Contacts of the strand formed by residues 128 - 140 (chain B) in PDB entry 1RVB
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 TYR 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B PRO* 3.6 13.4 - - + +
76B THR* 2.7 43.0 + - + +
86B LYS* 3.1 14.1 - - + +
87B ILE 3.8 2.7 - - - -
88B ALA* 3.5 35.0 - - + -
121B ILE* 3.9 11.0 - - + -
122B VAL* 3.9 0.5 - - - +
123B TYR* 3.3 46.2 + - + -
124B PRO 3.6 11.0 - - - -
125B PHE* 3.1 20.1 + - - +
126B ASP* 4.0 5.5 - - - +
127B GLN* 1.3 80.6 - - - +
129B ILE* 1.3 64.3 + - - +
130B ALA 4.4 1.3 - - - +
131B HIS* 3.7 23.5 + + + +
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Residues in contact with ILE 129 (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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84B ASN 3.8 21.5 - - - +
85B LYS* 3.9 32.3 - - + +
86B LYS 2.8 14.7 + - - +
87B ILE* 4.8 7.4 - - + -
126B ASP 5.6 1.1 - - - +
127B GLN 5.1 0.4 - - - -
128B TYR* 1.3 76.9 - - - +
130B ALA* 1.3 67.2 + - + +
131B HIS* 5.1 2.2 - - - -
209B GLU* 5.2 6.2 - - - +
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Residues in contact with ALA 130 (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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86B LYS 3.8 1.8 + - - +
87B ILE* 3.7 14.7 - - + -
88B ALA* 2.9 26.1 + - - +
128B TYR* 3.6 1.3 - - - +
129B ILE* 1.3 91.0 - - + +
131B HIS* 1.3 71.3 + - - +
132B TRP* 3.7 24.9 - - + +
172B ASP* 4.8 4.7 - - - +
209B GLU* 5.7 1.8 - - - -
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Residues in contact with HIS 131 (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* 2.8 32.9 + + - +
88B ALA* 3.5 9.1 - - - +
113B PHE* 5.4 0.4 - - - -
125B PHE* 3.4 42.0 + + - -
128B TYR* 3.7 36.2 + + + +
129B ILE 5.1 1.1 - - - -
130B ALA* 1.3 80.4 - - - +
132B TRP* 1.3 63.6 + - - +
172B ASP* 3.4 7.9 + - - +
173B LYS* 2.8 45.7 + - + +
209B GLU* 4.5 16.4 + - - +
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Residues in contact with TRP 132 (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* 4.2 12.3 - - + -
4B ARG* 3.6 58.6 - - + +
7B LEU* 4.0 17.0 - - + -
72B TYR* 5.3 1.2 + - - -
87B ILE* 4.0 41.3 - - + -
88B ALA 2.8 11.0 + - - +
89B ILE* 3.4 22.5 - - + -
90B ASP* 3.1 23.6 + - - +
130B ALA* 3.7 14.4 - - + +
131B HIS* 1.3 84.0 - - - +
133B ILE* 1.3 65.8 + - - +
170B LEU* 4.0 28.9 - - + -
171B GLN 3.4 5.2 - - - +
172B ASP* 3.6 17.5 + - - -
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Residues in contact with ILE 133 (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* 5.8 0.4 - - - +
90B ASP* 3.3 25.4 - - + -
92B LYS* 3.8 28.7 - - + -
105B PHE* 5.9 1.1 - - + -
107B LEU* 4.1 21.3 - - + -
132B TRP* 1.3 78.8 - - - +
134B ILE* 1.3 69.5 + - - +
135B GLY* 3.8 3.1 + - - +
169B PHE* 3.5 7.5 - - + +
170B LEU* 3.2 4.0 - - - -
171B GLN 2.8 33.4 + - - +
173B LYS* 3.9 39.7 - - + -
176B ILE* 4.2 18.4 - - + -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.7 2.5 - - + -
11B LEU* 4.1 22.4 - - + -
48B SER* 4.9 2.0 - - - +
52B ILE* 4.0 23.1 - - + -
89B ILE* 3.5 28.7 - - + -
90B ASP 2.9 9.6 + - - +
91B ILE* 3.3 12.0 - - + +
92B LYS 2.9 24.4 + - - +
133B ILE* 1.3 74.3 - - - +
135B GLY* 1.3 60.2 + - - +
136B TYR* 3.7 17.5 - - + +
168B VAL* 3.6 26.0 - - + -
169B PHE 3.2 5.2 - - - +
170B LEU* 4.0 20.2 - - + -
