Contacts of the helix formed by residues 640 - 653 (chain A) in PDB entry 2WXL
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 ASN 640 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLN 4.7 2.7 + - - +
165A TYR* 3.7 4.5 - - - -
168A PRO* 3.4 27.7 - - - +
605A ASP* 3.0 38.4 + - - +
636A ARG 3.1 5.5 + - - +
637A ALA 2.8 15.8 - - - +
638A LEU 3.4 0.8 - - - -
639A ALA* 1.3 82.1 - - - +
641A ARG* 1.3 58.8 + - - +
642A LYS* 2.9 23.5 + - - +
643A ILE* 3.1 28.7 + - + +
644A GLY 2.9 15.6 + - - -
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Residues in contact with ARG 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 2.9 48.1 + - + +
166A SER* 3.3 35.1 + - - +
167A PHE* 4.4 12.9 - - - -
247A HIS* 4.4 3.4 - - - +
289A GLN* 5.3 6.5 - - - -
637A ALA 4.4 2.2 - - - -
640A ASN* 1.3 71.9 - - - +
642A LYS* 1.3 58.3 + - - +
644A GLY* 3.6 3.0 - - - +
645A HIS* 2.8 28.9 + - - +
671A TYR* 4.8 1.3 - - - +
677A HIS* 6.2 1.8 - - - -
678A HIS* 3.8 37.3 + - + +
681A VAL* 5.4 1.0 - - - +
732A GLN* 2.7 41.8 + - - +
737A PRO* 4.2 21.4 + - - +
738A SER* 5.2 0.8 - - - +
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Residues in contact with LYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR 4.6 0.2 + - - -
166A SER 5.3 0.4 + - - +
168A PRO* 4.1 25.6 - - + +
170A GLN* 6.0 10.2 - - + +
606A ASP* 5.8 4.0 - - - -
609A PHE* 3.6 50.3 - - + -
640A ASN* 2.9 10.6 + - - +
641A ARG* 1.3 77.0 - - - +
643A ILE* 1.3 68.5 + - + +
645A HIS* 3.2 5.6 + - - +
646A PHE* 3.2 40.6 + - + -
736A ASP* 5.2 7.5 + - - -
737A PRO* 4.5 13.6 - - + +
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Residues in contact with ILE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ASP* 4.0 13.9 - - - +
608A LEU* 4.1 23.3 - - + -
609A PHE* 3.9 37.9 - - + +
612A LEU* 4.0 19.2 - - + +
633A LEU* 4.8 3.4 - - + +
636A ARG* 4.0 4.7 - - + +
637A ALA* 3.8 23.3 - - + +
640A ASN* 3.1 32.7 + - + +
642A LYS* 1.3 79.8 - - + +
644A GLY* 1.3 56.6 + - - +
646A PHE* 3.3 0.6 + - - -
647A LEU* 2.8 31.1 + - + +
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Residues in contact with GLY 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ALA* 3.7 22.4 + - - -
640A ASN 2.9 10.3 + - - -
641A ARG 3.3 2.0 + - - -
642A LYS 3.2 0.2 - - - -
643A ILE* 1.3 74.5 - - - +
645A HIS* 1.3 63.5 + - - +
647A LEU* 3.6 0.9 + - - +
648A PHE* 3.0 25.6 + - - +
671A TYR* 3.4 29.2 - - - -
678A HIS* 4.1 1.1 - - - -
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Residues in contact with HIS 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A ARG 2.8 17.0 + - - +
642A LYS 3.5 4.7 - - - +
644A GLY* 1.3 78.4 - - - +
646A PHE* 1.3 78.6 + + - +
648A PHE* 3.4 4.5 + - - +
649A TRP* 3.2 35.5 + + - -
678A HIS* 3.6 17.0 + - + +
682A LEU* 4.1 10.0 - - - +
685A GLN* 3.4 29.7 + - - -
733A SER 3.6 13.5 - - - -
734A PRO* 2.7 28.6 + - + -
737A PRO* 3.6 38.5 - - + +
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Residues in contact with PHE 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A PHE* 3.4 34.1 - + + -
612A LEU* 3.8 19.7 - - + -
642A LYS* 3.2 34.2 + - + +
645A HIS* 1.3 86.9 - + - +
647A LEU* 1.3 66.8 + - - +
649A TRP* 4.4 1.6 - - - +
650A HIS* 2.9 38.1 + + - +
734A PRO 3.8 15.3 - - - -
735A LEU* 3.4 24.2 - - - -
736A ASP* 4.2 1.1 - - - -
737A PRO* 3.7 23.1 - - + -
792A GLN* 6.3 1.1 - - - -
816A LEU* 4.2 24.5 - - + -
