Contacts of the strand formed by residues 318 - 331 (chain B) 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 LEU 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B LEU* 4.9 0.9 - - + -
172B ILE* 3.8 26.0 - - + -
173B LEU* 3.9 22.4 - - + -
307B ALA 3.5 14.4 + - - +
309B PHE* 3.0 36.4 + - + +
312B ILE* 4.1 20.9 - - + -
313B THR* 3.8 10.1 - - + -
316B ALA* 3.3 33.8 + - + +
317B GLN* 1.3 77.5 - - - +
319B LYS* 1.3 61.8 + - - +
346B ALA* 3.8 24.2 - - + -
347B ILE 3.5 7.2 - - - +
349B ARG* 3.7 4.0 - - - +
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Residues in contact with LYS 319 (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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302B LEU 3.6 7.6 - - - +
303B PHE 4.1 10.3 + - - +
304B THR 3.4 31.2 - - - +
305B THR* 4.0 20.7 + - - +
307B ALA* 3.8 1.1 - - + -
309B PHE* 3.7 8.1 - - - -
318B LEU* 1.3 75.7 - - - +
320B SER* 1.3 63.3 + - - +
321B SER* 3.7 0.4 + - - +
346B ALA* 3.3 5.5 - - - -
347B ILE* 2.9 62.6 + - + +
348B PRO 4.4 1.8 - - - -
349B ARG* 3.8 22.8 - - + +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 2.7 28.0 + - - -
303B PHE* 3.4 48.0 - - - +
309B PHE* 3.9 6.7 - - - -
319B LYS* 1.3 75.0 - - - +
321B SER* 1.3 60.3 + - - +
322B LYS 4.2 0.9 + - - -
323B VAL* 3.7 4.7 - - - +
344B LEU* 3.4 33.4 - - - +
345B GLU 3.4 6.6 + - - -
346B ALA* 4.5 0.2 - - - +
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Residues in contact with SER 321 (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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169B SER* 3.5 27.4 + - - -
303B PHE* 5.0 5.9 - - - -
319B LYS* 3.7 0.6 + - - +
320B SER* 1.3 74.5 - - - +
322B LYS* 1.3 65.1 + - - +
345B GLU* 3.0 24.4 + - - +
347B ILE* 3.5 33.0 - - - +
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Residues in contact with LYS 322 (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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165B SER 4.3 15.5 - - - -
169B SER* 4.7 7.6 - - - +
289B ASP* 3.3 23.8 + - - +
291B GLY* 6.4 0.2 - - - -
303B PHE* 5.5 1.3 - - - -
320B SER 3.8 0.8 - - - -
321B SER* 1.3 83.1 + - - +
323B VAL* 1.3 67.5 + - - +
324B VAL* 3.7 26.5 - - + -
343B PHE* 3.8 6.4 - - + +
344B LEU* 3.4 3.8 - - - -
345B GLU* 2.9 56.5 + - + +
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Residues in contact with VAL 323 (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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52B LEU* 5.2 0.9 - - + -
289B ASP* 3.6 5.6 + - - +
290B LEU* 2.9 49.5 + - + -
291B GLY* 4.0 5.5 + - - +
294B LEU* 4.0 17.7 - - + -
303B PHE* 3.9 16.1 - - + -
320B SER* 3.7 17.0 - - - +
322B LYS* 1.3 82.3 - - - +
324B VAL* 1.3 67.0 + - - +
342B MET* 3.7 28.3 - - + -
343B PHE 3.4 3.4 - - - +
344B LEU* 3.8 16.4 - - + -
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Residues in contact with VAL 324 (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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163B LEU* 4.3 10.3 - - + +
165B SER 5.2 3.8 - - - +
287B VAL* 4.1 23.8 - - + -
288B TYR 3.3 10.1 - - - +
289B ASP* 4.5 8.1 - - + +
290B LEU* 4.8 0.4 - - - +
322B LYS* 3.7 31.6 - - + +
323B VAL* 1.3 80.7 - - - +
325B HIS* 1.3 65.8 + - - +
326B LYS* 4.9 0.4 - - + +
341B ALA 4.0 0.3 - - - +
342B MET* 3.3 6.5 - - - +
