Contacts of the strand formed by residues 310 - 314 (chain B) in PDB entry 2PMW
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 VAL 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LEU 2.8 25.9 + - - +
284B VAL* 3.2 26.7 - - + +
285B VAL* 2.6 34.0 + - - +
308B GLY 4.3 0.8 + - - -
309B VAL* 1.3 72.7 - - - +
311B LEU* 1.3 63.1 + - - +
312B VAL* 4.3 7.9 - - + -
334B ILE* 4.2 17.5 - - + -
396B ALA* 5.1 1.1 - - + -
400B LEU* 4.0 11.4 - - + -
408B LEU* 4.9 11.2 - - + -
411B LEU* 3.9 25.8 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 5.0 2.7 - - + -
285B VAL* 3.3 15.0 - - + +
287B LEU* 4.2 13.0 - - + -
301B CYS* 3.6 48.0 - - + +
304B LEU* 4.3 16.4 - - + -
305B ALA* 4.3 9.9 - - + +
309B VAL* 3.4 30.7 + - + +
310B VAL* 1.3 81.6 - - - +
312B VAL* 1.3 61.9 + - - +
313B THR 4.2 0.2 - - - -
332B GLU 5.2 2.2 + - - -
333B VAL* 3.6 18.4 - - + +
334B ILE* 2.8 30.9 + - - +
408B LEU* 5.9 0.8 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 4.0 21.5 - - + -
285B VAL 2.7 12.3 + - - +
286B LEU* 3.4 8.3 - - + +
287B LEU* 2.8 27.3 + - - +
310B VAL* 4.3 9.6 - - + -
311B LEU* 1.3 77.5 - - - +
313B THR* 1.3 63.6 + - - +
334B ILE* 3.4 9.9 - - + +
336B VAL* 3.8 21.1 - - + -
389B ALA* 3.4 28.5 - - + +
392B VAL* 4.0 14.6 - - + +
393B ALA* 4.0 12.3 - - + +
396B ALA* 4.9 2.5 - - + -
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Residues in contact with THR 313 (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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287B LEU* 2.9 23.2 + - - -
289B LEU 3.9 2.6 + - - -
312B VAL* 1.3 76.0 - - - +
314B ALA* 1.3 64.7 + - - +
327B PRO* 3.2 24.7 - - - +
328B ALA* 3.7 19.3 - - - +
333B VAL* 3.8 12.8 - - + -
334B ILE 2.8 13.0 + - - +
335B THR* 3.4 24.6 - - - +
336B VAL* 2.9 30.0 + - - +
389B ALA* 3.8 6.5 - - - +
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Residues in contact with ALA 314 (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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152A GLN* 3.9 17.3 - - + -
287B LEU 3.3 10.9 + - - +
288B PRO* 4.3 0.2 - - + -
289B LEU 4.3 8.6 - - - +
290B ALA* 5.0 1.4 - - - +
313B THR* 1.3 80.6 + - - +
315B ALA* 1.3 64.7 + - - +
316B GLY* 3.3 2.0 + - - +
328B ALA* 3.5 15.2 - - - +
335B THR* 4.2 0.7 - - - -
336B VAL 4.0 0.9 - - - -
385B THR* 3.4 38.8 - - - +
386B SER* 3.9 7.6 - - - +
389B ALA* 3.9 2.3 - - + +
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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