Contacts of the strand formed by residues 82 - 96 (chain A) in PDB entry 2RVE
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 GLU 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TYR* 4.1 7.3 - - - +
79A LYS* 2.5 60.5 + - + +
80A PRO 4.4 1.1 - - - -
81A SER* 1.3 90.6 - - - +
83A PRO* 1.3 65.6 - - + +
84A ASN 3.7 1.3 - - - +
85A LYS* 4.4 26.9 + - + +
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Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TYR* 5.2 4.7 - - + -
80A PRO 4.6 5.6 - - - +
81A SER 3.8 8.7 - - - +
82A GLU* 1.3 83.5 - - - +
84A ASN* 1.3 73.0 + - - +
85A LYS 3.0 9.5 + - - -
86A LYS* 3.6 32.3 - - + +
127A GLN* 3.7 12.5 - - - +
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Residues in contact with ASN 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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82A GLU* 3.7 1.2 - - - +
83A PRO* 1.3 95.8 + - - +
85A LYS* 1.3 66.0 + - + +
126A ASP* 4.8 8.7 - - - +
127A GLN* 3.6 36.3 + - - +
129A ILE* 3.8 8.1 - - - +
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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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61A TYR* 5.3 2.9 + - - -
77A LEU 4.2 2.9 - - - +
78A TYR* 4.2 9.4 - - - +
79A LYS 5.3 0.5 + - - -
82A GLU* 4.7 25.7 - - + +
83A PRO 3.0 3.6 - - - -
84A ASN* 1.3 80.1 - - + +
86A LYS* 1.3 64.2 + - - +
87A ILE* 4.1 4.2 + - - +
129A ILE* 3.1 46.7 - - + +
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Residues in contact with LYS 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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76A THR* 4.1 3.8 - - + -
77A LEU 3.3 6.7 - - - +
78A TYR* 3.3 45.8 - - + -
83A PRO* 3.6 20.6 + - - +
85A LYS* 1.3 75.0 - - - +
87A ILE* 1.3 61.9 + - - +
88A ALA 4.1 0.2 - - - -
123A TYR* 3.3 54.0 - - + -
127A GLN* 3.0 36.0 + - - +
128A TYR* 3.5 18.6 - - + +
129A ILE* 2.8 33.5 + - - +
130A ALA 3.3 2.6 + - - -
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Residues in contact with ILE 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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3A LEU* 4.1 6.3 - - + -
61A TYR* 3.6 34.8 - - + +
75A PHE 3.5 2.4 - - - +
76A THR 3.4 1.0 - - - -
77A LEU* 2.5 50.8 + - + +
85A LYS 4.5 4.5 - - - +
86A LYS* 1.3 76.1 - - - +
88A ALA* 1.3 60.4 + - - +
89A ILE* 3.8 1.8 + - + -
128A TYR* 4.3 1.8 - - - -
129A ILE* 4.5 10.8 - - + -
130A ALA* 3.9 11.2 - - + +
132A TRP* 3.2 61.9 - - + -
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Residues in contact with ALA 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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72A TYR* 3.7 4.2 + - + +
73A PRO* 3.0 26.0 - - + -
75A PHE 3.4 5.2 - - - -
87A ILE* 1.3 73.1 - - - +
89A ILE* 1.4 60.3 + - - +
128A TYR* 3.3 22.8 - - + -
130A ALA 3.1 6.5 + - - -
131A HIS* 3.3 21.3 - - - +
132A TRP* 3.0 27.5 + - - +
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Residues in contact with ILE 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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7A LEU* 4.1 11.0 - - + -
52A ILE* 4.0 22.2 - - + -
73A PRO* 3.6 1.6 - - - +
74A ASP* 3.2 6.7 + - - +
75A PHE* 2.6 47.6 + - + +
77A LEU* 3.7 29.2 - - + -
87A ILE 4.6 2.2 - - - +
88A ALA* 1.4 74.3 - - - +
90A ASP* 1.3 65.0 + - - +
91A ILE* 4.8 1.1 - - + -
132A TRP* 3.4 45.3 - - + +
134A ILE* 3.5 34.3 - - + -
170A LEU* 5.0 0.2 - - + -
