Contacts of the strand formed by residues 318 - 331 (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 LEU 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.6 4.0 - - + -
172A ILE* 3.6 26.5 - - + -
173A LEU* 4.1 20.2 - - + -
307A ALA* 3.7 15.4 + - - +
309A PHE* 3.4 41.8 + - + +
312A ILE* 4.5 6.3 - - + -
313A THR* 4.4 15.5 - - + -
316A ALA* 3.6 32.8 + - + +
317A GLN* 1.3 76.3 - - - +
319A LYS* 1.3 61.0 + - - +
346A ALA* 4.0 18.8 - - + -
347A ILE 3.5 11.9 - - - +
348A PRO* 4.3 1.3 - - + -
349A ARG* 4.2 2.6 - - - -
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Residues in contact with LYS 319 (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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302A LEU 3.8 5.6 - - - +
303A PHE 3.8 15.6 + - - +
304A THR 3.5 29.6 - - - +
305A THR* 4.1 16.0 + - - +
307A ALA* 3.8 4.5 - - + -
309A PHE* 4.3 6.3 - - - -
318A LEU* 1.3 74.7 - - - +
320A SER* 1.3 63.4 + - - +
321A SER* 5.5 1.8 - - - +
346A ALA* 3.2 5.1 - - - -
347A ILE* 2.9 64.1 + - + +
348A PRO 4.5 4.3 - - - -
349A ARG* 4.0 20.3 - - + +
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 2.8 33.3 + - - -
303A PHE* 3.4 43.7 - - - +
309A PHE* 4.2 12.7 - - - -
319A LYS* 1.3 74.2 - - - +
321A SER* 1.3 60.8 + - - +
322A LYS 3.9 1.2 + - - -
323A VAL* 3.6 14.6 - - - +
344A LEU* 3.9 11.6 - - - +
345A GLU 3.4 11.1 + - - -
346A ALA* 4.4 1.3 - - - +
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Residues in contact with SER 321 (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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169A SER* 5.6 3.1 + - - -
170A PRO 5.3 0.5 + - - -
171A ALA* 4.8 0.2 - - - +
303A PHE* 4.8 6.5 - - - -
319A LYS* 3.7 4.4 + - - +
320A SER* 1.3 74.1 - - - +
322A LYS* 1.3 67.8 + - - +
345A GLU* 2.8 30.5 + - - +
347A ILE* 3.8 36.3 - - - +
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Residues in contact with LYS 322 (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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168A ASP* 3.3 42.6 - - + +
169A SER* 5.4 1.8 - - - +
289A ASP* 2.8 29.9 + - - +
303A PHE* 5.0 2.5 - - - -
320A SER* 3.6 1.4 + - - -
321A SER* 1.3 85.4 + - - +
323A VAL* 1.3 65.7 + - - +
324A VAL* 3.7 17.5 - - + -
343A PHE* 3.8 2.6 - - + +
344A LEU* 3.5 3.6 - - - -
345A GLU* 2.9 48.1 + - + +
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Residues in contact with VAL 323 (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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52A LEU* 5.3 2.5 - - + -
289A ASP* 3.5 9.0 + - - +
290A LEU* 2.9 43.7 + - + -
291A GLY* 5.0 0.6 - - - +
294A LEU* 4.1 16.2 - - + -
302A LEU* 5.4 2.0 - - + -
303A PHE* 3.7 21.9 - - + -
320A SER* 3.6 16.6 - - - +
322A LYS* 1.3 78.8 - - - +
324A VAL* 1.3 64.7 + - - +
342A MET* 3.7 31.0 - - + -
343A PHE 3.5 2.2 - - - -
344A LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 324 (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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163A LEU* 5.1 3.9 - - + +
168A ASP* 4.3 4.7 - - - +
287A VAL* 3.8 26.2 - - + -
288A TYR 3.3 9.9 - - - +
289A ASP* 4.4 8.5 - - + +
290A LEU* 4.8 0.7 - - - -
322A LYS* 3.7 28.0 - - + -
323A VAL* 1.3 79.2 - - - +
325A HIS* 1.3 67.0 + - - +
326A LYS* 5.4 1.6 - - + -
341A ALA 4.1 0.3 - - - +
342A MET* 3.4 6.6 - - - +
343A PHE* 2.9 71.2 + - + -
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Residues in contact with HIS 325 (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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43A ILE* 3.7 29.3 - - + -