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Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 3.6 13.9 - - + +
616A VAL* 3.8 24.5 - - + -
619A LEU* 5.4 0.7 - - + -
633A LEU* 4.0 28.3 - - + +
634A LEU* 4.3 19.5 - - + -
637A ALA* 3.6 24.7 - - + -
643A ILE* 2.8 24.6 + - + +
644A GLY 3.8 3.6 - - - +
646A PHE* 1.3 71.9 - - - +
648A PHE* 1.3 65.0 + - - +
650A HIS* 3.9 2.7 - - - +
651A LEU* 3.1 49.5 + - + +
667A ILE* 4.7 3.6 - - + -
671A TYR* 4.9 7.0 - - + -
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Residues in contact with PHE 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.5 53.2 - - + -
121A ILE* 4.6 1.6 - - + -
644A GLY 3.0 15.1 + - - +
645A HIS 3.4 8.7 - - - +
647A LEU* 1.3 77.9 - - - +
649A TRP* 1.3 93.4 + + - +
651A LEU* 3.2 8.4 + - - +
652A ARG* 2.8 48.1 + - + +
668A MET* 3.5 28.5 - - + -
671A TYR* 5.1 12.1 - + + -
672A CYS* 5.2 1.3 - - - -
682A LEU* 3.6 24.7 - - + -
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Residues in contact with TRP 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 5.9 0.7 - - + -
645A HIS* 3.2 42.3 + + - +
646A PHE* 3.3 3.6 + - - +
648A PHE* 1.3 97.0 - + - +
650A HIS* 1.3 66.7 + - - +
652A ARG* 3.8 18.1 - - + +
653A SER* 3.0 29.5 + - - -
682A LEU* 3.8 10.0 - - + +
685A GLN* 3.0 41.7 + - + -
686A GLY* 4.4 12.1 - - - -
689A LEU* 3.4 28.3 - - + -
734A PRO* 4.1 5.2 - - + +
816A LEU* 4.0 28.3 - - + -
817A PRO 4.6 2.2 - - - +
818A THR* 3.7 35.2 - - + -
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Residues in contact with HIS 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 6.3 0.4 - - - -
612A LEU* 4.0 24.4 - - + +
613A LEU* 4.2 28.3 + - + +
616A VAL* 4.0 23.1 - - + +
617A GLN* 5.6 1.2 - - - +
646A PHE* 2.9 33.2 + + - +
647A LEU 3.9 2.9 - - - +
649A TRP* 1.3 74.3 - - - +
651A LEU* 1.3 61.9 + - - +
653A SER* 3.2 17.2 + - - -
654A GLU* 3.8 13.7 - - - +
664A PHE* 4.5 2.4 - - - -
788A MET* 3.6 38.6 - - + +
792A GLN* 4.5 9.5 + - - -
816A LEU* 4.2 14.6 - - + +
817A PRO* 5.5 1.2 + - - +
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Residues in contact with LEU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A VAL* 4.1 13.5 - - + -
619A LEU* 4.1 10.8 - - + -
647A LEU* 3.1 38.9 + - + +
648A PHE* 3.7 3.1 - - - +
650A HIS* 1.3 74.8 - - - +
652A ARG* 1.3 65.9 + - - +
654A GLU 3.3 9.0 + - - -
655A MET* 3.8 10.4 + - - +
664A PHE* 3.5 53.8 - - + +
667A ILE* 3.7 32.3 - - + -
668A MET* 3.7 26.9 - - + +
671A TYR* 6.3 0.9 - - + -
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Residues in contact with ARG 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU 4.8 2.6 + - - -
120A LEU 2.9 25.7 + - - +
121A ILE* 3.4 22.1 - - - +
122A GLY* 3.6 16.9 - - - +
648A PHE* 2.8 36.3 + - + +
649A TRP* 3.8 27.4 - - + -
651A LEU* 1.3 74.0 - - - +
653A SER* 1.3 58.9 - - - +
654A GLU 3.0 5.5 + - - -
655A MET* 3.2 22.4 + - - +
668A MET* 3.7 9.9 - - - -
818A THR 4.1 5.7 + - - +
819A GLY* 4.8 4.6 - - - -
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Residues in contact with SER 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A TRP 3.0 15.3 + - - -
650A HIS* 3.2 17.7 + - - -
651A LEU 3.3 0.2 - - - -
652A ARG* 1.3 76.6 - - - +
654A GLU* 1.3 62.5 + - - +
655A MET 3.6 0.2 - - - -
656A HIS* 3.1 21.6 - - - -
785A ARG* 6.0 1.0 - - - +
817A PRO* 3.3 34.2 + - - +
818A THR 3.5 20.3 + - - -
819A GLY* 3.6 8.6 - - - +
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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