Contacts of the strand formed by residues 348 - 351 (chain B) in PDB entry 2P3Z
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 SER 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ILE* 3.5 25.4 - - - -
169B GLN 2.8 7.7 + - - -
170B PHE* 3.3 12.8 - - - -
171B TYR* 3.0 34.9 + - - -
327B VAL* 4.5 4.5 - - - -
328B PRO* 4.7 4.9 + - - +
330B GLY* 5.2 1.6 - - - -
335B SER* 4.1 16.3 + - - -
336B HIS* 4.9 2.9 + - - -
339B VAL* 4.4 13.0 - - - +
345B THR* 5.2 0.2 - - - -
347B PHE* 1.3 76.5 - - - +
349B GLU* 1.3 69.8 + - - +
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Residues in contact with GLU 349 (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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170B PHE* 3.7 12.0 - - - -
171B TYR* 3.2 28.4 + - + +
173B THR* 2.5 34.5 + - - +
189B LYS* 3.0 15.7 + - - -
328B PRO 4.1 8.2 + - - +
329B HIS* 3.3 21.4 + - - -
330B GLY* 2.7 48.3 + - - +
332B SER 5.8 0.2 + - - -
336B HIS* 5.3 1.7 - - - -
348B SER* 1.3 81.1 + - - +
350B PHE* 1.3 67.9 + - - +
351B LEU* 4.1 8.9 - - - +
363B GLN* 4.2 1.6 - - - +
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Residues in contact with PHE 350 (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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170B PHE* 3.8 10.9 - + + -
171B TYR 3.0 8.0 + - - +
172B ALA* 3.4 1.9 - - - +
173B THR 2.7 31.7 + - - -
185B PHE* 3.8 33.0 - + + -
336B HIS* 6.0 3.1 - + - -
349B GLU* 1.3 76.1 - - - +
351B LEU* 1.3 65.4 + - - +
352B MET* 3.7 19.7 + - + -
360B LEU* 4.1 21.5 - - + -
361B ARG 3.3 27.6 - - - -
362B PRO* 4.7 0.2 - - + -
363B GLN* 4.0 26.5 - - + -
372B PRO 5.3 2.0 - - - -
373B VAL* 4.8 5.4 - - + -
374B PRO* 3.4 30.1 - - + -
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Residues in contact with LEU 351 (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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32B TYR* 3.8 37.0 - - + -
33B HIS* 5.7 2.5 - - - +
40B TRP* 3.8 22.2 - - + -
41B ILE* 4.4 11.9 - - + -
173B THR* 3.7 31.2 - - + -
329B HIS* 4.1 24.2 - - + +
330B GLY 5.1 1.8 - - - +
349B GLU* 4.0 9.3 - - - +
350B PHE* 1.3 79.3 - - - +
352B MET* 1.3 63.0 + - - +
353B THR* 3.2 5.5 + - + +
363B GLN* 2.7 40.1 + - - +
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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