Contacts of the strand formed by residues 86 - 96 (chain B) in PDB entry 1RVC
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 LYS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B THR* 3.9 15.9 - - + -
77B LEU 3.4 8.1 - - - +
78B TYR* 3.8 30.5 - - + -
83B PRO* 2.8 31.8 + - - +
85B LYS* 1.3 76.4 - - - +
87B ILE* 1.3 60.7 + - - +
123B TYR* 3.7 40.1 - - + -
127B GLN* 2.6 43.6 + - + +
128B TYR* 3.1 18.9 - - + +
129B ILE* 2.8 30.8 + - - +
130B ALA 3.7 0.9 + - - -
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Residues in contact with ILE 87 (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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3B LEU* 3.6 30.1 - - + -
61B TYR* 4.2 17.3 - - + +
75B PHE 3.8 0.7 - - - +
76B THR* 3.5 4.0 - - - -
77B LEU* 2.8 41.8 + - + +
85B LYS 4.3 7.0 - - - +
86B LYS* 1.3 77.5 - - - +
88B ALA* 1.3 66.7 + - - +
89B ILE* 4.1 5.3 + - + -
128B TYR* 3.8 3.3 - - - -
129B ILE* 4.6 8.3 - - + -
130B ALA* 3.7 15.9 - - + -
132B TRP* 3.9 46.2 - - + -
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Residues in contact with ALA 88 (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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72B TYR* 3.6 12.1 - - + +
73B PRO* 3.7 13.9 - - + -
75B PHE 3.7 4.5 - - - -
87B ILE* 1.3 73.9 - - - +
89B ILE* 1.3 64.2 + - - +
128B TYR* 3.6 17.0 - - + -
130B ALA 2.9 7.7 + - - +
131B HIS* 3.5 28.4 - - - +
132B TRP* 2.8 28.7 + - - +
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Residues in contact with ILE 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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7B LEU* 3.9 26.5 - - + -
52B ILE* 4.3 15.9 - - + -
73B PRO* 4.0 1.5 - - - +
74B ASP* 3.2 8.4 + - - +
75B PHE* 2.9 44.4 + - + +
77B LEU* 3.9 28.3 - - + -
87B ILE* 4.3 5.2 - - + -
88B ALA* 1.3 80.0 - - - +
90B ASP* 1.3 64.5 + - - +
91B ILE* 5.1 0.7 - - + -
132B TRP* 3.4 26.5 - - + +
134B ILE* 3.6 33.0 - - + -
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Residues in contact with ASP 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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72B TYR* 3.6 32.7 - - + -
73B PRO* 3.7 2.1 - - - +
74B ASP* 3.0 32.7 + - - +
89B ILE* 1.3 74.1 - - - +
91B ILE* 1.3 65.5 + - - +
92B LYS* 3.2 27.0 + - - -
107B LEU 4.9 1.4 - - - +
108B GLY* 5.7 0.2 - - - -
132B TRP 3.0 7.2 + - - +
133B ILE* 3.3 24.2 - - + +
134B ILE 2.9 22.7 + - - -
403B MG 4.2 0.5 - - - -
6E T 5.2 2.4 - - - +
7F A 4.8 5.4 - - - -
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Residues in contact with ILE 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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41B SER 5.4 0.9 - - - +
45B GLU* 3.8 30.9 - - + +
48B SER* 3.5 30.5 - - - +
52B ILE* 4.6 1.6 - - + -
74B ASP* 2.9 16.1 + - - +
75B PHE* 3.5 27.4 - - + -
89B ILE* 5.1 0.2 - - + -
90B ASP* 1.3 76.5 - - - +
92B LYS* 1.3 76.2 + - - +
93B THR* 4.7 4.0 - - - +
134B ILE* 3.3 24.9 - - + +
136B TYR* 3.9 23.3 - - + -
403B MG 4.0 6.8 - - - -
7F A 5.1 0.7 - - - +
8F T 4.1 7.4 + - - -
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Residues in contact with LYS 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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90B ASP* 3.2 31.2 + - - -
91B ILE* 1.3 81.3 + - - +
93B THR* 1.3 64.0 + - - +
105B PHE* 3.8 20.9 - - + -
106B THR 3.3 21.1 + - - +
107B LEU* 3.7 30.8 + - + +
108B GLY* 3.8 8.1 - - - +
133B ILE* 4.0 26.0 - - + -
134B ILE 3.0 6.2 + - - +
135B GLY* 3.3 3.9 - - - -
136B TYR* 2.9 24.1 + - - +
188B ASN* 5.1 1.2 + - - -
6E T 5.1 7.9 + - - -
7F A 5.6 4.0 - - - -
8F T 3.6 19.3 + - - +
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Residues in contact with THR 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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37B THR* 4.0 14.6 - - + -
41B SER* 3.5 27.1 + - - +
44B PHE* 3.7 37.4 - - + +
91B ILE* 4.7 4.2 - - - +
92B LYS* 1.3 78.3 + - - +
94B THR* 1.3 72.2 - - - +
105B PHE* 4.0 4.7 - - - -
106B THR 6.0 0.2 + - - -
136B TYR* 3.4 12.0 - - - +
138B TYR* 4.0 4.7 - - + -
8F T 3.1 37.8 + - - +
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Residues in contact with THR 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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37B THR* 4.5 0.2 - - - -
93B THR* 1.3 76.0 - - - +
95B TYR* 1.3 71.0 + - - +
103B ILE* 4.2 15.9 - - + -
104B LYS 3.3 22.1 + - - +
105B PHE* 3.5 31.2 - - + -
136B TYR 3.1 2.6 + - - +
137B VAL* 3.4 13.1 - - + -
138B TYR* 3.3 28.4 + - - -
9F C 3.0 26.2 + - - -
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Residues in contact with TYR 95 (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 THR* 3.9 1.1 - - - -
94B THR* 1.3 85.0 + - - +
96B THR* 1.3 80.4 + - - +
97B ASN* 3.9 25.7 + - - -
103B ILE* 4.3 6.6 - - - +
137B VAL* 4.4 2.5 - - - -
138B TYR* 3.2 36.6 - - + +
140B ARG* 3.0 49.2 + - + -
9F C 3.3 29.6 - - - -
10F T 2.6 24.6 + - - -
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Residues in contact with THR 96 (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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95B TYR* 1.3 83.4 - - - +
97B ASN* 1.3 62.0 + - - +
98B LYS 3.7 20.5 + - - +
99B GLU* 4.7 4.7 + - - +
101B GLU* 4.1 19.3 - - + +
102B LYS 4.3 2.5 - - - +
103B ILE* 3.2 35.4 - - + -
137B VAL* 3.9 9.2 - - + +
138B TYR 3.0 8.9 + - - -
139B THR* 3.2 15.8 + - - -
140B ARG 3.0 24.8 + - - -
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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