44A SER* 3.1 34.1 + - - -
47A SER* 4.0 14.8 - - - -
48A ILE* 4.0 10.3 - - + +
287A VAL* 3.5 1.9 - - - -
288A TYR* 2.7 47.6 + + + +
290A LEU* 3.9 20.8 - - + +
324A VAL* 1.3 76.9 - - - +
326A LYS* 1.3 63.9 - - - +
327A ALA* 4.0 5.6 - - + +
340A GLY* 4.3 1.1 - - - -
341A ALA 3.1 34.1 + - - -
342A MET* 3.5 17.5 - - + +
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Residues in contact with LYS 326 (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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160A ILE* 3.8 21.6 - - + +
161A VAL 2.8 30.8 + - - +
162A ASP* 3.6 14.7 + - - +
163A LEU* 3.8 22.4 - - + +
285A SER* 5.4 6.3 - - - -
286A GLY 3.3 13.0 - - - +
287A VAL* 3.9 26.2 - - + +
324A VAL* 5.4 0.2 - - + -
325A HIS* 1.3 77.0 - - - +
327A ALA* 1.3 65.2 + - - +
328A VAL* 5.1 11.9 - - - -
340A GLY* 3.3 1.0 - - - -
341A ALA 2.8 37.4 + - - -
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Residues in contact with ALA 327 (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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42A PHE* 3.3 38.9 + - + +
43A ILE* 4.4 3.1 - - - -
160A ILE* 4.1 1.6 - - - -
285A SER* 3.3 4.0 - - - -
286A GLY 3.1 31.1 + - - +
325A HIS* 4.0 13.2 - - - +
326A LYS* 1.3 75.5 - - - +
328A VAL* 1.3 64.2 + - - +
339A ALA 3.2 14.8 - - - +
340A GLY* 4.0 2.9 - - - -
375A PHE* 5.4 0.9 - - + -
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Residues in contact with VAL 328 (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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42A PHE* 3.3 8.8 - - - -
159A LYS* 3.7 41.1 - - + +
160A ILE* 3.9 7.4 - - + -
284A ILE 3.4 6.5 - - - +
285A SER* 3.6 21.5 - - - -
326A LYS* 5.1 8.7 - - - -
327A ALA* 1.3 75.6 - - - +
329A LEU* 1.3 61.1 + - - +
330A GLN* 6.2 2.5 - - + +
337A GLU 4.6 1.1 - - - +
338A ALA* 3.4 2.5 - - - -
339A ALA* 2.9 51.3 + - + +
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Residues in contact with LEU 329 (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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42A PHE* 3.6 43.3 - - + -
282A VAL* 3.4 11.2 - - + +
283A THR* 3.3 6.8 - - - +
284A ILE* 2.8 53.3 + - + +
328A VAL* 1.3 75.5 - - - +
330A GLN* 1.3 72.3 + - - +
331A LEU* 4.1 12.3 - - + -
336A THR* 3.7 27.1 - - + -
337A GLU 3.7 0.7 - - - -
338A ALA* 4.4 3.4 - - + -
363A ILE* 3.8 26.2 - - + -
365A ILE* 4.8 4.9 - - + -
377A ALA* 4.7 0.2 - - + -
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Residues in contact with GLN 330 (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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159A LYS* 3.9 29.5 + - + +
282A VAL 3.3 3.6 - - - -
283A THR* 4.2 23.6 - - + +
328A VAL* 6.2 2.6 - - + +
329A LEU* 1.3 77.4 - - - +
331A LEU* 1.3 63.4 + - - +
332A ASN* 5.4 8.2 + - - +
336A THR* 3.4 9.0 - - - +
337A GLU* 2.8 57.1 + - + +
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Residues in contact with LEU 331 (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* 4.1 14.1 - - + -
212A MET* 4.3 6.3 - - + -
235A TYR* 5.0 0.7 - - - +
243A PHE* 4.3 15.3 - - + -
279A ILE* 4.3 5.8 - - + -
280A PRO 4.1 9.0 - - - +
281A LYS* 3.4 24.1 - - - +
282A VAL* 2.8 46.0 + - + +
283A THR* 5.4 1.0 + - - -
329A LEU* 4.1 9.9 - - + -
330A GLN* 1.3 74.1 - - - +
332A ASN* 1.3 62.5 + - - +
335A GLY 3.9 1.1 - - - -
336A THR* 3.3 36.6 - - + +
361A PHE* 5.2 2.2 - - + -
363A ILE* 4.2 21.1 - - + -
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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