Contacts of the strand formed by residues 325 - 333 (chain B) in PDB entry 2ZV6
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 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LEU* 5.4 3.8 - - + -
41B VAL* 4.4 11.4 - - + -
174B LEU* 3.8 22.6 - - + +
175B VAL 4.2 0.2 - - - +
176B LEU* 3.8 33.2 - - + +
296B LYS* 3.9 1.9 + - - -
304B MET* 5.6 1.1 - - + -
307B ILE* 2.8 43.0 + - + +
308B PHE* 3.4 34.7 - - + +
314B LEU* 4.3 5.3 - - + +
324B VAL* 1.3 68.2 - - - +
326B SER* 1.3 60.9 + - - +
327B GLY 3.1 27.1 - - - +
328B VAL* 4.2 18.6 - - + -
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Residues in contact with SER 326 (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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168B ILE* 5.6 1.6 - - - +
171B ASN 5.1 1.7 + - - -
172B THR* 3.8 18.6 - - - +
173B THR* 2.9 31.3 + - - -
174B LEU 3.2 23.1 + - - +
175B VAL* 4.5 4.3 - - - +
296B LYS* 4.2 13.7 - - - +
324B VAL 3.0 2.5 + - - -
325B LEU* 1.3 70.0 - - - +
327B GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 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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175B VAL* 4.1 3.2 - - - -
176B LEU 3.5 10.7 + - - -
294B ASP* 4.3 7.6 - - - -
296B LYS* 3.9 22.6 - - - +
308B PHE* 4.5 1.4 - - - -
325B LEU* 3.1 25.4 + - - +
326B SER* 1.3 77.8 - - - +
328B VAL* 1.3 63.7 + - - -
329B LEU* 4.1 6.7 - - - -
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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
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34B ILE* 6.4 0.2 - - + -
37B ALA* 6.1 1.1 - - + -
38B LEU* 5.1 9.6 - - + -
176B LEU* 3.7 20.2 - - + +
178B ASN* 5.4 5.6 - - + +
294B ASP* 3.1 30.3 + - - -
295B LEU* 3.2 30.6 + - + +
296B LYS 4.4 3.1 - - - +
299B LEU* 4.6 10.3 - - + -
308B PHE* 3.8 29.2 - - + -
325B LEU* 4.2 12.6 - - + -
327B GLY* 1.3 76.0 - - - +
329B LEU* 1.3 64.7 + - - +
330B HIS* 3.5 3.3 + - + -
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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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162B LEU* 3.1 49.8 - - + +
163B ILE* 4.0 17.9 - - + -
164B PRO* 5.6 0.9 - - + -
167B ASN* 5.4 8.7 - - - +
175B VAL* 5.7 7.3 - - + +
176B LEU 3.3 7.2 + - - +
177B VAL* 4.6 6.5 - - + -
178B ASN* 2.5 37.9 + - - +
292B SER* 4.7 5.2 - - - +
293B TYR 3.6 13.5 - - - +
294B ASP* 3.8 22.2 - - + +
327B GLY* 4.1 4.2 - - - -
328B VAL* 1.3 78.6 - - - +
330B HIS* 1.3 54.6 + - - +
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Residues in contact with HIS 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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29B TYR* 3.9 11.4 - - - +
30B SER* 3.0 52.0 + - - -
33B SER* 3.8 2.5 + - - -
34B ILE* 3.2 32.5 - - + +
162B LEU* 4.6 0.8 - - - +
178B ASN* 3.1 33.2 + - + +
180B ILE* 4.6 0.8 - - - +
291B GLU 5.4 0.2 + - - -
292B SER* 3.8 1.2 + - - -
293B TYR* 2.8 43.0 + - + +
295B LEU* 4.5 15.7 - - + -
328B VAL* 3.5 3.6 + - + +
329B LEU* 1.3 75.0 - - - +
331B LYS* 1.3 67.7 + - - +
332B ALA* 4.1 10.3 + - + -
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Residues in contact with LYS 331 (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 ILE* 3.5 25.7 - - + +
160B LYS 4.2 14.7 + - - +
161B ASN 4.4 7.9 + - - -
162B LEU* 3.5 28.9 - - + +
178B ASN 2.9 6.9 + - - -
179B ALA* 3.5 2.1 - - - -
180B ILE* 3.1 31.3 + - - +
290B GLU* 3.4 34.5 - - - +
291B GLU 3.5 15.5 - - - +
292B SER* 3.6 23.6 + - - +
330B HIS* 1.3 79.8 + - - +
332B ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 332 (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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28B PHE* 3.9 28.6 - - + +
29B TYR* 4.2 9.9 - - - -
180B ILE* 3.6 14.8 - - + -
289B VAL 3.5 1.5 - - - +
290B GLU* 3.5 6.7 - - - +
291B GLU 3.1 29.6 + - - +
330B HIS* 4.1 14.0 - - + -
331B LYS* 1.3 74.4 - - - +
333B PHE* 1.3 61.8 + - - +
334B VAL 4.1 0.7 - - - -
383B PHE* 4.2 6.7 - - + -
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Residues in contact with PHE 333 (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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28B PHE* 4.8 0.7 - - - -
158B LYS* 3.7 37.9 - - - -
159B ILE* 3.9 16.6 - - + -
180B ILE* 3.1 6.9 + - - +
181B TYR* 3.4 16.4 - + + -
182B PHE* 3.0 27.4 + - - +
288B LYS* 4.1 28.3 - - + -
289B VAL 3.3 10.3 - - - -
290B GLU* 3.7 32.8 - - + +
332B ALA* 1.3 75.9 - - - +
334B VAL* 1.3 76.0 + - - +
335B GLU* 4.0 20.0 - - - -
383B PHE* 4.8 2.5 - - - -
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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