Contacts of the strand formed by residues 271 - 280 (chain A) in PDB entry 2VDY
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 THR 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A SER* 4.1 2.5 - - - -
220A TYR* 2.8 41.8 + - + +
221A LEU* 5.5 2.0 - - + -
269A GLY 3.9 9.0 - - - +
270A LEU* 1.3 75.2 - - - +
272A SER* 1.3 70.3 + - - +
273A SER* 3.1 16.8 + - - +
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Residues in contact with SER 272 (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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217A THR* 3.9 21.9 - - - +
218A ILE 3.8 8.1 - - - -
219A SER* 4.4 9.2 + - - +
271A THR* 1.3 76.7 + - - +
273A SER* 1.3 61.2 + - - +
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Residues in contact with SER 273 (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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217A THR* 3.2 7.9 - - - +
218A ILE* 2.8 32.9 + - - +
220A TYR* 3.9 23.1 - - - +
271A THR* 3.1 23.4 + - - +
272A SER* 1.3 73.9 + - - +
274A GLN* 1.3 63.7 + - - +
275A VAL* 3.6 1.6 + - - +
353A ILE* 4.1 17.5 - - - +
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Residues in contact with GLN 274 (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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215A SER* 4.4 15.8 + - - -
216A SER* 3.7 14.7 + - - +
217A THR* 2.6 31.2 + - - +
273A SER* 1.3 71.5 - - - +
275A VAL* 1.3 58.1 + - - +
351A LYS 4.2 10.2 - - - +
352A PRO* 3.4 20.0 - - + +
353A ILE* 2.7 34.7 + - - +
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Residues in contact with VAL 275 (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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214A GLN 3.2 13.7 - - - +
215A SER* 3.4 1.5 - - - -
216A SER 3.1 21.3 + - - +
218A ILE* 4.0 20.4 - - + +
220A TYR* 4.0 32.3 - - + -
231A VAL* 4.7 4.7 - - + -
273A SER* 4.0 10.5 - - - +
274A GLN* 1.3 81.1 - - - +
276A ASP* 1.3 74.6 + - - +
277A LEU* 3.3 16.8 + - + +
352A PRO* 4.3 2.0 - - - +
353A ILE* 3.2 14.6 - - + +
355A LEU* 4.1 15.9 - - + -
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Residues in contact with ASP 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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213A LEU* 4.2 7.4 - - + +
214A GLN 3.7 3.6 - - - -
215A SER* 2.7 33.1 + - - -
275A VAL* 1.3 69.0 - - - +
277A LEU* 1.3 59.4 + - - +
278A TYR* 3.3 30.2 + - + -
352A PRO* 3.5 24.0 - - - +
353A ILE 2.8 11.1 + - - +
354A ILE* 4.2 16.5 - - + +
355A LEU 3.0 22.0 + - - -
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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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189A PHE* 3.6 18.3 - - + -
212A MET 3.5 0.7 - - - +
213A LEU* 3.4 6.3 - - - +
214A GLN* 3.0 34.9 + - + +
218A ILE* 3.9 29.8 - - + -
231A VAL* 3.8 31.2 - - + -
233A MET* 3.7 30.7 - - + -
275A VAL* 3.3 3.6 + - + -
276A ASP* 1.3 70.0 - - - +
278A TYR* 1.3 60.8 + - - +
279A ILE* 4.0 11.9 - - + -
355A LEU* 3.7 11.2 - - + +
357A PHE* 3.8 20.6 - - + -
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Residues in contact with TYR 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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197A GLU* 3.4 18.2 - - - -
211A MET* 3.8 11.3 - - + +
212A MET 3.2 15.7 - - - +
213A LEU* 3.5 37.8 - - + +
276A ASP* 3.3 26.9 + - + +
277A LEU* 1.3 71.3 - - - +
279A ILE* 1.3 61.1 + - - +
354A ILE* 3.8 17.8 - - + +
355A LEU 2.8 15.0 + - - +
356A ARG* 3.4 43.8 + - + -
357A PHE* 2.8 34.3 + - - -
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Residues in contact with ILE 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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185A TRP* 4.5 5.2 - - + -
189A PHE* 3.4 30.5 - - + -
211A MET* 3.5 4.7 - - - -
212A MET* 2.9 47.1 + - + +
243A PHE* 3.8 39.5 - - + -
277A LEU* 3.9 20.0 + - + -
278A TYR* 1.3 78.8 - - - +
280A PRO* 1.3 67.2 - - + +
331A LEU* 4.3 10.8 - - + -
357A PHE* 3.6 22.7 - - + -
361A PHE* 5.7 1.6 - - + -
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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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199A PHE* 4.3 8.1 - - + -
209A VAL* 3.8 32.5 - - + -
210A PRO 3.4 7.2 - - - +
211A MET* 3.5 7.1 - - + -
212A MET* 3.5 9.2 - - - +
279A ILE* 1.3 90.1 - - + +
281A LYS* 1.3 60.7 + - - +
282A VAL* 3.0 28.5 + - + +
331A LEU* 4.1 5.5 - - - +
357A PHE* 3.3 29.6 - - + +
361A PHE* 4.1 13.7 - - + -
382A PRO* 4.4 1.3 - - + -
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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