Contacts of the helix formed by residues 651 - 662 (chain A) in PDB entry 4H1J
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 PRO 651 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A VAL* 3.9 16.2 - - + -
527A VAL* 4.7 2.9 - - + -
619A LEU* 4.2 0.9 - - + -
649A LEU 3.4 6.9 - - - +
650A CYS* 1.4 90.8 - - - +
652A PRO* 1.4 72.7 - - + +
653A VAL* 4.6 3.1 - - + +
654A LEU* 3.0 34.8 + - + +
655A TYR* 3.2 9.5 + - - +
682A VAL* 5.0 4.0 - - + -
685A MET* 6.4 1.6 - - + -
686A GLU* 3.6 38.6 - - + +
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Residues in contact with PRO 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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646A LYS* 4.2 21.3 - - + -
650A CYS 3.5 4.2 - - - +
651A PRO* 1.4 81.4 - - + +
653A VAL* 1.3 58.7 + - + +
655A TYR* 3.2 5.2 + - - +
656A THR* 3.0 29.9 + - - -
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Residues in contact with VAL 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 PRO* 3.3 3.8 - - + +
652A PRO* 1.3 78.7 - - + +
654A LEU* 1.4 61.2 + - - +
656A THR* 3.3 10.7 + - - -
657A LEU* 3.2 24.9 + - + +
682A VAL* 3.9 20.2 - - + -
685A MET* 3.9 27.6 - - + -
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Residues in contact with LEU 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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527A VAL* 4.2 22.4 - - + -
530A SER* 5.2 1.3 - - - +
615A MET* 4.2 14.6 - - + -
619A LEU* 3.8 35.7 - - + -
650A CYS* 3.9 4.7 - - - -
651A PRO* 3.0 20.1 + - + +
653A VAL* 1.4 74.6 - - - +
655A TYR* 1.4 61.2 + - - +
657A LEU* 3.2 12.5 + - + +
658A MET* 3.0 35.1 + - + +
679A LEU* 3.5 32.8 - - + -
682A VAL* 4.2 18.4 - - + +
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Residues in contact with TYR 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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643A ARG* 4.6 5.7 + - - +
644A LEU 2.6 30.0 + - - -
645A PRO* 3.8 3.8 - - - +
646A LYS* 3.5 58.9 + - + -
647A PRO* 4.5 0.9 - - + -
650A CYS* 3.8 5.3 - - - -
651A PRO 3.2 4.9 + - - -
652A PRO* 3.6 7.6 - - + +
654A LEU* 1.4 72.5 - - - +
656A THR* 1.3 68.0 + - - +
658A MET* 3.2 19.1 + - - +
659A THR* 3.0 42.3 + - + +
662A TRP* 4.0 14.7 - + - -
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Residues in contact with THR 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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652A PRO 3.0 14.6 + - - -
653A VAL* 3.5 13.8 - - + +
654A LEU 3.3 0.2 - - - -
655A TYR* 1.3 76.4 - - - +
657A LEU* 1.3 60.4 + - + +
659A THR* 2.8 23.3 + - - +
660A ARG* 3.1 44.5 + - + +
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Residues in contact with LEU 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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615A MET* 5.2 2.5 - - + -
653A VAL* 3.2 14.6 + - + +
654A LEU* 3.2 12.7 + - + +
656A THR* 1.3 75.7 - - + +
658A MET* 1.4 60.5 + - - +
660A ARG* 3.2 37.9 + - + +
661A CYS* 3.2 19.5 + - - -
670A PRO* 5.3 2.4 - - + +
675A LEU* 4.5 14.3 - - + +
678A SER* 3.7 37.5 - - - +
679A LEU* 4.0 16.2 - - + -
682A VAL* 3.8 28.5 - - + -
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Residues in contact with MET 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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612A ALA* 4.0 13.9 - - - +
615A MET* 3.9 47.5 - - + +
616A TRP* 4.0 13.7 - - - +
619A LEU* 4.3 3.8 - - + -
647A PRO* 4.8 0.9 - - + -
650A CYS* 3.7 25.4 - - - -
654A LEU* 3.0 26.0 + - + +
655A TYR* 3.2 28.2 + - + +
657A LEU* 1.4 74.4 - - - +
659A THR* 1.4 63.5 + - - +
661A CYS* 3.2 6.7 + - - +
662A TRP* 3.1 50.0 + - + -
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Residues in contact with THR 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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643A ARG* 5.5 7.8 + - + -
655A TYR* 3.0 52.1 + - + +
656A THR* 2.8 23.6 + - - +
658A MET* 1.4 75.9 - - - +
660A ARG* 1.3 61.1 + - - +
662A TRP* 3.2 31.8 + - + +
663A ASP* 3.5 2.4 + - - +
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Residues in contact with ARG 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 THR* 3.1 36.8 + - + +
657A LEU* 3.2 30.4 + - + +
659A THR* 1.3 73.6 - - - +
661A CYS* 1.3 62.6 + - - +
662A TRP 3.1 0.4 - - - -
663A ASP* 3.3 22.5 + - - +
668A ASP 3.9 4.9 - - - +
669A ARG* 3.6 12.3 - - - -
670A PRO* 4.1 16.2 - - + -
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Residues in contact with CYS 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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608A VAL* 3.6 33.2 - - + +
609A TRP* 3.4 12.0 - - - +
612A ALA* 3.5 22.9 - - + -
615A MET* 4.9 2.9 - - - -
657A LEU 3.2 15.9 + - - -
658A MET* 3.2 9.3 + - - +
660A ARG* 1.3 76.1 - - - +
662A TRP* 1.3 58.2 + - - +
663A ASP 3.3 0.9 - - - -
669A ARG* 3.2 25.2 + - - -
670A PRO* 4.1 9.4 - - - -
675A LEU* 4.0 23.8 - - - -
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Residues in contact with TRP 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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609A TRP* 3.2 53.5 + + + -
612A ALA* 3.4 31.3 - - + +
613A VAL* 3.5 10.0 - - + +
616A TRP* 4.2 6.7 - + + -
643A ARG* 3.0 50.0 + - + +
644A LEU* 3.8 51.1 - - + -
655A TYR* 4.0 14.1 - + - -
658A MET* 3.1 37.4 + - + +
659A THR* 3.2 18.1 + - + +
660A ARG 3.1 1.0 - - - -
661A CYS* 1.3 78.1 - - - +
663A ASP* 1.3 62.9 + - - -
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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
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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