Contacts of the strand formed by residues 335 - 340 (chain A) in PDB entry 2CVP
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 THR 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ILE* 6.0 0.9 - - - +
333A CYS* 3.3 4.6 - - - +
334A GLU* 1.3 85.2 - - + +
336A HIS* 1.3 62.5 + - - +
377A PRO* 4.2 4.5 - - - +
378A ILE* 3.1 17.0 - - + +
380A TRP* 3.0 23.8 + - + +
401A MET 5.0 0.6 + - - -
402A ILE* 3.8 11.4 - - - +
403A PRO* 3.4 24.0 - - - +
334B GLU* 3.9 6.5 + - - +
335B THR* 3.6 31.6 - - + -
378B ILE* 3.5 21.7 - - + +
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Residues in contact with HIS 336 (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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324A GLY* 6.2 1.8 - - - -
335A THR* 1.3 74.9 - - - +
337A ALA* 1.3 60.3 + - - +
338A LEU* 3.6 21.8 + - + +
356A ASP* 5.4 2.0 - - - -
377A PRO* 4.2 19.1 - - + -
378A ILE 2.9 6.6 + - - +
379A VAL* 3.3 14.4 - - + +
380A TRP* 3.2 23.4 + - - +
403A PRO* 3.5 27.7 + - + +
405A ASP* 3.1 43.5 + - - -
475A ASN* 5.1 1.8 - - - -
497A LYS* 3.4 26.2 + - - -
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Residues in contact with ALA 337 (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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336A HIS* 1.3 74.1 + - - +
338A LEU* 1.3 63.2 + - - +
339A LEU* 4.3 14.6 - - + -
380A TRP* 3.2 37.4 - - + +
395A ILE* 5.3 0.7 - - + -
402A ILE* 4.0 1.7 - - + +
403A PRO 3.0 7.9 + - - +
404A CYS* 3.4 22.2 - - - +
405A ASP* 2.9 27.2 + - - +
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Residues in contact with LEU 338 (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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336A HIS* 3.6 28.0 - - + +
337A ALA* 1.3 73.1 - - - +
339A LEU* 1.3 65.1 + - - +
340A PRO* 3.4 12.8 - - + +
348A PHE* 4.5 9.2 - - + -
349A ALA* 3.8 23.6 - - + +
352A PHE* 3.7 36.6 - - + -
379A VAL* 3.8 19.5 - - + -
380A TRP 2.9 7.9 + - - +
381A GLY* 3.6 12.3 - - - -
382A GLU 3.9 1.0 + - - -
405A ASP* 3.8 16.2 - - + +
407A LEU* 4.9 3.6 - - + -
494A TYR* 3.9 21.1 - - + +
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Residues in contact with LEU 339 (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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337A ALA* 4.3 11.0 - - + -
338A LEU* 1.3 83.3 - - - +
340A PRO* 1.3 66.3 - - - +
341A TYR* 3.4 13.9 - - + -
381A GLY* 4.1 4.3 - - - -
382A GLU 3.6 18.6 - - - +
384A GLY 4.8 0.2 - - - -
391A PHE* 4.0 25.4 - - + -
392A TYR* 3.6 28.9 - - + +
395A ILE* 4.6 3.1 - - + -
404A CYS* 3.9 20.9 - - + -
405A ASP 2.8 15.7 + - - +
406A PHE* 3.5 29.0 - - + -
407A LEU* 3.2 18.1 + - - +
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Residues in contact with PRO 340 (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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338A LEU* 3.4 11.4 - - + +
339A LEU* 1.3 86.9 - - - +
341A TYR* 1.3 59.1 + - - +
342A ASP 2.9 9.7 + - - -
345A MET* 3.6 58.8 - - + +
348A PHE* 4.2 10.5 - - + -
349A ALA* 5.2 3.8 - - + +
382A GLU 4.1 1.1 - - - +
383A PRO* 3.0 21.1 - - + +
384A GLY 2.9 15.6 + - - -
407A LEU* 3.4 16.4 - - + +
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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