Contacts of the strand formed by residues 132 - 142 (chain B) in PDB entry 1VE3
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 LEU 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 3.3 17.1 - - - +
104B PHE 3.6 14.4 - - - +
106B TYR* 3.8 8.7 - - - -
107B VAL* 3.3 25.4 - - + -
128B VAL* 3.1 35.2 + - + +
129B ARG* 3.7 10.1 - - - +
130B ARG 3.2 4.2 - - - +
131B VAL* 1.3 79.3 - - - +
133B LYS* 1.3 67.9 + - - +
134B PRO 3.9 0.2 - - - -
136B GLY* 4.4 0.2 - - - -
137B LYS 3.5 39.9 - - - +
138B PHE* 4.0 6.3 - - + -
207B PHE* 4.2 3.4 - - + -
226B PRO* 4.1 21.6 - - + +
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Residues in contact with LYS 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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34A LYS* 5.3 11.8 - - - +
41B LYS* 5.4 2.8 - - - +
102B LYS* 3.4 24.5 - - + +
103B THR 3.5 20.4 + - - -
104B PHE 2.9 18.1 + - - +
105B ASP* 3.3 34.4 + - - +
132B LEU* 1.3 78.5 - - - +
134B PRO* 1.3 67.7 - - + +
135B SER* 4.2 9.9 - - - +
136B GLY* 2.7 30.0 + - - +
226B PRO* 3.9 4.6 - - - +
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Residues in contact with PRO 134 (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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102B LYS* 3.6 35.4 - - + -
132B LEU 3.9 0.4 - - - +
133B LYS* 1.3 86.3 - - + +
135B SER* 1.3 58.1 + - - +
136B GLY 3.2 1.3 + - - +
225B ASN* 5.7 1.9 - - - +
226B PRO* 4.2 19.2 - - + +
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 5.1 3.5 + - - -
133B LYS* 4.2 12.6 - - - +
134B PRO* 1.3 77.5 - - - +
136B GLY* 1.3 68.5 + - - +
137B LYS* 4.3 6.2 - - - +
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Residues in contact with GLY 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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105B ASP* 3.1 23.3 - - - -
132B LEU* 4.4 4.9 - - - -
133B LYS* 2.7 20.0 + - - +
134B PRO 3.2 1.1 - - - +
135B SER* 1.3 85.7 + - - +
137B LYS* 1.3 64.5 + - - +
225B ASN* 3.7 12.5 + - - +
226B PRO* 3.9 12.2 - - - +
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Residues in contact with LYS 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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35B TYR* 2.7 32.8 + - - +
105B ASP 2.9 7.4 + - - +
106B TYR* 3.3 31.3 + - + +
107B VAL 3.1 23.6 + - - +
132B LEU* 3.5 9.2 - - - +
135B SER 4.3 5.2 - - - +
136B GLY* 1.3 77.1 - - - +
138B PHE* 1.3 60.0 + - - +
139B ILE* 4.0 7.9 + - + +
210B GLU* 2.9 39.9 + - - +
223B VAL* 3.8 11.7 - - + -
224B TYR 3.5 5.8 - - - +
225B ASN* 3.6 8.7 - - - +
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Residues in contact with PHE 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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107B VAL* 3.4 12.1 - - + -
109B PHE* 3.7 27.1 - + + -
124B VAL* 5.9 0.2 - - + -
125B PHE* 3.7 39.5 - + - -
128B VAL* 3.6 23.8 - - + -
132B LEU* 4.0 6.7 - - + +
137B LYS* 1.3 71.0 - - - +
139B ILE* 1.3 62.4 + - - +
140B MSE 3.9 23.7 + - + -
203B ALA* 5.6 0.2 - - + -
207B PHE* 3.7 35.0 - + + -
222B THR 3.6 1.4 - - - +
223B VAL* 3.5 2.1 - - - -
224B TYR* 2.7 67.0 + + + +
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Residues in contact with ILE 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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32B LEU* 3.7 24.7 - - + +
35B TYR* 4.3 17.7 - - + +
36B MSE 3.6 37.7 - - + -
106B TYR* 4.4 9.6 - - + -
107B VAL 3.0 10.6 + - - +
108B ILE* 3.1 13.0 - - + +
109B PHE* 2.9 23.2 + - - +
110B ILE* 5.3 1.6 - - + +
137B LYS* 4.5 7.9 - - + +
138B PHE* 1.3 79.2 - - - +
140B MSE 1.3 63.3 + - - +
221B LEU* 4.1 20.9 - - + -
222B THR 3.4 8.1 - - - +
223B VAL* 4.4 15.3 - - + -
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Residues in contact with MSE 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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109B PHE* 3.1 36.8 - - + +
110B ILE* 5.6 0.9 - - - -
113B ILE* 3.9 14.4 - - + -
125B PHE* 3.9 31.4 - - + -
138B PHE* 3.9 13.4 + - + -
139B ILE* 1.3 77.0 - - - +
141B TYR* 1.3 67.3 + - - +
142B PHE* 3.7 31.4 - - + -
199B VAL* 3.8 20.4 - - + -
220B TYR 3.9 0.5 - - - +
221B LEU* 3.4 1.9 - - - +
222B THR* 2.9 46.4 + - - +
224B TYR* 4.8 7.2 - - + -
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Residues in contact with TYR 141 (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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28B LEU* 3.9 38.4 - - + -
109B PHE* 2.9 9.9 + - - +
110B ILE* 4.0 8.3 - - + +
111B ASP* 2.8 57.5 + - - -
112B SER 4.6 0.7 + - - -
140B MSE 1.3 80.0 - - - +
142B PHE* 1.3 70.4 + - - +
143B THR* 3.3 16.4 + - - +
151B ARG* 4.7 4.7 + - - -
215B VAL* 4.0 21.2 - - + +
219B SER* 3.4 27.7 + - - -
220B TYR 2.9 31.9 - - - +
221B LEU* 3.9 13.0 - - + -
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Residues in contact with PHE 142 (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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111B ASP* 3.7 13.9 - - - +
113B ILE* 3.5 34.5 - - + -
114B VAL* 6.3 0.4 - - + -
140B MSE 3.7 20.2 - - + -
141B TYR* 1.3 86.4 - - - +
143B THR* 1.3 75.7 + - - +
144B ASP* 3.6 9.5 + - + -
145B LEU 5.7 0.2 - - - -
194B TRP* 3.6 27.1 - - + -
196B LYS* 4.5 13.9 - - + -
199B VAL* 3.7 30.3 - - + -
218B TYR 6.0 2.0 - - - -
219B SER* 3.6 18.1 - - - -
220B TYR* 3.8 12.3 + + + -
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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