Contacts of the helix formed by residues 652 - 664 (chain A) in PDB entry 1Q2L
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 LYS 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650A LYS* 2.9 8.9 + - + +
651A GLY* 1.3 78.8 - - - +
653A ALA* 1.3 65.8 + - - +
654A PHE* 3.3 16.7 - - + +
655A GLU* 2.9 53.4 + - + +
656A GLN* 3.1 13.2 + - - +
819A GLN* 4.2 7.2 - - - +
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Residues in contact with ALA 653 (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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651A GLY 3.4 6.6 + - - +
652A LYS* 1.3 70.0 - - - +
654A PHE* 1.3 58.5 + - - +
656A GLN* 3.2 10.6 + - - +
657A ALA 2.9 22.3 + - - -
752A ASN* 5.3 3.1 + - - +
753A SER* 5.7 0.7 - - - +
755A ASP* 4.0 14.4 - - + +
756A SER 4.0 6.7 - - - +
757A ALA* 3.4 18.4 - - + +
819A GLN* 3.0 28.4 + - + +
925A ILE* 3.5 13.6 - - + +
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Residues in contact with PHE 654 (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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652A LYS* 4.8 15.5 - - + -
653A ALA* 1.3 73.9 - - - +
655A GLU* 1.3 104.5 + - + +
657A ALA* 4.1 0.2 - - - -
658A ILE* 3.0 26.3 + - + +
757A ALA* 3.8 5.5 - - + +
800A ALA* 4.2 16.2 - - + +
802A PHE* 4.7 17.9 - + + -
817A LEU* 3.5 42.1 - - + +
819A GLN* 3.1 47.8 + - + +
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Residues in contact with GLU 655 (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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650A LYS* 4.3 13.2 - - + +
652A LYS* 2.9 42.1 + - + +
654A PHE* 1.3 102.2 - - + +
656A GLN* 1.3 63.0 + - + +
658A ILE* 3.4 9.3 - - + +
659A MET* 3.2 25.3 + - - +
662A GLN* 5.5 0.2 + - - -
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Residues in contact with GLN 656 (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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648A ALA 3.0 21.1 - - - +
649A GLU* 3.1 32.0 + - - +
650A LYS* 3.1 16.4 + - - +
652A LYS 3.3 16.4 - - - +
653A ALA* 3.4 8.7 - - - +
655A GLU* 1.3 76.4 - - + +
657A ALA* 1.3 65.5 + - - +
659A MET* 3.7 13.0 - - - +
660A PRO* 3.1 21.5 - - - +
749A LYS* 3.6 24.9 + - - +
752A ASN* 4.7 8.9 + - - +
923A SER* 4.4 0.2 + - - -
925A ILE* 3.6 23.4 - - + +
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Residues in contact with ALA 657 (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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653A ALA 2.9 13.0 + - - +
654A PHE 3.2 8.3 + - - +
656A GLN* 1.3 78.5 - - - +
658A ILE* 1.3 61.5 + - - +
660A PRO* 3.3 2.4 - - - +
661A ALA* 4.8 0.7 + - - +
757A ALA* 3.9 9.9 - - + -
759A ALA* 3.8 6.3 - - + +
817A LEU* 3.9 14.4 - - + -
923A SER* 2.6 50.7 + - - +
925A ILE* 3.7 13.9 - - + +
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Residues in contact with ILE 658 (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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654A PHE* 3.0 15.7 + - + +
655A GLU* 3.4 17.5 - - + +
657A ALA* 1.3 76.9 - - - +
659A MET* 1.3 69.4 + - - +
660A PRO 3.4 0.2 - - - -
661A ALA* 3.1 14.4 + - + +
662A GLN* 3.2 36.9 + - + +
759A ALA* 4.0 11.6 - - + +
761A VAL* 4.2 12.8 - - + -
804A PHE* 3.7 23.1 - - + -
806A MET* 3.6 27.6 - - + -
817A LEU* 4.2 13.5 - - + -
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Residues in contact with MET 659 (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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648A ALA* 4.2 26.0 - - + +
649A GLU* 5.8 2.7 - - + -
655A GLU 3.2 14.3 + - - +
656A GLN* 3.7 18.2 - - - +
658A ILE* 1.3 80.3 - - - +
660A PRO* 1.3 82.0 - - + +
662A GLN* 2.9 26.7 + - - +
663A MET* 3.0 31.9 + - + +
669A TYR* 5.5 7.0 - - - +
672A ARG* 5.4 13.2 - - + +
749A LYS* 4.5 14.1 - - + +
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Residues in contact with PRO 660 (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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656A GLN 3.1 21.8 - - - +
657A ALA 3.3 8.7 - - - +
659A MET* 1.3 95.7 - - + +
661A ALA* 1.3 61.7 + - - +
663A MET* 3.3 3.2 + - + +
664A LEU* 3.1 18.5 + - - +
747A PHE* 3.9 25.6 - - + -
923A SER* 3.7 11.2 - - - +
947A VAL* 3.3 38.5 - - + +
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Residues in contact with ALA 661 (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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657A ALA 4.8 1.9 + - - +
658A ILE* 3.1 12.8 + - + +
660A PRO* 1.3 79.6 - - - +
662A GLN* 1.3 61.5 + - - +
664A LEU* 3.6 16.7 - - - +
665A SER* 4.5 1.7 + - - -
747A PHE* 5.0 1.2 - - - -
759A ALA* 5.9 0.9 - - + -
761A VAL* 3.8 22.4 - - + -
806A MET* 3.3 26.6 - - + +
807A SER 4.8 3.5 - - - +
808A VAL* 5.2 3.5 - - - +
921A ILE* 4.5 21.8 - - + -
923A SER* 5.4 2.2 + - - -
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Residues in contact with GLN 662 (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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658A ILE* 3.2 36.7 + - + +
659A MET* 2.9 20.5 + - - +
661A ALA* 1.3 78.4 - - - +
663A MET* 1.3 80.0 + - + +
664A LEU 3.2 1.0 + - - -
665A SER* 3.2 18.5 + - - -
666A GLN* 3.9 7.1 - - - +
806A MET* 3.9 13.0 - - + -
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Residues in contact with MET 663 (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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659A MET* 3.0 32.1 + - + +
660A PRO* 3.9 7.4 - - + +
662A GLN* 1.3 93.7 - - + +
664A LEU* 1.3 66.3 + - - +
665A SER 3.0 2.7 - - - -
666A GLN* 2.9 45.0 + - + +
669A TYR* 3.8 46.4 - - + +
672A ARG* 5.6 5.6 - - - +
947A VAL* 4.3 4.3 - - + -
951A GLN* 3.4 8.0 + - - -
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Residues in contact with LEU 664 (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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660A PRO 3.1 7.6 + - - +
661A ALA* 3.6 13.2 - - - +
662A GLN 3.2 0.6 - - - -
663A MET* 1.3 76.4 - - - +
665A SER* 1.3 55.3 + - - +
737A VAL* 3.7 10.9 - - + +
747A PHE* 5.9 0.7 - - + -
808A VAL* 3.9 26.9 - - + -
919A MET* 3.9 13.7 - - + -
921A ILE* 3.9 26.9 - - + -
947A VAL* 3.5 24.4 - - + +
950A LEU* 3.9 15.9 - - + -
951A GLN* 2.8 36.3 + - + +
954A MET* 3.8 20.4 - - - -
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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