Contacts of the strand formed by residues 275 - 281 (chain B) in PDB entry 3NVQ
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 PHE 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B LEU* 4.1 23.1 - - + -
265B ALA* 4.9 0.7 - - + -
266B ARG 3.8 2.5 - - - -
267B ILE* 3.5 22.8 - - + +
273B VAL* 3.9 4.4 + - + +
274B LEU* 1.3 77.8 - - - +
276B GLN* 1.3 59.7 + - - +
277B GLY* 3.2 34.5 - - - -
278B GLN* 3.9 13.2 - - + -
342B ARG* 3.1 41.0 + - + +
343B VAL 3.4 23.3 - - - -
347B PHE* 4.2 26.7 - + + -
348B LYS 5.2 0.9 - - - +
349B THR* 3.9 22.0 - - + -
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Residues in contact with GLN 276 (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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242B GLY 5.4 0.8 + - - -
243B SER* 2.6 28.0 + - - -
266B ARG* 2.9 51.6 + - - +
267B ILE 3.1 13.2 - - - -
268B ALA* 3.5 22.9 - - + +
274B LEU* 3.3 18.6 - - + +
275B PHE* 1.3 75.9 - - - +
277B GLY* 1.3 58.0 + - - +
340B ALA 3.4 12.6 - - - +
342B ARG* 3.7 36.2 + - - +
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Residues in contact with GLY 277 (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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265B ALA* 3.7 0.3 - - - -
266B ARG* 2.9 28.9 + - - -
275B PHE* 3.2 21.2 - - - -
276B GLN* 1.3 82.0 - - - +
278B GLN* 1.3 60.1 + - - +
340B ALA* 3.7 11.0 - - - -
341B LYS 3.2 21.1 - - - -
342B ARG* 4.0 0.4 - - - +
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Residues in contact with GLN 278 (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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248B TYR* 3.2 20.5 + - - +
263B SER* 4.5 7.9 + - - -
264B MET 3.4 9.6 - - - +
265B ALA* 5.1 0.4 - - - -
275B PHE* 3.9 10.3 - - + -
277B GLY* 1.3 75.4 - - - +
279B ALA* 1.3 68.0 + - - +
280B SER* 5.7 0.2 + - - -
339B ARG 4.1 1.6 - - - +
340B ALA* 3.3 11.4 - - - +
341B LYS* 3.2 14.8 + - - +
343B VAL* 4.5 8.0 - - + +
345B TRP* 3.6 11.0 + - - +
346B ASP* 2.8 46.2 + - - +
347B PHE* 4.0 8.9 - - + -
360B PRO* 3.5 34.9 - - - +
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Residues in contact with ALA 279 (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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263B SER* 3.2 5.3 - - - -
264B MET* 3.0 31.8 + - - +
278B GLN* 1.3 82.2 - - - +
280B SER* 1.3 62.2 + - - +
281B LEU* 4.3 2.1 - - + +
336B ILE* 4.6 8.3 - - + +
339B ARG 3.9 4.5 - - - +
340B ALA* 3.7 21.8 - - + +
360B PRO* 4.5 2.5 - - - -
361B GLU 3.6 13.5 - - - +
363B VAL* 3.9 16.8 - - + -
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Residues in contact with SER 280 (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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261B TRP* 3.4 38.9 - - - +
262B PRO 3.4 10.8 - - - -
263B SER* 4.0 4.8 + - - -
279B ALA* 1.3 73.2 - - - +
281B LEU* 1.3 56.9 + - - +
360B PRO* 3.9 17.5 + - - +
361B GLU 3.0 10.0 + - - -
362B ARG* 3.9 10.5 - - - -
363B VAL* 2.7 37.7 + - - +
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Residues in contact with LEU 281 (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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261B TRP* 5.2 2.8 - - - +
262B PRO* 2.9 29.2 + - + +
263B SER* 3.8 26.0 - - - +
264B MET* 3.9 13.7 - - + -
279B ALA* 4.3 4.3 - - + +
280B SER* 1.3 82.5 - - - +
282B ASP* 1.3 61.1 + - - +
283B CYS 3.6 2.8 + - - -
291B ARG 5.6 0.2 - - - +
294B LEU* 5.3 2.0 - - + -
306B TRP* 3.8 28.3 - - + -
310B PHE* 4.0 19.1 - - + -
331B PHE* 3.9 17.3 - - + -
336B ILE* 3.4 34.3 - - + -
363B VAL* 3.9 7.4 - - + -
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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