Contacts of the helix formed by residues 675 - 695 (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 GLN 675 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A GLU* 5.0 3.1 - - + +
671A VAL* 3.5 14.6 - - + -
672A SER* 2.8 17.5 + - - +
674A GLY* 1.3 97.2 + - - +
676A PHE* 1.3 66.2 + - - +
677A GLN 3.4 2.5 - - - -
678A GLN* 3.1 28.8 + - - +
679A VAL* 3.0 31.7 + - + +
11B C 2.8 27.5 + - - +
12B C 3.4 39.9 + - - +
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Residues in contact with PHE 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A VAL* 3.2 31.6 - - + -
672A SER 3.3 11.2 - - - -
673A GLU* 3.2 34.6 + - + +
674A GLY 3.7 0.4 - - - -
675A GLN* 1.3 78.3 - - - +
677A GLN* 1.3 69.1 + - + +
679A VAL* 4.0 0.6 - - - +
680A LEU* 2.9 34.3 + - - +
706A VAL* 3.7 11.9 - - + -
708A GLN* 3.8 18.8 - - - -
745A GLU* 5.4 1.6 - - - -
766A HIS* 3.5 41.7 - + + -
768A LEU* 3.7 30.7 - - + +
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Residues in contact with GLN 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.2 28.0 + - - +
24A LYS* 4.6 15.3 + - - +
25A PRO* 3.9 29.3 - - - +
673A GLU 5.0 0.2 + - - -
675A GLN 3.4 0.6 - - - -
676A PHE* 1.3 82.6 - - + +
678A GLN* 1.3 71.7 + - - +
680A LEU* 4.0 5.5 - - - +
681A HIS* 3.0 26.7 + - - +
768A LEU* 5.7 0.2 - - - +
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Residues in contact with GLN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ILE* 4.1 16.9 - - + +
674A GLY 3.2 16.7 + - - +
675A GLN* 3.1 33.8 - - + +
676A PHE 3.3 0.2 - - - -
677A GLN* 1.3 90.2 + - + +
679A VAL* 1.3 64.4 - - + +
681A HIS* 3.6 6.0 + - - +
682A HIS* 3.3 20.4 + - - +
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Residues in contact with VAL 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 4.5 11.7 - - + -
638A ILE* 4.2 20.9 - - + -
668A ARG* 4.1 2.5 - - + +
671A VAL* 3.7 35.2 - - + -
675A GLN* 3.0 26.3 + - + +
676A PHE* 4.1 1.8 - - - +
678A GLN* 1.3 73.7 - - + +
680A LEU* 1.3 62.4 + - - +
681A HIS 3.3 0.2 + - - -
682A HIS* 3.3 1.2 + - - -
683A GLU* 2.9 58.6 + - - +
704A PHE* 4.3 10.3 - - + -
768A LEU* 5.8 1.8 - - + -
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 4.5 2.9 - - - +
23A PHE* 3.2 34.3 - - - +
25A PRO* 5.2 1.3 - - + -
676A PHE 2.9 20.1 + - - +
677A GLN* 4.0 8.1 - - - +
679A VAL* 1.3 78.9 - - - +
681A HIS* 1.3 63.5 + - - +
684A LEU* 3.0 56.8 + - + +
704A PHE* 4.0 20.9 - - + -
768A LEU* 3.6 43.7 - - + +
769A TRP* 4.2 7.6 - - + -
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Residues in contact with HIS 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 4.3 17.9 + - + +
23A PHE* 6.2 2.9 - - + -
677A GLN 3.0 19.9 + - - +
678A GLN* 3.6 5.9 + - - +
679A VAL 3.2 0.4 - - - -
680A LEU* 1.3 78.4 - - - +
682A HIS* 1.3 66.1 + - - +
685A LEU* 3.2 47.8 - - + +
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Residues in contact with HIS 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ILE* 3.5 32.9 - - + +
639A ILE 3.2 23.7 + - - -
640A GLN* 3.5 31.6 + - - -
642A LEU 5.1 0.2 - - - -
678A GLN 3.3 10.1 + - - +
679A VAL 3.3 2.5 + - - +
681A HIS* 1.3 85.5 - - - +
683A GLU* 1.3 63.8 + - - +
685A LEU* 3.6 3.1 + - - +
686A ALA* 3.0 34.2 + - + +
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Residues in contact with GLU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ILE* 3.8 2.5 - - + -
639A ILE* 2.9 36.3 + - - +
642A LEU* 3.5 19.1 - - + +
666A PHE* 4.0 4.0 - - - -
668A ARG* 2.8 42.4 + - - -
679A VAL* 2.9 30.3 + - + +
682A HIS* 1.3 86.0 - - + +
684A LEU* 1.3 66.1 + - - +
686A ALA* 3.2 4.0 + - - +
687A ILE* 3.1 27.7 + - - +
704A PHE* 3.6 15.9 - - + -
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Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.8 34.8 - - + -
680A LEU* 3.0 34.6 + - + +
681A HIS 4.8 0.2 - - - +
683A GLU* 1.3 76.2 - - - +
685A LEU* 1.3 62.5 + - + +
687A ILE* 3.2 7.5 + - - +
688A ARG* 3.1 30.7 + - - +
702A ILE* 3.8 37.0 - - + -
704A PHE* 4.1 9.6 - - + -
769A TRP* 3.8 39.5 - - + +
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Residues in contact with LEU 685 (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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22A ALA* 3.8 28.3 - - + -
