Contacts of the helix formed by residues 641 - 658 (chain A) in PDB entry 4Z4H
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 ASP 641 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A ARG* 3.2 42.5 + - + +
632A GLN* 4.8 0.4 + - - -
639A ILE* 3.4 2.4 - - - +
640A GLN* 1.3 79.3 - - + +
642A LEU* 1.3 62.8 + - - +
643A ALA* 3.2 4.4 + - - +
644A ALA* 3.2 27.1 + - - +
645A MET* 3.2 14.1 + - - +
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Residues in contact with LEU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A VAL* 3.7 29.2 - - + -
639A ILE* 3.7 27.2 + - + +
640A GLN 3.3 4.6 + - - -
641A ASP* 1.3 75.7 - - - +
643A ALA* 1.3 58.1 + - - +
645A MET* 3.0 5.4 + - + +
646A VAL* 2.8 45.5 + - + +
666A PHE* 4.0 24.2 - - + -
682A HIS* 5.1 0.2 - - - -
683A GLU* 3.5 49.1 - - + +
686A ALA* 3.9 9.4 - - + -
687A ILE* 4.2 3.1 - - + -
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Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ASP* 3.2 1.7 + - - +
642A LEU* 1.3 76.9 - - - +
644A ALA* 1.3 62.5 + - - +
646A VAL* 3.4 0.6 + - - -
647A ARG* 3.1 21.3 + - - +
686A ALA* 3.5 32.6 - - + +
689A GLU* 3.6 31.9 - - + +
690A ALA* 3.4 12.3 - - - +
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Residues in contact with ALA 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A ARG* 4.2 8.7 - - - +
641A ASP* 3.2 32.6 + - - +
643A ALA* 1.3 77.7 - - - +
645A MET* 1.3 63.0 + - - +
647A ARG* 3.4 9.6 + - - +
648A GLU* 3.2 29.4 + - - +
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Residues in contact with MET 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA* 3.6 20.0 - - - +
614A VAL* 3.7 26.7 - - + -
628A THR* 3.3 51.7 - - - +
629A VAL* 3.7 4.7 - - - +
630A ARG* 3.7 31.4 - - + -
639A ILE* 3.9 20.0 - - - -
641A ASP* 3.3 14.8 - - - +
642A LEU* 3.0 7.7 + - + +
644A ALA* 1.3 77.9 - - - +
646A VAL* 1.3 60.5 + - - +
648A GLU* 3.5 10.2 + - - +
649A LEU* 3.3 28.5 + - - +
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Residues in contact with VAL 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A LEU* 4.0 27.6 - - + -
614A VAL* 5.1 1.3 - - + -
642A LEU* 2.8 41.0 + - + +
643A ALA* 4.6 0.4 - - - -
645A MET* 1.3 74.5 - - - +
647A ARG* 1.3 59.8 + - - +
649A LEU* 3.1 8.2 + - + +
650A LEU* 2.8 44.8 + - + +
664A ILE* 5.3 2.0 - - + -
687A ILE* 4.3 24.9 - - + -
690A ALA* 3.8 20.2 - - + -
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Residues in contact with ARG 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ALA 3.1 17.2 + - - +
644A ALA* 3.6 9.0 - - - +
646A VAL* 1.3 78.7 - - - +
648A GLU* 1.3 63.6 + - - +
650A LEU* 3.3 6.6 + - - +
651A ILE* 3.0 47.5 + - + +
690A ALA* 3.9 12.9 + - + +
693A LYS* 3.4 37.2 + - - +
694A LEU* 3.4 29.6 - - + +
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Residues in contact with GLU 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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628A THR* 3.5 22.6 - - + +
630A ARG* 2.5 36.7 + - - -
644A ALA* 3.2 13.7 + - - +
645A MET* 3.6 6.9 - - - +
647A ARG* 1.3 79.2 - - + +
649A LEU* 1.3 59.0 + - - +
651A ILE* 3.4 8.2 + - - +
652A GLN* 3.0 28.8 + - - +
853A LEU* 5.2 9.9 - - - +
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Residues in contact with LEU 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 4.6 3.1 - - + -
594A LEU* 4.2 15.5 - - + -
614A VAL* 3.8 38.1 - - + +
615A VAL 4.1 8.1 - - - -
616A GLY 3.7 6.5 - - - +
618A MET* 3.5 19.0 - - + +
626A CYS* 3.5 33.7 - - + +
627A ALA 4.4 0.2 - - - +
628A THR* 4.1 14.8 - - + +
645A MET 3.3 17.2 + - - +
646A VAL* 3.1 10.3 + - + +
648A GLU* 1.3 74.6 - - - +
650A LEU* 1.3 60.7 + - + +
652A GLN* 3.2 2.9 + - + +
653A PHE* 2.8 30.6 + - - +
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Residues in contact with LEU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 4.5 10.5 - - + -
