Contacts of the strand formed by residues 331 - 335 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLY* 5.1 0.8 - - - -
37D VAL 3.6 17.2 + - - +
38D CYS* 3.4 28.2 - - - +
62D GLU* 3.0 33.3 + - - -
145D PRO* 3.9 20.3 - - + +
148D CYS* 3.9 7.3 - - - -
149D ALA* 3.6 29.8 - - + +
175D GLY* 4.4 18.6 - - - +
176D PHE* 3.9 8.7 - - - -
178D HIS* 4.8 0.4 - - + -
306D THR* 4.4 14.8 - - + -
307D ILE 2.9 11.4 + - - +
308D ILE* 3.2 7.4 - - + -
309D GLU* 2.8 24.9 + - - +
323D MET* 6.1 1.6 - - - -
328D ILE* 4.3 3.6 - - - -
329D ASN 3.7 2.3 + - - +
330D GLY* 1.3 82.6 - - - +
332D VAL* 1.3 66.3 + - - +
333D VAL* 5.3 0.7 - - + -
342D SO4 4.9 6.1 + - - -
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLY* 3.8 0.5 - - - -
37D VAL* 3.2 42.4 + - + +
309D GLU* 3.3 35.0 - - + +
311D GLN* 4.6 6.5 - - + -
319D VAL* 4.0 33.4 - - + -
322D ARG* 4.7 0.9 - - - +
323D MET* 5.6 1.5 - - + +
328D ILE* 3.8 34.5 - - + +
331D ARG* 1.3 77.3 + - - +
333D VAL* 1.3 71.6 + - - +
334D LEU* 4.6 3.6 - - + +
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Residues in contact with VAL 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA* 3.9 26.5 - - + -
35D CYS 4.0 11.9 - - - +
36D GLY* 4.4 3.8 - - - +
141D GLU* 3.6 33.0 - - + +
144D ALA* 4.4 3.8 - - + -
145D PRO* 3.8 16.2 - - + -
308D ILE* 3.8 21.5 - - + -
309D GLU 2.8 10.5 + - - +
310D VAL* 3.1 15.6 - - + +
311D GLN 3.1 20.3 + - - -
331D ARG* 4.9 1.8 - - + +
332D VAL* 1.3 79.7 - - - +
334D LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA* 3.2 9.7 - - - +
35D CYS* 3.0 33.7 + - + +
37D VAL* 3.9 26.2 - - + -
120D TYR* 4.0 17.9 - - + -
310D VAL* 4.8 0.4 - - - -
311D GLN* 3.0 27.8 - - + +
312D PRO 3.6 15.3 - - - +
313D LEU* 3.9 26.7 - - + +
315D LYS 5.3 0.2 - - - -
316D ILE* 4.0 24.7 - - + -
319D VAL* 5.3 1.6 - - + -
332D VAL* 4.2 4.0 - - + -
333D VAL* 1.3 72.3 - - - +
335D THR* 1.3 64.3 + - - +
336D LEU* 4.1 9.0 - - + +
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Residues in contact with THR 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LYS 4.1 7.2 + - - -
34D ALA* 4.8 2.2 - - - +
141D GLU* 6.0 2.4 - - - +
310D VAL* 3.7 20.2 - - + -
311D GLN 2.7 11.6 + - - +
312D PRO* 3.5 26.2 - - + +
313D LEU 3.4 21.0 + - - -
333D VAL 3.7 2.0 + - - -
334D LEU* 1.3 73.4 - - - +
336D LEU* 1.3 65.1 + - - +
337D GLU* 4.1 16.7 + - - +
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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