Contacts of the strand formed by residues 234 - 239 (chain K) in PDB entry 3VD1
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 GLN 234 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K MET* 3.5 14.8 - - - +
179K PRO* 3.6 14.8 - - + +
190K VAL* 5.2 4.8 - - + +
191K VAL 3.4 23.9 + - - +
192K LYS* 3.0 27.7 + - + +
212K SER* 3.1 35.5 + - - -
213K HIS* 3.3 34.7 - - + +
214K LEU 4.4 1.0 - - - +
226K VAL 3.8 1.3 - - - -
227K ASP* 3.3 19.5 - - - +
232K GLY 3.6 5.1 + - - +
233K ARG* 1.3 78.1 - - - +
235K SER* 1.3 63.3 + - - +
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Residues in contact with SER 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K ARG* 3.2 35.6 + - - -
177K ALA 3.5 7.2 - - - -
178K MET* 3.4 26.9 - - - +
179K PRO* 5.2 0.4 - - - -
213K HIS* 3.7 7.6 - - - -
215K ILE* 5.5 1.8 - - - -
225K TYR* 3.4 4.0 - - - -
226K VAL* 2.9 40.6 + - - +
233K ARG* 4.8 1.4 + - - +
234K GLN* 1.3 73.3 - - - +
236K VAL* 1.3 61.3 + - - +
237K VAL 4.2 0.2 - - - -
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Residues in contact with VAL 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K ILE 3.6 1.6 - - - +
176K ARG* 3.5 2.2 - - - -
177K ALA* 3.1 31.9 + - + +
215K ILE* 3.4 38.8 - - + +
217K VAL* 4.1 21.5 - - + +
223K SER* 4.8 0.4 - - - -
224K GLN 3.5 11.0 - - - +
225K TYR* 3.8 34.1 - - + +
235K SER* 1.3 76.1 - - - +
237K VAL* 1.3 66.7 + - - +
238K VAL* 4.0 3.1 + - + +
254K TYR* 4.4 10.0 + - + -
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Residues in contact with VAL 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174K ALA* 3.3 31.4 - - + -
175K ILE 3.2 10.1 - - - +
176K ARG* 4.1 29.2 - - + +
222K LEU 4.6 1.2 - - - +
223K SER* 4.1 1.2 - - - -
224K GLN* 2.9 59.3 + - - +
226K VAL* 3.6 14.8 - - + -
236K VAL* 1.3 73.9 - - - +
238K VAL* 1.3 59.2 + - - +
239K PRO* 4.7 0.5 - - - +
278K GLU* 4.6 2.5 - - - +
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Residues in contact with VAL 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174K ALA* 4.2 2.5 - - - -
175K ILE* 2.6 43.2 + - + +
217K VAL* 4.1 15.7 - - + -
220K ASN* 3.2 44.4 - - + +
223K SER* 4.2 11.9 - - - -
236K VAL* 4.0 3.5 + - + -
237K VAL* 1.3 72.7 - - - +
239K PRO* 1.3 71.5 - - + +
252K ILE* 4.1 31.6 - - + -
254K TYR* 5.4 2.7 - - + +
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Residues in contact with PRO 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K GLY* 5.6 6.3 - - - +
173K THR 3.8 7.6 - - - +
174K ALA* 4.0 6.0 - - + -
220K ASN* 3.8 12.1 + - - +
222K LEU* 4.1 32.5 - - + +
237K VAL 4.5 0.6 - - - +
238K VAL* 1.3 102.6 - - + +
240K TYR* 1.3 66.2 + - - +
241K GLU* 3.5 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