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Residues in contact with GLY 135 (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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92B LYS 3.1 9.4 - - - -
105B PHE* 4.2 4.5 - - - -
133B ILE* 3.8 4.9 - - - -
134B ILE* 1.3 75.1 - - - +
136B TYR* 1.3 61.8 + - - -
167B LYS 3.7 0.3 - - - +
168B VAL* 3.1 6.4 - - - +
169B PHE* 2.9 58.6 + - - -
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Residues in contact with TYR 136 (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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11B LEU* 4.1 14.9 - - - +
15B ASN* 3.6 19.6 - - + +
44B PHE* 3.8 46.0 - + + -
47B PHE* 4.1 12.6 - + - -
48B SER* 2.6 31.2 + - - -
51B ILE* 5.0 0.2 - - - +
91B ILE* 3.9 18.4 - - + -
92B LYS 2.8 7.2 + - - -
93B THR* 3.2 7.4 - - + -
94B THR 3.1 24.5 + - - +
105B PHE* 3.8 3.5 - - - -
134B ILE* 3.7 15.7 - - + -
135B GLY* 1.3 77.0 - - - -
137B VAL* 1.3 60.8 + - - +
138B TYR* 4.2 0.4 - - - -
166B VAL* 3.9 17.7 - - + -
167B LYS 3.2 3.6 - - - -
168B VAL* 3.6 23.3 - - + +
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Residues in contact with VAL 137 (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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94B THR* 3.4 10.5 - - + +
95B TYR 4.7 0.2 - - - -
96B THR* 4.2 16.4 - - + +
103B ILE* 3.5 47.1 - - + -
105B PHE* 3.9 11.2 - - + -
136B TYR* 1.3 77.9 - - - +
138B TYR* 1.3 63.0 + - - +
165B GLY 3.8 0.3 - - - +
166B VAL* 3.3 3.9 - - - -
167B LYS* 2.8 48.6 + - + +
169B PHE* 4.5 3.6 - - + -
196B TYR* 4.3 17.3 - - + -
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Residues in contact with TYR 138 (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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35B SER 5.6 0.9 - - - -
37B THR* 3.4 36.7 + - - -
40B LEU* 3.3 34.9 - - + +
44B PHE* 3.7 22.7 - + + -
93B THR* 4.3 8.3 - - - -
94B THR 3.3 22.9 + - - -
95B TYR* 3.1 30.1 - - + +
96B THR* 2.9 24.2 + - - -
136B TYR 4.8 1.3 - - - -
137B VAL* 1.3 76.5 - - - +
139B THR* 1.3 65.3 + - - +
140B ARG* 4.1 13.4 + - + -
163B TYR* 4.2 17.0 - - + -
165B GLY 3.1 11.4 - - - +
166B VAL* 4.3 9.2 - - + -
9D C 4.2 1.7 + - - -
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Residues in contact with THR 139 (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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96B THR* 3.1 23.3 + - - +
97B ASN 3.6 17.5 - - - +
98B LYS* 4.5 1.3 - - - +
99B GLU* 4.3 21.5 - - + +
138B TYR* 1.3 73.7 - - - +
140B ARG* 1.3 73.3 + - - +
163B TYR* 3.5 2.9 - - - -
164B LYS* 2.8 45.7 + - + -
165B GLY* 3.0 21.9 + - - -
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Residues in contact with ARG 140 (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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67A LYS 5.7 2.6 + - - -
69A GLN* 3.6 27.9 + - - +
35B SER* 4.8 14.8 + - - +
37B THR* 5.2 0.8 - - - +
40B LEU* 6.0 0.2 - - + -
95B TYR* 3.1 56.9 + - + +
96B THR 3.2 10.6 + - - +
97B ASN* 4.4 16.7 + - - +
138B TYR* 3.8 21.7 + - + -
139B THR* 1.3 89.5 - - - +
141B VAL* 1.3 70.0 + - - +
142B ALA 4.2 0.2 + - - -
162B PRO 4.1 9.6 - - - +
164B LYS* 4.2 4.5 - - - +
9D C 5.1 0.2 - - - -
10D T 3.6 15.6 + - - -
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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