Contacts of the strand formed by residues 192 - 198 (chain B) in PDB entry 5VEB
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 VAL 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B LYS 3.7 1.6 - - - +
151B VAL* 3.4 6.9 - - - +
152B ASP* 2.9 57.6 + - - +
153B ASN 5.1 1.3 - - - +
191B LYS* 1.3 72.6 - - + +
193B TYR* 1.3 63.8 + - - +
194B ALA* 4.5 6.5 - - + +
209B SER* 3.9 22.7 - - - +
210B PHE 3.4 9.0 - - - +
211B ASN* 3.8 17.0 - - - +
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Residues in contact with TYR 193 (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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118B ILE* 3.4 9.0 - - - +
133B VAL* 4.5 7.9 - - + -
149B TRP* 5.3 1.6 - - + -
150B LYS 3.8 2.2 - - - -
151B VAL* 3.7 29.9 - - + +
180B LEU* 4.4 10.3 - - + -
182B LEU* 3.8 12.2 - - + +
186B ASP 3.7 2.1 + - - -
187B TYR* 2.7 63.9 + + - -
190B HIS* 3.5 35.8 - - + +
191B LYS 3.5 13.5 - - - -
192B VAL* 1.3 68.5 - - - +
194B ALA* 1.3 60.0 + - - +
209B SER* 3.3 4.4 - - - -
210B PHE* 3.1 58.3 + + + -
212B ARG* 4.2 3.4 - - + -
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Residues in contact with ALA 194 (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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118B ILE* 4.1 0.4 - - - -
148B GLN 3.8 0.2 - - - +
149B TRP* 3.3 12.1 - - - -
150B LYS* 2.9 52.2 + - + +
153B ASN* 6.3 0.4 - - - +
192B VAL* 3.9 7.2 - - + -
193B TYR* 1.3 74.3 - - - +
195B CYS* 1.3 60.0 + - - +
196B GLU* 5.2 0.4 - - + +
207B THR* 3.8 22.9 - - + -
208B LYS 3.4 4.0 - - - -
209B SER* 3.8 9.2 - - - -
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Residues in contact with CYS 195 (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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116B VAL* 4.3 1.2 - - - +
118B ILE* 3.9 15.0 - - + +
135B CYS* 2.0 53.4 - - + -
147B VAL* 3.8 20.6 - - - -
148B GLN 3.6 3.6 - - - -
149B TRP* 4.1 5.8 - - + -
194B ALA* 1.3 72.9 - - - +
196B GLU* 1.3 56.8 + - - +
197B VAL* 4.0 10.2 - - - +
206B VAL 3.6 2.4 - - - +
207B THR* 3.4 2.4 - - - -
208B LYS* 2.8 34.3 + - + +
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Residues in contact with GLU 196 (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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146B LYS 3.4 4.7 - - - +
147B VAL* 3.5 1.0 - - - -
148B GLN* 2.8 73.5 + - + +
150B LYS* 2.9 35.2 + - + +
194B ALA 4.1 0.6 - - - -
195B CYS* 1.3 72.3 - - - +
197B VAL* 1.3 63.1 + - - +
198B THR* 5.1 0.4 - - - +
205B PRO* 3.6 29.2 - - + +
206B VAL 3.4 3.1 - - - +
207B THR* 3.7 23.7 + - + +
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Residues in contact with VAL 197 (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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114B PRO* 3.9 20.2 - - + -
116B VAL* 3.6 26.5 - - + -
137B LEU* 3.6 46.7 - - + -
146B LYS 3.3 3.4 - - - +
147B VAL* 4.7 2.7 - - + -
195B CYS* 4.0 7.2 - - - -
196B GLU* 1.3 77.5 - - - +
198B THR* 1.3 68.3 + - - +
199B HIS* 4.7 1.1 - - + -
202B LEU* 3.4 13.9 - - + +
205B PRO* 3.3 5.5 - - - +
206B VAL 2.8 39.5 + - - +
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Residues in contact with THR 198 (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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145B ALA* 3.6 3.6 - - - +
146B LYS* 2.9 50.2 + - + +
148B GLN* 4.3 13.3 + - - -
197B VAL* 1.3 74.0 - - - +
199B HIS* 1.3 67.1 + - - +
202B LEU* 4.7 0.2 - - - -
205B PRO* 4.0 24.7 - - + +
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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