRO* 1.3 77.0 - - + +
107A ASN 4.0 4.0 - - - -
108A MET 2.9 21.3 + - - -
109A ILE* 2.8 49.0 + - + +
110A VAL 4.0 2.8 + - - -
111A GLU* 2.8 57.4 + - - +
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU 4.7 0.9 - - - +
87A ARG* 1.3 94.3 - - + +
89A MET* 1.3 63.4 + - - +
104A ASP* 4.4 16.4 - - + +
105A ILE 2.9 18.4 - - - +
106A GLN* 3.6 34.8 - - - +
107A ASN 4.1 0.4 - - - -
109A ILE* 3.9 8.7 - - - +
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.5 1.6 - - + -
32A PRO* 3.8 23.6 - - + -
35A TYR* 3.5 44.0 - - + -
88A PRO* 1.3 78.1 - - - +
90A SER* 1.3 72.3 + - - +
91A MET* 3.4 24.8 + - + +
104A ASP* 4.1 2.9 - - - -
105A ILE 2.9 27.0 + - - +
108A MET* 3.4 37.2 - - + -
109A ILE* 4.1 12.1 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 3.8 10.9 - - - +
89A MET* 1.3 84.2 - - - +
91A MET* 1.3 63.9 + - - +
102A LYS* 3.9 26.0 - - - +
103A LYS 3.6 6.8 + - - -
104A ASP* 3.6 18.4 + - - -
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Residues in contact with MET 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.4 5.6 - - - -
28A TRP* 5.1 3.4 - - + -
29A ILE* 3.9 33.4 - - + -
31A ALA 3.5 6.7 - - - +
32A PRO* 5.1 0.7 - - - -
89A MET* 3.5 23.3 - - + +
90A SER* 1.3 83.8 + - - +
92A LEU* 1.3 59.0 + - - +
93A TYR* 3.7 22.3 - - + -
101A ILE 3.4 1.4 - - - +
102A LYS* 3.2 4.8 - - - +
103A LYS 2.8 31.7 + - - -
105A ILE* 3.6 19.3 - - + -
108A MET* 3.1 31.2 - - + -
58B PHE* 4.4 13.0 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.7 1.6 - - - +
30A ILE* 2.7 53.7 + - + -
31A ALA* 2.8 31.2 + - + +
91A MET* 1.3 72.8 - - - +
93A TYR* 1.3 61.9 + - - +
100A ILE* 3.6 18.6 - - + -
101A ILE 3.1 17.7 - - - +
102A LYS* 3.9 22.7 - - + +
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 3.1 26.9 - + + +
29A ILE* 4.0 13.2 - - + -
30A ILE* 4.1 7.4 - - - +
91A MET* 3.7 29.6 - - + -
92A LEU* 1.3 80.6 - - - +
94A TYR* 1.3 74.6 + - - +
95A ASP* 3.8 20.2 - - + -
100A ILE* 3.3 0.9 - - - -
101A ILE* 2.6 60.7 + - + +
103A LYS* 3.2 37.5 - - + +
105A ILE* 3.8 17.2 - - + +
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Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP 3.9 16.4 - - - +
28A TRP* 2.7 43.4 + - + +
30A ILE* 3.6 21.8 - - + +
93A TYR* 1.3 81.8 - - - +
95A ASP* 1.3 61.1 + - - +
98A GLN 6.0 0.7 - - - -
99A ASN* 3.5 10.1 - - - -
100A ILE* 3.5 33.7 - - + +
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.7 23.1 + - + -
94A TYR* 1.3 75.3 - - - +
96A ASP* 1.3 65.6 + - - +
97A GLY* 3.3 15.1 + - - -
98A GLN* 2.9 9.4 + - - -
99A ASN* 2.6 48.4 + - - +
101A ILE* 3.3 13.3 - - + +
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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