681A HIS* 3.2 45.6 + - + +
682A HIS* 3.6 4.4 + - - +
684A LEU* 1.3 75.8 - - - +
686A ALA* 1.3 60.6 + - - +
688A ARG* 3.7 22.8 - - + +
689A GLU* 2.9 30.2 + - - +
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Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A LEU* 3.9 14.6 - - + -
643A ALA* 3.5 39.8 - - + +
682A HIS* 3.0 27.3 + - + +
683A GLU* 3.5 7.6 - - - +
684A LEU 3.2 0.6 - - - -
685A LEU* 1.3 74.3 - - - +
687A ILE* 1.3 63.9 + - - +
689A GLU* 3.3 7.0 + - - +
690A ALA* 3.0 18.4 + - - +
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Residues in contact with ILE 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A LEU* 4.2 9.6 - - + -
646A VAL* 4.3 19.5 - - + -
664A ILE* 4.0 26.2 - - + -
666A PHE* 3.7 39.0 - - + -
683A GLU 3.1 15.2 + - - +
684A LEU* 3.2 7.6 + - - +
686A ALA* 1.3 76.7 - - - +
688A ARG* 1.3 61.5 + - - +
690A ALA* 3.3 9.0 + - - +
691A CYS* 3.2 19.8 + - - -
702A ILE* 3.5 35.0 - - + -
704A PHE* 4.3 7.2 - - + -
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Residues in contact with ARG 688 (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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22A ALA* 3.9 23.2 - - - +
684A LEU* 3.1 21.9 + - - +
685A LEU* 3.7 24.0 - - + +
687A ILE* 1.3 78.0 - - - +
689A GLU* 1.3 57.7 + - - +
691A CYS* 3.0 5.5 + - - +
692A ILE* 2.8 36.9 + - + +
702A ILE* 3.9 4.7 - - + -
769A TRP* 3.6 31.7 - - - +
771A ASP* 4.9 0.4 + - - -
904A IPH 3.0 61.6 + - + -
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Residues in contact with GLU 689 (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 ALA* 3.6 23.3 - - + +
685A LEU 2.9 18.3 + - - +
686A ALA* 3.5 9.3 - - - +
688A ARG* 1.3 75.0 - - - +
690A ALA* 1.3 65.3 + - - +
692A ILE* 3.3 7.2 + - - +
693A LYS* 2.9 63.3 + - + +
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Residues in contact with ALA 690 (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 ALA* 3.4 26.9 - - - +
646A VAL* 3.8 21.3 - - + -
647A ARG* 3.9 12.4 + - - +
650A LEU* 4.6 2.7 - - + -
686A ALA 3.0 11.7 + - - +
687A ILE 3.4 9.9 - - - +
688A ARG 3.2 0.2 - - - -
689A GLU* 1.3 78.1 - - - +
691A CYS* 1.3 60.9 + - - +
693A LYS* 4.0 4.8 - - - +
694A LEU* 3.2 27.7 + - - +
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Residues in contact with CYS 691 (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* 4.0 7.6 - - - -
664A ILE* 3.8 15.9 - - - -
687A ILE* 3.2 16.2 + - - -
688A ARG* 3.0 9.2 + - - +
690A ALA* 1.3 76.5 - - - +
692A ILE* 1.3 64.9 + - - +
694A LEU* 3.1 14.3 + - - +
695A GLU 3.2 14.7 + - - +
698A TYR* 3.5 36.8 - - + +
700A PRO* 3.7 30.3 - - + -
904A IPH 4.5 7.6 - - + -
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Residues in contact with ILE 692 (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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688A ARG* 2.8 28.4 + - + +
689A GLU* 3.8 6.7 - - - +
691A CYS* 1.3 72.1 - - - +
693A LYS* 1.3 67.2 + - + +
694A LEU 3.5 0.2 + - - -
695A GLU* 3.5 15.3 + - - +
696A LYS 3.9 7.4 - - - +
697A ASP 4.4 12.1 - - - +
698A TYR 4.0 14.8 - - - +
699A GLN* 4.3 20.0 - - + +
904A IPH 5.0 3.6 - - + -
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Residues in contact with LYS 693 (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* 3.4 20.9 + - - +
689A GLU* 2.9 50.6 + - + +
690A ALA* 4.1 3.1 - - - +
692A ILE* 1.3 79.3 - - + +
694A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ARG* 3.4 37.2 - - + +
650A LEU* 3.7 41.1 - - + -
651A ILE* 4.0 17.3 - - + -
690A ALA 3.2 13.1 + - - +
691A CYS* 3.1 11.0 + - - +
693A LYS* 1.3 78.7 - - - +
695A GLU* 1.3 65.4 + - - +
902A IPH 3.9 36.2 - - + -
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Residues in contact with GLU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A LYS* 3.4 31.9 + - - +
691A CYS 3.2 11.1 + - - +
692A ILE* 3.5 6.7 - - - +
693A LYS 3.4 1.2 - - - -
694A LEU* 1.3 84.1 - - - +
696A LYS* 1.3 104.5 + - + +
698A TYR* 3.1 25.8 + - + +
902A IPH 3.1 26.3 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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