Contacts of the strand formed by residues 256 - 263 (chain B) in PDB entry 3DVA
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 ALA 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ILE* 4.1 1.9 - - - +
205B THR* 3.2 22.7 - - + +
207B ILE* 4.8 1.3 - - + -
250B VAL* 3.9 19.1 - - + -
255B ARG* 1.3 76.5 - - - +
257B ILE* 1.3 72.6 + - - +
276B ILE* 4.5 6.1 - - + -
284B LEU* 5.0 0.8 - - - +
286B ALA 5.4 1.2 + - - -
287B PRO 4.0 3.1 - - - +
288B VAL* 3.3 43.4 - - + +
289B LEU 3.5 0.3 + - - -
321B VAL* 4.3 3.4 - - - +
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Residues in contact with ILE 257 (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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204B ILE* 4.1 6.7 - - + -
205B THR 2.9 6.6 + - - +
206B ILE* 3.5 37.5 - - + -
207B ILE* 3.0 26.7 + - - +
256B ALA* 1.3 80.5 - - - +
258B VAL* 1.3 66.7 + - - +
259B VAL* 4.3 7.6 - - + -
288B VAL* 4.3 0.7 - - - -
289B LEU 3.1 15.0 - - - +
291B VAL* 4.4 7.4 - - + -
314B VAL* 3.9 22.2 - - + +
317B THR* 4.0 12.3 - - + +
318B ALA* 4.0 15.9 - - + +
321B VAL* 3.4 26.5 - - + -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.4 20.9 - - + +
208B ALA* 5.6 0.7 - - - -
209B TYR* 5.8 2.0 - - + -
235B LEU* 5.7 1.1 - - + -
257B ILE* 1.3 78.6 - - - +
259B VAL* 1.3 63.4 + - - +
260B GLN 4.2 0.2 + - - -
268B ILE* 5.4 2.9 - - + -
269B ALA* 3.6 32.8 - - + +
272B VAL* 3.9 28.3 - - + -
273B VAL* 3.8 23.1 - - + -
276B ILE* 4.8 0.7 - - + -
288B VAL* 4.1 9.0 - - + -
289B LEU 2.9 6.7 + - - -
290B ARG* 3.3 9.0 - - + +
291B VAL 2.8 31.4 + - - +
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Residues in contact with VAL 259 (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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206B ILE* 4.0 19.5 - - + -
207B ILE 2.7 17.0 + - - +
208B ALA* 3.5 26.3 - - + +
209B TYR* 4.1 6.6 + - - -
212B MET* 3.8 29.3 - - + +
216B SER* 4.1 2.7 - - - +
257B ILE* 4.3 4.3 - - + -
258B VAL* 1.3 79.3 - - - +
260B GLN* 1.3 64.5 + - - +
291B VAL* 3.4 35.0 - - + -
314B VAL* 3.8 26.0 - - + -
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Residues in contact with GLN 260 (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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209B TYR* 3.3 23.4 + - + +
212B MET* 3.5 9.9 - - - +
259B VAL* 1.3 76.2 - - - +
261B GLU* 1.3 60.3 + - - +
262B ALA* 3.4 10.4 + - - +
263B GLN 2.9 28.9 + - - -
264B ARG* 4.1 4.0 + - - +
266B ALA 3.1 12.0 + - - -
267B GLY* 3.3 6.3 - - - -
268B ILE 3.1 26.0 + - - -
269B ALA* 3.2 23.6 + - + +
290B ARG* 6.0 0.8 - - - +
291B VAL 2.8 17.5 + - - +
292B ALA* 3.5 24.5 - - + +
309B PRO* 3.6 8.8 - - - +
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Residues in contact with GLU 261 (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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118B PHE* 5.8 2.0 - - + -
119B GLY* 3.3 6.7 - - - -
120B GLY* 2.8 32.7 + - - +
129B SER 4.5 1.9 - - - +
131B SER* 4.1 14.0 + - - +
172B HIS* 2.9 26.3 + - - -
209B TYR* 5.0 3.6 + - + -
211B ALA* 3.8 10.8 + - - +
212B MET* 3.4 26.5 - - + +
260B GLN* 1.3 70.7 - - - +
262B ALA* 1.3 65.7 + - - +
293B ALA* 3.5 16.0 - - - +
298B TYR* 4.7 2.8 + - + -
307B TRP* 4.3 6.4 - - - -
308B LEU* 3.8 22.7 - - + +
309B PRO* 4.1 5.4 - - + +
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Residues in contact with ALA 262 (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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131B SER* 3.5 33.5 + - - +
133B GLU* 3.5 14.3 + - - +
260B GLN* 3.3 12.2 + - - +
261B GLU* 1.3 80.6 - - - +
263B GLN* 1.3 70.3 + - - +
267B GLY* 3.7 24.2 - - - +
292B ALA* 3.5 1.9 - - - +
293B ALA* 3.1 16.7 + - - -
307B TRP* 5.7 0.2 - - - -
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Residues in contact with GLN 263 (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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130B ASP* 5.4 4.2 + - - +
131B SER* 4.3 10.8 + - - +
132B LEU* 6.0 0.5 - - - +
260B GLN* 2.9 16.8 + - - -
261B GLU 4.0 0.2 + - - -
262B ALA* 1.3 77.4 - - - +
264B ARG* 1.3 60.8 + - - +
265B GLN* 4.2 2.7 - - + +
266B ALA* 2.9 30.6 + - + +
293B ALA* 3.5 9.6 - - - +
294B PRO 3.3 16.6 - - - +
295B ASP* 3.6 12.3 - - - +
296B THR 3.2 23.1 + - - +
297B VAL* 4.5 0.4 - - - +
298B TYR* 3.8 20.2 - - - +
307B TRP* 4.0 14.5 - - + -
140D PRO* 3.9 21.2 - - + +
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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