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Residues in contact with ASP 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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72A TYR* 3.2 32.8 - - + +
73A PRO* 3.2 7.6 - - + +
74A ASP* 2.7 35.8 + - - +
89A ILE* 1.3 75.8 - - - +
91A ILE* 1.3 64.9 + - - +
92A LYS* 3.5 21.8 + - - -
107A LEU 5.5 0.7 - - - -
132A TRP 3.2 11.8 + - - +
133A ILE* 3.7 15.0 - - + +
134A ILE 3.3 20.7 + - - -
173A LYS* 3.5 9.5 + - - -
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Residues in contact with ILE 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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41A SER* 5.6 2.5 + - - +
44A PHE* 3.8 24.2 - - + +
45A GLU* 4.6 11.8 - - + +
48A SER* 3.5 27.8 - - - +
52A ILE* 4.0 9.4 - - + -
74A ASP* 2.8 27.0 + - - +
75A PHE* 3.9 17.3 - - + -
89A ILE* 4.8 0.2 - - + -
90A ASP* 1.3 72.2 - - - +
92A LYS* 1.3 74.6 + - - +
93A THR* 4.5 0.8 + - - +
134A ILE* 3.8 29.6 - - + +
136A TYR* 4.1 18.4 - - + -
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Residues in contact with LYS 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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74A ASP* 5.6 1.0 + - - -
90A ASP* 4.0 25.9 + - - +
91A ILE* 1.3 86.0 + - - +
93A THR* 1.3 65.0 + - - +
105A PHE* 4.0 19.3 - - + -
106A THR* 3.3 32.6 + - + +
107A LEU* 4.3 14.6 - - + +
108A GLY* 4.8 7.7 - - - +
133A ILE* 3.8 24.7 - - + -
134A ILE 3.0 14.5 + - - +
135A GLY* 3.6 1.1 - - - -
136A TYR* 3.0 27.1 + - - +
8F G 6.0 0.2 + - - -
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Residues in contact with THR 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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37A THR 5.6 2.2 - - - +
41A SER* 3.3 36.4 + - - +
44A PHE* 2.9 40.2 - - + +
91A ILE* 4.5 1.9 + - - +
92A LYS* 1.3 76.6 + - - +
94A THR* 1.3 71.0 + - - +
95A TYR* 6.4 0.2 - - + -
105A PHE* 4.1 5.7 - - - -
136A TYR* 3.6 5.3 - - - +
138A TYR* 4.1 14.4 - - + +
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Residues in contact with THR 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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93A THR* 1.3 80.2 - - - +
95A TYR* 1.3 83.1 + - - +
103A ILE* 4.4 10.4 - - + +
104A LYS 4.2 12.1 + - - +
105A PHE* 3.0 43.1 - - + -
136A TYR 3.0 11.8 + - - +
137A VAL* 3.4 14.0 - - + -
138A TYR* 3.0 31.1 + - - -
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Residues in contact with TYR 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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37A THR* 4.4 9.0 - - + -
94A THR* 1.3 93.9 + - - +
96A THR* 1.3 71.2 - - - +
97A ASN* 3.8 8.7 - - - -
103A ILE* 5.2 1.0 - - - +
137A VAL* 5.1 0.4 - - - -
138A TYR* 2.9 35.2 - + + +
140A ARG* 3.2 53.2 + - + -
3C A 3.7 43.1 + - - +
4C G 4.8 1.2 + - - -
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Residues in contact with THR 96 (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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95A TYR* 1.3 83.7 - - - +
97A ASN* 1.3 61.6 + - - +
98A LYS 3.1 20.0 + - - -
99A GLU* 4.8 1.5 - - - -
100A ASN 5.2 1.4 + - - +
101A GLU* 3.7 26.5 - - + +
102A LYS 5.3 1.3 - - - +
103A ILE* 3.7 27.6 - - + -
137A VAL* 4.3 8.5 - - + +
138A TYR 2.6 17.5 + - - -
139A THR* 3.2 13.2 + - - -
140A ARG* 2.7 32.7 + - - +
167A LYS* 5.8 1.6 + - - +
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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