Contacts of the strand formed by residues 323 - 329 (chain A) in PDB entry 2V90
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 CYS 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A LEU 3.4 5.2 - - - +
253A GLU* 3.5 32.3 - - - +
320A GLN* 2.9 28.0 + - - +
321A GLY 4.5 0.7 - - - -
322A SER* 1.3 84.8 - - - +
324A VAL* 1.3 61.6 + - - +
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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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250A LEU 3.9 0.5 - - - +
251A HIS* 3.5 2.9 - - - -
252A LEU* 2.9 38.9 + - + +
259A PHE* 3.3 38.1 - - + -
300A VAL* 4.0 7.6 - - + -
317A ILE* 4.3 9.6 - - + +
320A GLN* 3.8 26.7 - - + -
323A CYS* 1.3 75.6 - - - +
325A SER* 1.3 74.3 + - - +
326A LEU* 3.7 24.8 + - + -
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Residues in contact with SER 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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249A CYS* 3.2 26.7 - - - -
250A LEU 3.4 5.6 - - - -
251A HIS* 3.9 17.9 + - - -
300A VAL* 3.5 0.3 - - - -
301A ALA* 2.9 40.9 + - - +
302A GLY* 4.5 5.6 + - - -
320A GLN* 5.4 1.4 + - - -
324A VAL* 1.3 81.0 - - - +
326A LEU* 1.3 60.9 + - - +
327A THR* 4.9 1.2 + - - -
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Residues in contact with LEU 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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248A ARG 3.6 1.2 - - - +
249A CYS* 3.5 1.2 - - - -
250A LEU* 2.8 42.6 + - + +
252A LEU* 3.8 15.7 - - + -
261A PHE* 3.8 18.2 - - + -
291A MET* 2.8 38.4 - - + -
297A LEU* 4.0 21.8 - - + -
299A ALA 3.6 2.2 - - - -
300A VAL* 4.0 13.9 - - + -
317A ILE* 4.1 12.3 - - + -
324A VAL* 3.7 23.6 - - + -
325A SER* 1.3 84.0 + - - +
327A THR* 1.3 61.1 + - - +
328A VAL* 4.8 2.2 - - + -
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Residues in contact with THR 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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247A PRO* 3.7 20.2 - - + -
248A ARG 3.3 12.8 - - - +
249A CYS* 3.9 17.8 - - + +
297A LEU* 3.7 1.7 - - - +
298A VAL* 2.8 41.8 + - + +
299A ALA* 2.8 34.8 + - + +
302A GLY* 5.6 3.1 + - - -
325A SER* 4.3 1.2 + - - -
326A LEU* 1.3 73.7 - - - +
328A VAL* 1.3 66.2 + - - +
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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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246A LYS 4.5 0.2 - - - +
247A PRO* 3.1 5.7 - - - +
248A ARG* 2.8 48.4 + - + +
250A LEU* 3.6 24.9 - - + -
277A LEU* 4.0 23.6 - - + -
291A MET* 4.7 4.0 - - + -
295A ASP* 3.5 28.9 - - + +
296A ARG 3.2 10.8 - - - +
297A LEU* 4.2 8.1 - - + -
298A VAL* 4.6 1.8 - - - -
326A LEU 4.7 0.9 - - - +
327A THR* 1.3 81.2 - - - +
329A VAL* 1.3 63.3 + - - +
330A ASP* 4.2 9.0 + - - +
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Residues in contact with VAL 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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245A MET* 3.8 24.0 - - + +
247A PRO* 4.1 24.7 - - + -
294A GLY 4.4 0.5 - - - +
295A ASP* 3.6 2.5 - - - -
296A ARG* 2.9 47.1 + - + +
298A VAL* 4.0 18.8 - - + -
328A VAL* 1.3 76.5 - - - +
330A ASP* 1.3 72.4 + - - +
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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