Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 3VI4
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 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLY 3.6 2.3 + - - -
256A ASN* 3.0 43.5 + - - +
257A LEU* 2.8 25.6 + - + -
258A THR* 1.3 80.4 - - - +
260A GLY* 1.3 63.1 + - - +
278A GLY 4.2 8.7 - - - +
279A GLU 3.4 29.8 - - - -
280A GLN* 3.7 16.2 - - - +
281A MET* 3.6 20.4 - - + -
2007A NAG 3.8 33.7 - - - +
327B GLU* 3.0 43.7 + - + +
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Residues in contact with GLY 260 (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 VAL 3.8 3.4 - - - -
253A PRO 3.6 15.4 + - - -
256A ASN* 4.5 2.5 - - - +
258A THR 3.8 1.2 + - - -
259A TYR* 1.3 78.7 - - - +
261A TYR* 1.3 63.1 + - - +
277A SER* 3.4 4.0 - - - -
278A GLY* 2.7 29.9 + - - +
280A GLN 4.8 2.0 + - - -
283A SER* 6.1 0.2 - - - -
284A TYR 5.9 0.6 - - - +
285A PHE* 3.8 26.9 - - - +
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Residues in contact with TYR 261 (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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226A TYR* 5.1 4.0 - + - -
229A SER* 4.9 4.0 + - - -
252A VAL* 2.9 58.1 + - + +
255A GLY* 3.6 33.0 - - - -
256A ASN* 4.1 11.7 - - + -
260A GLY* 1.3 74.2 - - - +
262A VAL* 1.3 65.1 + - - +
263A THR* 3.5 21.1 - - - -
275A ASN* 3.5 26.7 - - + -
276A PHE 3.0 20.4 - - - +
277A SER* 3.9 8.5 - - - +
285A PHE* 4.0 4.0 + - - +
1K NAG 3.3 32.3 - - - -
2K NAG 5.0 5.2 + - - +
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Residues in contact with VAL 262 (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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249A VAL* 3.6 30.7 - - + -
250A ALA 3.5 11.7 - - - +
261A TYR* 1.3 80.1 - - - +
263A THR* 1.3 65.5 + - - +
264A ILE* 5.2 0.2 - - + -
275A ASN* 3.4 6.6 - - - +
276A PHE* 2.9 40.3 + - + +
285A PHE* 3.7 13.9 - - + -
286A GLY* 4.2 5.4 - - - -
289A VAL* 4.1 10.1 - - + -
302A LEU* 4.6 8.5 - - + -
304A VAL* 3.4 37.5 - - + -
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Residues in contact with THR 263 (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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231A LEU* 4.4 5.3 - - - +
249A VAL* 3.4 4.0 - - - -
250A ALA* 2.9 35.9 + - - -
252A VAL* 3.5 11.3 - - - +
261A TYR* 3.5 20.0 - - + -
262A VAL* 1.3 75.4 - - - +
264A ILE* 1.3 65.0 + - - +
265A LEU* 3.8 23.1 - - + -
272A SER* 3.7 18.2 - - - +
274A TYR 3.3 9.0 - - - +
275A ASN* 3.2 17.0 - - - +
1K NAG 4.7 3.4 - - - -
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Residues in contact with ILE 264 (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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240A PHE* 3.8 52.7 - - + -
247A ASP* 4.2 9.9 - - + -
248A PHE 3.0 15.0 - - - +
249A VAL* 4.0 9.9 - - + -
262A VAL* 5.2 0.4 - - + -
263A THR* 1.3 77.4 - - - +
265A LEU* 1.3 61.9 + - - +
272A SER* 4.2 0.7 - - - -
273A LEU* 3.0 31.3 + - + +
274A TYR* 3.0 19.9 + - + +
276A PHE* 3.7 29.6 - - + -
302A LEU* 4.1 12.6 - - + -
334A ILE* 3.9 9.2 - - + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ILE* 3.8 34.1 - - + -
219A THR* 3.8 11.2 - - + -
231A LEU* 5.5 3.6 - - + -
247A ASP* 3.3 4.7 - - - +
248A PHE* 2.7 52.1 + - + +
250A ALA* 4.9 3.8 - - + -
263A THR* 3.8 27.8 - - + +
264A ILE* 1.3 73.2 - - - +
266A ASN* 1.3 60.3 + - - +
267A GLY 3.1 3.3 + - - -
270A ILE* 3.8 36.1 - - + +
271A ARG 3.4 3.6 - - - +
272A SER* 4.2 12.8 - - - +
273A LEU* 4.1 2.7 - - - -
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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