Contacts of the strand formed by residues 275 - 280 (chain A) in PDB entry 5NV6
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 TYR 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ILE* 4.2 15.0 - - + +
268A MET* 4.2 38.0 - - + +
269A LEU* 6.0 1.3 - - + -
271A GLY 5.0 1.6 - - - -
272A ASN 4.8 4.1 + - - -
273A GLY* 4.1 16.8 - - - -
274A GLN* 1.3 76.2 - - - +
276A THR* 1.3 64.7 + - - +
277A LEU 4.2 0.4 - - - -
311A ILE* 4.0 17.9 - - + -
312A LEU 3.3 17.9 - - - +
313A LYS* 4.0 15.5 - - - -
315A ALA* 3.7 3.8 - - - +
330A LEU* 4.5 13.5 - - + -
361A ASN* 2.9 21.0 + - + +
362A GLY* 3.1 3.6 - - - -
363A VAL 3.0 23.2 + - - +
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Residues in contact with THR 276 (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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275A TYR* 1.3 72.4 + - - +
277A LEU* 1.3 62.2 + - - +
278A LEU* 3.9 3.5 + - + -
310A HIS 3.5 1.7 - - - +
311A ILE* 3.4 4.6 - - - -
312A LEU* 2.8 59.1 + - + +
314A SER 2.7 26.6 + - - -
315A ALA* 3.1 2.6 - - - -
316A MET* 2.9 24.8 + - + +
363A VAL* 3.3 7.1 - - - +
365A HIS* 3.8 29.2 - - + -
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Residues in contact with LEU 277 (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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243A ILE* 3.7 25.5 - - + +
247A ILE* 3.7 31.9 - - + -
256A LEU* 4.5 11.7 - - + -
269A LEU* 4.7 11.9 - - + -
275A TYR 4.2 0.8 - - - -
276A THR* 1.3 72.6 - - - +
278A LEU* 1.3 60.8 + - - +
279A ALA* 3.0 20.6 + - + +
307A LEU 5.1 0.4 - - - +
310A HIS* 3.4 22.2 - - + +
311A ILE* 3.7 22.7 - - + -
363A VAL 2.9 9.7 + - - -
364A ILE* 3.4 14.3 - - + +
365A HIS 2.9 25.7 + - - -
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Residues in contact with LEU 278 (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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276A THR* 4.8 4.5 - - + -
277A LEU* 1.3 68.8 - - - +
279A ALA* 1.3 61.9 + - - +
280A PRO* 3.4 1.2 - - - +
310A HIS* 2.8 46.6 + - - +
312A LEU* 4.6 22.0 - - + -
335A LEU* 4.0 16.2 - - + -
337A VAL* 5.9 0.4 - - + -
346A ILE* 4.2 17.3 - - + -
352A ILE* 3.9 24.5 - - + -
365A HIS* 3.3 26.9 - - + -
367A ILE* 3.4 16.8 - - + +
371A LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 279 (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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247A ILE* 4.2 1.6 - - + -
253A PHE* 3.5 27.4 - - + -
256A LEU* 3.8 7.0 - - + -
277A LEU* 3.0 26.3 + - + -
278A LEU* 1.3 70.6 - - - +
280A PRO* 1.4 69.0 - - - +
281A THR 3.6 0.3 + - - -
364A ILE* 3.8 14.4 - - + -
365A HIS 3.0 7.6 + - - +
366A TYR* 3.5 4.5 - - - -
367A ILE* 2.9 22.5 + - - -
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Residues in contact with PRO 280 (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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252A THR 4.4 0.3 - - - +
253A PHE* 3.4 13.2 - - - -
256A LEU* 3.7 24.4 - - + +
277A LEU* 5.6 0.2 - - + -
278A LEU 3.4 8.7 - - - +
279A ALA* 1.4 82.6 - - - +
281A THR* 1.3 63.6 + - - +
284A ALA* 3.9 8.3 - - + -
285A PHE* 3.7 28.3 - - + -
307A LEU* 6.1 0.7 - - + -
310A HIS* 4.0 18.2 - - + +
367A ILE* 3.4 17.5 - - + +
369A GLU 4.5 0.2 - - - +
370A LEU* 3.7 23.8 - - + -
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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