Contacts of the strand formed by residues 174 - 178 (chain D) in PDB entry 5VQ9
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 174 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ASN* 3.2 18.1 + - + +
173D ARG* 1.3 82.5 - - + +
175D VAL* 1.3 65.1 + - - +
288D LYS* 4.5 20.6 - - + +
295D ILE* 3.6 28.5 - - + -
297D THR* 4.2 11.7 - - + +
309D PHE* 4.9 1.3 - - + +
312D ARG* 3.5 42.8 - - + +
313D ALA* 3.7 19.2 - - + +
314D ASP 3.7 1.9 + - - -
315D ILE* 3.7 14.7 + - - +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LEU* 4.3 8.1 - - + -
153D VAL* 3.6 28.3 - - + -
172D ASN 5.9 0.4 - - - +
173D ARG 5.0 1.6 - - - +
174D VAL* 1.3 77.6 - - - +
176D LEU* 1.3 61.2 + - - +
177D LEU* 3.5 24.4 - - + +
192D LEU* 5.1 3.4 - - + -
294D VAL* 4.6 7.6 - - + -
295D ILE 2.9 12.8 + - - +
296D LEU* 3.6 17.3 - - + -
297D THR* 2.9 30.3 + - - +
313D ALA* 4.4 0.2 - - - -
315D ILE* 3.4 28.5 - - + +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D VAL* 1.3 71.7 - - - +
177D LEU* 1.3 82.3 + - - +
178D HIS* 4.2 17.5 - - + -
254D VAL* 4.8 3.4 - - + -
297D THR* 3.4 24.0 - - - +
298D THR 4.2 0.4 - - - +
299D SER* 4.0 23.1 - - - +
306D ASP* 6.2 3.6 - - + -
309D PHE* 4.4 19.7 - - + +
310D VAL* 4.8 3.1 - - + +
313D ALA* 3.7 14.4 - - + +
315D ILE 2.8 11.6 + - - +
316D LYS* 3.4 26.5 - - + -
317D GLN* 3.0 24.9 + - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LEU* 4.0 20.4 - - + -
175D VAL* 3.5 23.6 - - + +
176D LEU* 1.3 80.0 - - - +
178D HIS* 1.3 60.6 + - - +
185D LYS* 3.5 29.6 - - + +
188D LEU* 3.7 35.0 - - + -
189D CYS* 4.0 13.9 - - - -
192D LEU* 5.7 2.9 - - + -
297D THR 3.0 14.2 + - - +
298D THR* 3.1 13.1 - - + -
299D SER 3.1 19.9 + - - -
317D GLN* 3.5 7.0 - - + +
319D ILE* 4.4 10.5 - - + -
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Residues in contact with HIS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 4.2 24.0 - - + -
177D LEU* 1.3 75.2 - - - +
179D GLY* 1.3 59.3 + - - +
185D LYS* 4.0 4.3 - - - -
299D SER* 3.1 16.6 - - - +
301D ILE 5.1 0.4 - - - +
302D THR* 2.7 43.5 + - - -
316D LYS* 4.2 14.2 - - + +
317D GLN 3.0 35.3 + - - -
318D TYR* 3.4 27.9 + + + -
319D ILE* 3.0 25.3 + - - +
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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