Contacts of the strand formed by residues 331 - 335 (chain B) in PDB entry 3PII
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 ARG 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY* 5.4 0.2 - - - -
37B VAL 3.6 17.0 + - - +
38B CYS* 3.4 26.6 - - - +
62B GLU* 3.2 31.1 + - - -
145B PRO* 4.0 21.4 + - + +
149B ALA* 3.6 14.9 - - + +
175B GLY* 4.4 17.9 - - - +
176B PHE* 3.5 30.3 - - - -
306B THR* 4.3 16.8 - - + -
307B ILE 2.9 11.9 + - - +
308B ILE* 3.2 9.3 - - + -
309B GLU* 2.8 31.5 + - - +
323B MET* 6.2 1.6 - - - -
328B ILE* 4.4 3.1 - - - -
329B ASN 3.7 2.1 + - - +
330B GLY* 1.3 81.6 - - - +
332B VAL* 1.3 59.1 + - - +
333B VAL* 5.3 0.4 - - + -
340B ZN 4.1 5.1 - - - -
342B SO4 4.6 6.9 + - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY* 4.0 0.3 - - - -
37B VAL* 3.1 39.7 + - + +
309B GLU* 3.3 31.4 - - + +
311B GLN* 4.5 5.4 - - + -
319B VAL* 3.9 33.7 - - + -
322B ARG* 4.9 1.6 - - - +
323B MET* 5.7 1.2 - - + +
328B ILE* 3.7 36.1 - - + +
331B ARG* 1.3 78.2 + - - +
333B VAL* 1.3 71.7 + - - +
334B LEU* 4.5 5.6 - - + -
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.9 18.8 - - + -
35B CYS 3.7 14.4 - - - +
36B GLY* 4.3 3.6 - - - -
141B GLU* 3.6 28.9 - - + +
144B ALA* 4.2 8.1 - - + -
145B PRO* 3.9 13.7 - - + -
308B ILE* 3.8 23.1 - - + -
309B GLU 3.0 8.1 + - - +
310B VAL* 3.3 14.5 - - + +
311B GLN 3.2 20.8 + - - -
331B ARG* 4.9 1.3 - - + +
332B VAL* 1.3 79.3 - - - +
334B LEU* 1.3 70.3 + - - +
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Residues in contact with LEU 334 (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 ALA* 3.2 8.3 - - - +
35B CYS* 2.7 39.2 + - + +
37B VAL* 3.7 26.9 - - + -
120B TYR* 3.9 25.8 - - + -
310B VAL* 4.8 0.4 - - - -
311B GLN* 3.2 20.4 - - + +
312B PRO 4.1 12.8 - - - +
313B LEU* 4.0 24.7 - - + +
316B ILE* 4.1 21.5 - - + -
319B VAL* 5.1 1.6 - - + -
332B VAL* 4.2 5.6 - - + -
333B VAL* 1.3 72.0 - - - +
335B THR* 1.3 61.3 + - - +
336B LEU* 4.1 11.7 - - + +
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Residues in contact with THR 335 (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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33B LYS 4.0 9.9 + - - -
34B ALA* 4.7 2.7 - - - +
141B GLU* 5.7 3.6 - - - +
310B VAL* 3.7 21.0 - - + +
311B GLN 2.9 8.8 + - - +
312B PRO* 3.7 21.8 - - + +
313B LEU* 3.1 23.9 + - - +
333B VAL 3.7 0.8 + - - -
334B LEU* 1.3 73.9 - - - +
336B LEU* 1.3 65.4 + - - +
337B GLU* 4.4 16.5 + - - +
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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