Contacts of the strand formed by residues 250 - 254 (chain A) in PDB entry 2VLH
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 GLY 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A PHE* 3.4 18.9 - - - -
212A PHE* 3.5 15.9 - - - -
213A TYR 3.0 19.2 + - - -
248A ALA* 3.4 5.6 - - - +
249A ASP* 1.3 77.9 - - - +
251A CYS* 1.3 61.9 + - - +
268A CYS 3.0 17.3 - - - -
269A MET* 3.9 0.2 - - - -
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Residues in contact with CYS 251 (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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88A PHE* 4.0 8.7 - - - -
90A PHE* 3.5 23.8 - - + -
106A LEU* 5.7 0.2 - - - -
212A PHE* 4.4 4.2 - - - +
213A TYR* 3.1 24.5 - - + +
215A ALA* 4.0 19.7 - - + -
245A PHE* 4.2 0.7 - - + -
250A GLY* 1.3 75.3 - - - +
252A THR* 1.3 66.0 + - - +
266A PHE* 4.4 5.6 - - - -
267A LEU* 3.4 10.8 - - - +
268A CYS* 2.9 47.6 + - - -
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Residues in contact with THR 252 (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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99A GLY* 4.8 1.6 - - - -
102A ALA* 3.8 35.2 - - + +
103A GLU* 3.9 17.5 + - + +
106A LEU* 3.8 26.0 - - + +
126A THR* 5.9 1.4 - - - +
213A TYR 2.9 10.0 + - - -
214A ASP* 3.6 18.2 + - - +
215A ALA* 2.8 28.6 + - - +
251A CYS* 1.3 76.2 - - - +
253A MET* 1.3 61.1 + - - +
254A SER 4.4 0.2 - - - -
266A PHE 3.7 3.8 - - - -
267A LEU* 4.0 4.3 - - + -
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Residues in contact with MET 253 (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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88A PHE* 3.4 33.7 - - + -
99A GLY* 3.7 10.7 - - - -
102A ALA* 4.5 0.6 - - - +
215A ALA* 3.5 30.5 - - + +
216A THR* 3.9 4.9 - - - +
218A CYS* 4.5 2.9 - - - -
251A CYS* 4.7 0.4 - - - -
252A THR* 1.3 77.7 - - - +
254A SER* 1.3 78.5 + - - +
255A GLY* 3.7 2.7 - - - +
258A ASP* 5.6 1.3 - - + -
259A CYS* 3.4 27.8 - - - +
265A GLY* 3.1 4.7 - - - -
266A PHE* 2.9 64.1 + - + +
306A LEU* 4.4 2.9 - - + -
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Residues in contact with SER 254 (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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99A GLY* 3.8 9.3 - - - +
216A THR* 3.3 27.7 + - - +
253A MET* 1.3 80.7 - - - +
255A GLY* 1.3 59.8 + - - +
256A LYS* 3.0 14.1 + - - +
257A LYS* 3.1 27.6 + - - +
258A ASP 4.4 0.7 + - - -
1457A PM9 2.5 40.9 + - - -
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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