Contacts of the helix formed by residues 337 - 350 (chain B) in PDB entry 2VDP
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 SER 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B ASN* 4.4 6.1 + - - +
134B LEU* 3.7 31.5 - - - +
137B LYS* 3.7 26.2 - - - +
332B VAL 5.8 0.4 - - - -
334B SER 5.3 0.4 - - - -
335B MET 4.0 1.4 + - - -
336B ASP* 1.3 72.9 + - - +
338B SER* 1.3 65.5 + - - +
339B ASN 3.3 2.9 + - - -
340B VAL* 3.5 4.9 + - - +
341B LEU* 3.1 41.9 + - - +
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASP* 2.4 37.8 + - - -
337B SER* 1.3 73.2 + - - +
339B ASN* 1.3 63.6 + - - +
341B LEU* 3.5 7.4 + - - +
342B GLN* 3.1 30.7 + - - +
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Residues in contact with ASN 339 (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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330B VAL 4.9 0.9 - - - +
331B GLY* 3.8 11.3 - - - -
332B VAL* 3.4 50.7 - - + +
336B ASP* 4.4 2.9 + - - +
337B SER 3.3 0.8 - - - -
338B SER* 1.3 81.5 - - - +
340B VAL* 1.3 62.9 + - - +
342B GLN* 3.3 16.0 + - - +
343B LEU* 3.6 11.4 + - - +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.8 34.5 - - + -
138B LEU* 4.8 8.5 - - + -
247B VAL* 4.4 11.4 - - + -
307B ILE* 4.7 10.1 - - + -
309B ALA* 3.9 26.0 - - + -
331B GLY* 4.0 13.7 - - - -
332B VAL 3.7 20.6 - - - +
333B LEU* 4.5 0.9 - - - +
337B SER* 3.5 2.9 + - - +
339B ASN* 1.3 73.2 - - - +
341B LEU* 1.3 67.5 + - - +
343B LEU* 3.1 24.0 + - + +
344B ILE* 3.4 9.1 + - + +
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Residues in contact with LEU 341 (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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134B LEU* 3.8 15.5 - - + -
137B LYS* 4.4 4.5 - - + +
138B LEU* 3.8 29.6 - - + +
141B GLN* 4.0 28.0 - - + -
142B MET* 3.4 26.8 - - + +
337B SER* 3.1 39.1 + - - +
338B SER* 3.9 6.1 - - - +
340B VAL* 1.3 74.6 - - - +
342B GLN* 1.3 57.8 + - + +
344B ILE* 3.1 3.8 + - - -
345B VAL* 2.9 29.5 + - + +
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Residues in contact with GLN 342 (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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338B SER* 3.1 19.9 + - - +
339B ASN* 3.5 11.2 - - - +
340B VAL 3.2 0.2 - - - -
341B LEU* 1.3 72.6 - - - +
343B LEU* 1.3 57.9 + - + +
345B VAL* 4.3 16.0 - - - +
346B ASP* 2.7 64.1 + - - +
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Residues in contact with LEU 343 (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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307B ILE* 3.9 30.4 - - + +
329B THR* 4.2 20.6 - - + +
330B VAL 3.5 28.0 - - - +
331B GLY* 3.6 20.0 - - - +
339B ASN* 3.9 12.3 - - - +
340B VAL* 3.1 13.4 + - - +
342B GLN* 1.3 76.7 - - + +
344B ILE* 1.3 58.7 + - - +
346B ASP* 3.6 11.2 - - + +
347B ALA* 2.9 27.8 + - - +
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Residues in contact with ILE 344 (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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112B VAL* 5.4 2.5 - - + -
114B ILE* 3.9 13.0 - - + -
138B LEU* 3.7 20.0 - - + -
142B MET* 3.7 21.1 - - + -
145B LEU* 5.8 0.2 - - + -
245B LEU* 3.7 26.2 - - + +
247B VAL* 4.1 18.4 - - + -
307B ILE* 3.3 30.3 - - + -
340B VAL* 3.6 15.0 - - + +
341B LEU 3.1 6.2 + - - +
343B LEU* 1.3 73.9 - - - +
345B VAL* 1.3 60.5 + - - +
347B ALA* 3.1 7.3 + - - +
348B TYR* 2.8 29.4 + - + +
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Residues in contact with VAL 345 (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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142B MET* 4.2 9.0 - - + -
145B LEU* 3.6 31.2 - - + -
341B LEU* 2.9 21.7 + - + +
342B GLN* 3.7 18.2 - - - +
344B ILE* 1.3 74.4 - - - +
346B ASP* 1.3 60.0 + - - +
348B TYR* 3.1 4.0 + - - +
349B GLY* 2.7 32.4 + - - -
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Residues in contact with ASP 346 (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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342B GLN* 2.7 50.0 + - - +
343B LEU* 3.6 13.3 - - + +
345B VAL* 1.3 74.8 - - - +
347B ALA* 1.3 60.8 + - - +
349B GLY* 3.3 10.5 + - - +
350B LYS* 3.4 32.4 + - - +
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Residues in contact with ALA 347 (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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243B SER* 5.3 4.1 + - - +
245B LEU* 4.1 28.0 - - + -
305B ASN* 5.5 4.5 - - - +
307B ILE* 5.7 0.9 - - + -
343B LEU 2.9 15.6 + - - +
344B ILE 3.1 10.3 + - - +
346B ASP* 1.3 76.3 - - - +
348B TYR* 1.3 61.2 + - - +
350B LYS* 3.4 19.9 + - - +
351B ILE* 3.6 13.5 + - - +
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Residues in contact with TYR 348 (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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109B ASP* 3.6 14.2 + - - +
110B TYR* 3.0 54.5 + + + +
112B VAL* 3.6 20.6 - - + -
145B LEU* 3.9 40.5 + - + -
146B THR* 3.7 25.4 - - + -
344B ILE* 2.8 14.5 + - + +
345B VAL 3.4 7.9 - - - +
347B ALA* 1.3 74.3 - - - +
349B GLY* 1.3 65.7 + - - +
351B ILE* 3.2 26.5 + - + +
391B ILE* 4.1 11.2 - - + +
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Residues in contact with GLY 349 (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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345B VAL 2.7 18.7 + - - -
346B ASP* 3.3 5.4 + - - -
347B ALA 3.3 0.2 - - - -
348B TYR* 1.3 76.6 - - - +
350B LYS* 1.3 52.0 + - - +
351B ILE 3.6 0.7 + - - +
352B ARG* 2.8 27.4 + - - -
390B LYS* 5.5 2.1 - - - +
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Residues in contact with LYS 350 (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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346B ASP* 3.4 30.5 + - - +
347B ALA* 3.9 12.0 - - - +
348B TYR 3.2 1.4 - - - -
349B GLY* 1.3 74.9 - - - +
351B ILE* 1.3 62.8 + - - +
352B ARG* 3.4 18.7 + - - +
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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