343B PHE* 3.0 62.5 + - + -
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Residues in contact with HIS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.7 19.1 - - + -
44B SER* 3.0 50.0 + - - -
47B SER* 4.1 9.2 - - - -
48B ILE* 3.8 20.2 - - + +
287B VAL* 3.6 0.9 - - - -
288B TYR* 2.9 48.8 + + + +
290B LEU* 3.9 18.4 - - + +
324B VAL* 1.3 76.9 - - - +
326B LYS* 1.3 66.1 + - - +
327B ALA* 3.8 8.9 - - + +
341B ALA 3.1 25.6 + - - -
342B MET* 3.8 11.0 - - + +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LYS 5.7 0.2 - - - -
160B ILE* 3.6 18.7 - - + +
161B VAL* 2.8 36.0 + - - +
162B ASP* 4.3 10.7 + - - +
163B LEU* 3.8 19.1 - - + +
285B SER* 5.3 7.0 - - - -
286B GLY 3.3 11.9 - - - +
287B VAL* 4.0 26.5 - - + +
324B VAL* 5.6 0.4 - - + -
325B HIS* 1.3 76.7 - - - +
327B ALA* 1.3 66.3 + - - +
328B VAL* 5.0 12.8 - - - -
340B GLY* 3.4 1.6 - - - -
341B ALA 2.8 37.4 + - - +
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Residues in contact with ALA 327 (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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42B PHE* 3.4 37.5 - - + +
43B ILE* 4.3 3.8 - - - -
44B SER* 4.5 0.7 - - - +
160B ILE* 4.0 1.1 - - - -
285B SER* 3.2 5.7 - - - -
286B GLY 3.1 31.1 + - - -
325B HIS* 3.8 14.8 - - - +
326B LYS* 1.3 77.4 - - - +
328B VAL* 1.3 63.5 + - - +
339B ALA 3.2 10.8 - - - +
340B GLY* 4.2 4.3 - - - -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.1 11.7 - - - -
159B LYS* 3.5 52.3 - - + +
160B ILE* 3.8 6.3 - - + -
284B ILE 3.5 4.7 - - - +
285B SER* 3.7 17.9 - - - -
326B LYS* 5.0 9.0 - - - -
327B ALA* 1.3 78.5 - - - +
329B LEU* 1.3 60.8 + - - +
330B GLN* 6.3 1.8 - - + +
337B GLU 4.6 0.7 - - - +
338B ALA* 3.4 1.7 - - - -
339B ALA* 2.8 43.4 + - + +
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Residues in contact with LEU 329 (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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42B PHE* 3.5 42.8 - - + -
282B VAL* 4.0 14.8 - - + -
283B THR* 3.4 6.6 - - - +
284B ILE* 2.8 54.2 + - + +
328B VAL* 1.3 75.6 - - - +
330B GLN* 1.3 70.3 + - - +
331B LEU* 3.8 21.8 - - + -
336B THR* 3.8 17.0 - - + -
337B GLU 3.5 2.5 - - - -
338B ALA* 4.0 4.3 - - + -
363B ILE* 4.0 22.2 - - + -
365B ILE* 4.6 6.5 - - + -
377B ALA* 4.5 0.2 - - + -
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Residues in contact with GLN 330 (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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159B LYS* 3.5 36.1 + - + +
282B VAL 3.2 4.3 - - - +
283B THR* 4.0 22.2 - - + +
328B VAL* 6.3 1.7 - - + +
329B LEU* 1.3 79.8 - - - +
331B LEU* 1.3 65.4 + - - +
332B ASN* 5.5 5.9 + - - +
335B GLY 4.2 0.2 - - - +
336B THR* 3.4 5.4 - - - +
337B GLU* 2.7 57.0 + - + +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TRP* 4.4 10.1 - - + -
212B MET* 4.7 3.8 - - + -
235B TYR* 5.3 0.4 - - - +
243B PHE* 3.9 30.7 - - + -
279B ILE* 4.2 13.9 - - + -
280B PRO 4.4 2.5 - - - +
281B LYS* 3.5 11.6 - - - +
282B VAL* 2.7 54.4 + - + +
283B THR* 5.4 0.2 + - - -
329B LEU* 3.8 26.0 - - + -
330B GLN* 1.3 77.6 - - - +
332B ASN* 1.3 63.0 + - - +
335B GLY 3.9 1.8 - - - -
336B THR* 3.5 23.3 - - + +
361B PHE* 5.4 0.2 - - + -
363B ILE* 4.3 8.7 - - + -
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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