646A VAL* 2.8 37.6 + - + +
647A ARG 3.7 0.4 - - - +
649A LEU* 1.3 76.0 - - - +
651A ILE* 1.3 63.5 + - - +
653A PHE* 3.3 6.3 + - - +
654A TYR 3.1 17.5 + - - -
661A PRO* 3.8 29.6 - - + -
664A ILE* 4.4 12.1 - - + -
690A ALA* 4.6 1.3 - - + -
691A CYS* 4.0 27.8 - - - +
694A LEU* 3.7 28.3 - - + -
698A TYR* 4.1 13.5 - - + +
902A IPH 3.5 13.6 + - + -
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Residues in contact with ILE 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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647A ARG* 3.0 50.2 + - + +
648A GLU* 3.6 7.2 - - - +
650A LEU* 1.3 77.4 - - - +
652A GLN* 1.3 64.8 + - - +
654A TYR* 3.2 5.5 + - - +
655A LYS* 3.0 24.5 + - + +
694A LEU* 4.0 19.5 - - + -
902A IPH 3.6 9.9 - - - +
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Residues in contact with GLN 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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618A MET* 3.6 17.5 - - + -
626A CYS* 3.9 18.1 - - + -
648A GLU 3.0 17.4 + - - +
649A LEU* 3.2 5.8 + - + +
651A ILE* 1.3 79.4 - - - +
653A PHE* 1.3 53.6 + - - +
655A LYS* 3.4 24.5 + - - +
656A SER* 2.8 56.7 + - - +
854A ARG* 3.1 46.5 + - + +
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Residues in contact with PHE 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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590A PRO* 4.8 0.4 - - + -
591A VAL 3.6 25.4 - - - -
592A ILE* 3.6 20.2 - - + -
617A SER* 3.2 27.6 - - - -
618A MET* 3.5 11.6 - - - -
619A ASP 4.8 4.7 - - - -
649A LEU 2.8 17.7 + - - +
650A LEU* 3.4 7.0 - - - +
651A ILE 3.2 0.2 - - - -
652A GLN* 1.3 77.4 - - - +
654A TYR* 1.3 53.5 + - - +
656A SER* 3.2 1.2 + - - -
657A THR* 2.8 57.7 + - + +
659A PHE* 3.5 19.3 - - + -
661A PRO* 3.6 28.7 - - + -
903A IPH 3.2 25.6 - + - -
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Residues in contact with TYR 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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650A LEU 3.1 7.3 + - - +
651A ILE 3.6 3.8 - - - +
653A PHE* 1.3 73.9 - - - +
655A LYS* 1.3 64.2 + - - +
658A ARG* 2.7 78.1 + - - -
659A PHE 3.3 27.1 - - - +
660A LYS* 3.7 33.1 - - + -
902A IPH 3.2 26.9 - + + +
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Residues in contact with LYS 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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651A ILE* 3.0 17.2 + - + +
652A GLN* 3.6 33.0 - - - +
653A PHE 3.3 0.2 - - - -
654A TYR* 1.3 81.6 - - + +
656A SER* 1.3 60.8 + - - +
658A ARG* 4.7 11.3 + - - +
854A ARG* 4.3 20.4 - - - +
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Residues in contact with SER 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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618A MET* 3.4 34.3 - - - +
652A GLN* 2.8 36.2 + - - -
653A PHE 3.7 2.2 - - - -
654A TYR 3.2 0.2 - - - -
655A LYS* 1.3 80.1 - - - +
657A THR* 1.3 60.8 + - - +
658A ARG* 5.5 1.0 - - - +
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Residues in contact with THR 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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618A MET 3.3 30.7 - - - +
619A ASP* 3.9 10.3 - - + -
620A ALA* 5.0 0.4 - - + +
653A PHE* 2.8 39.9 + - + +
656A SER* 1.3 76.7 - - - +
658A ARG* 1.3 69.9 + - - +
659A PHE* 3.0 31.4 + - - +
903A IPH 3.9 17.7 - - - +
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Residues in contact with ARG 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 TYR* 2.7 69.9 + - - +
655A LYS* 4.9 10.2 + - - +
656A SER 5.5 0.9 - - - +
657A THR* 1.3 74.7 + - - +
659A PHE* 1.3 64.7 + - - +
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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