Contacts of the strand formed by residues 644 - 650 (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 644 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B GLY* 4.4 7.6 - - - +
495B ARG* 3.6 28.3 + - - +
566B TRP* 6.4 0.4 - - + -
637B ALA* 4.5 12.6 - - + -
638B LEU 6.1 0.4 - - - +
642B SER* 3.0 33.8 + - - +
643B HIS* 1.3 74.0 - - - +
645B LEU* 1.3 64.6 + - - +
646B GLY* 4.2 3.4 - - - +
656B VAL* 4.3 19.3 - - + -
657B ARG 3.3 11.2 - - - +
658B SER* 4.2 2.0 - - - +
672B VAL* 4.5 12.3 - - + -
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Residues in contact with LEU 645 (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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489B PHE* 3.7 12.3 - - + -
490B SER 3.0 35.2 + - - +
491B ARG* 3.6 17.5 - - - +
492B SER 3.7 6.3 - - - +
493B GLY* 3.4 29.4 - - - +
495B ARG* 3.4 12.4 + - - -
643B HIS 4.5 0.7 - - - +
644B VAL* 1.3 76.7 - - - +
646B GLY* 1.3 55.1 + - - +
657B ARG* 2.5 44.4 + - + +
658B SER 4.4 10.8 - - - +
659B ARG* 4.2 27.6 - - + +
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Residues in contact with GLY 646 (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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488B SER 3.2 13.7 - - - -
489B PHE* 4.2 7.6 - - - -
495B ARG* 3.8 16.6 - - - +
637B ALA* 6.0 0.9 - - - -
644B VAL* 3.3 4.3 - - - +
645B LEU* 1.3 82.3 - - - +
647B ALA* 1.3 61.7 + - - +
648B TYR* 5.1 0.2 - - - -
656B VAL* 3.6 6.1 - - - +
657B ARG* 2.9 25.4 + - - +
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Residues in contact with ALA 647 (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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487B SER* 2.6 29.4 + - - -
488B SER 3.2 10.5 + - - +
523B ILE* 3.6 3.6 - - - +
635B CYS* 4.1 12.8 - - - +
636B SER* 4.1 15.5 - - - -
637B ALA* 4.5 2.9 - - + +
646B GLY* 1.3 75.0 - - - +
648B TYR* 1.3 65.8 + - - +
655B VAL 3.1 12.8 - - - +
656B VAL* 3.9 17.3 - - + -
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Residues in contact with TYR 648 (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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435B VAL* 3.3 30.6 - - + +
461B TRP* 3.7 31.9 - + + -
487B SER* 3.8 7.0 - - - -
489B PHE* 4.3 14.4 - + + -
523B ILE* 3.8 20.2 - - + -
621B GLN* 4.7 1.7 + - - -
635B CYS* 3.6 7.6 - - - -
647B ALA* 1.3 82.7 - - - +
649B ALA* 1.3 64.7 + - - +
650B VAL* 3.7 20.9 - - + -
655B VAL* 3.0 54.5 + - + +
657B ARG* 3.4 33.0 + - + +
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Residues in contact with ALA 649 (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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459B THR* 3.1 39.0 + - + +
461B TRP* 5.3 1.0 + - - -
487B SER* 5.0 0.4 + - - -
523B ILE* 5.1 1.8 - - - +
525B ARG* 3.9 21.8 - - - +
632B LEU* 3.5 25.1 - - + -
634B GLY 6.0 0.2 - - - -
635B CYS* 4.1 9.1 - - + +
648B TYR* 1.3 75.4 - - - +
650B VAL* 1.3 61.3 + - - +
651B ASP 4.4 0.7 - - - +
653B THR 3.4 5.6 - - - -
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Residues in contact with VAL 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ASP* 6.0 2.0 - - - +
426B GLU* 5.6 5.4 - - - +
439B ASN* 5.9 7.2 - - + +
648B TYR* 3.7 19.3 - - + -
649B ALA* 1.3 74.0 - - - +
651B ASP* 1.3 75.2 + - + +
653B THR* 2.8 31.6 + - - +
655B VAL* 3.5 26.9 - - + -
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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
------------------------------------------------------------
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