Contacts of the helix formed by residues 680 - 701 (chain A) in PDB entry 4PK7
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 680 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A GLU 3.5 4.3 + - - +
679A PRO* 1.3 74.6 - - - +
681A GLU* 1.3 65.8 + - + +
682A ASP* 3.0 25.6 + - - +
683A ASP* 2.8 30.1 + - - +
684A ALA* 3.2 20.8 + - - +
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Residues in contact with GLU 681 (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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680A ASP* 1.3 75.2 - - + +
682A ASP* 1.3 68.0 + - - +
684A ALA* 3.7 7.3 - - - +
685A TYR* 3.4 20.8 + - - +
726A PRO* 6.4 0.7 - - - -
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Residues in contact with ASP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A ASP* 3.0 16.6 + - - +
681A GLU* 1.3 87.0 - - - +
683A ASP* 1.3 69.0 - - - +
684A ALA 2.9 2.2 + - - -
685A TYR* 3.2 15.2 + - - +
686A GLN* 3.2 15.0 + - - +
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Residues in contact with ASP 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LEU* 5.5 0.3 - - - +
671A ASP* 5.1 7.3 - - - +
672A PHE* 4.2 4.7 - - + -
677A GLU* 4.4 14.2 - - - +
679A PRO* 3.6 31.5 - - + +
680A ASP* 2.8 24.5 + - - +
682A ASP* 1.3 78.8 - - - +
684A ALA* 1.3 59.9 + - - +
686A GLN* 3.3 22.4 - - - +
687A VAL* 3.3 13.6 - - - +
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Residues in contact with ALA 684 (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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672A PHE* 4.1 17.4 - - + -
679A PRO 5.4 0.7 - - - +
680A ASP 3.2 15.5 + - - +
681A GLU* 3.7 9.2 - - - +
682A ASP 2.9 0.4 - - - -
683A ASP* 1.3 74.0 - - - +
685A TYR* 1.3 57.9 + - - +
686A GLN 3.1 1.6 - - - -
687A VAL* 2.7 26.4 + - - +
688A LEU* 2.8 13.1 + - - +
726A PRO* 4.2 26.2 - - + -
729A ILE* 3.8 8.8 - - + +
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Residues in contact with TYR 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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624A THR* 2.8 27.6 + - + +
681A GLU 3.4 10.1 + - - +
682A ASP* 3.2 9.9 + - - +
684A ALA* 1.3 77.7 - - - +
686A GLN* 1.3 59.9 + - - +
688A LEU* 4.0 24.5 - - + -
689A SER* 2.6 64.3 + - - -
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Residues in contact with GLN 686 (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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664A LYS* 4.6 13.7 + - - +
668A LEU* 3.8 27.4 - - + +
682A ASP 3.2 12.3 + - - +
683A ASP* 3.3 19.5 - - - +
685A TYR* 1.3 86.3 - - - +
687A VAL* 1.3 61.1 + - - +
689A SER* 3.9 5.2 + - - -
690A THR* 3.3 23.6 + - - -
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Residues in contact with VAL 687 (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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665A PHE* 4.1 20.2 - - + -
668A LEU* 4.4 19.3 - - + +
669A LEU* 4.2 15.3 - - + -
672A PHE* 3.9 31.6 - - + -
683A ASP 3.3 17.7 - - - +
684A ALA 2.7 12.7 + - - +
686A GLN* 1.3 71.0 - - + +
688A LEU* 1.3 54.7 + - - +
690A THR* 3.1 3.3 + - - -
691A LEU* 2.7 39.3 + - + +
715A LEU* 4.8 7.2 - - + -
729A ILE* 4.2 13.7 - - + -
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Residues in contact with LEU 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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684A ALA 2.8 14.8 + - - +
685A TYR* 3.7 28.3 - - + +
687A VAL* 1.3 72.8 - - - +
689A SER* 1.3 65.1 + - - +
691A LEU* 3.1 7.6 + - + -
692A LYS* 2.8 58.5 + - + +
728A GLN* 3.7 49.1 - - + +
729A ILE* 4.0 17.2 - - + +
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Residues in contact with SER 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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624A THR* 3.4 27.5 - - - +
685A TYR* 2.6 56.9 + - - -
686A GLN* 3.9 8.2 + - - -
688A LEU* 1.3 75.1 - - - +
690A THR* 1.3 61.7 + - - +
692A LYS* 3.8 5.0 + - - +
693A ARG* 3.1 35.3 + - - +
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Residues in contact with THR 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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661A LEU* 4.1 26.2 - - + +
664A LYS* 3.3 20.8 + - + -
665A PHE* 3.7 22.7 - - + +
668A LEU* 3.3 27.6 - - + +
686A GLN 3.3 6.1 + - - -
687A VAL 3.1 7.6 + - - -
689A SER* 1.3 75.4 - - - +
691A LEU* 1.3 65.5 + - - +
693A ARG* 3.3 25.9 + - - +
694A ILE* 3.3 12.8 + - + +
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Residues in contact with LEU 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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665A PHE* 3.7 31.6 - - + -
687A VAL* 2.7 22.3 + - + +
688A LEU* 3.6 6.5 - - + +
690A THR* 1.3 70.9 - - - +
692A LYS* 1.3 56.4 + - + +
694A ILE* 3.0 9.0 + - + +
695A THR* 2.7 52.7 + - - +
712A ASN* 3.8 19.5 - - - +
715A LEU* 4.3 9.9 - - + -
729A ILE* 3.6 46.4 - - + +
732A HIS* 4.6 10.3 - - - -
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Residues in contact with LYS 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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624A THR* 3.0 31.0 + - - -
625A ASP 4.9 0.2 - - - -
626A THR* 2.9 32.0 + - - +
629A LEU* 3.9 11.6 - - + +
688A LEU* 2.8 53.2 + - + +
689A SER* 3.8 6.7 - - - +
691A LEU* 1.3 72.0 - - + +
693A ARG* 1.3 53.7 + - - +
695A THR* 3.2 7.3 + - - -
696A ALA* 2.8 36.7 + - - +
728A GLN* 5.3 8.7 + - - +
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Residues in contact with ARG 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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620A VAL* 3.1 33.5 + - + -
621A GLU* 3.3 25.1 + - - +
622A LYS 4.8 0.8 - - - -
623A HIS 3.2 8.9 + - - +
624A THR* 3.3 25.3 - - - +
629A LEU* 4.0 18.8 - - + -
661A LEU* 3.7 30.1 - - + +
664A LYS* 4.2 14.6 - - - +
689A SER* 3.1 24.7 + - - +
690A THR* 3.5 28.7 + - - +
691A LEU 3.2 0.6 - - - -
692A LYS* 1.3 75.0 - - - +
694A ILE* 1.3 63.3 + - - +
696A ALA* 3.7 2.3 + - - +
697A PHE* 3.3 31.9 + - - +
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Residues in contact with ILE 694 (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* 6.2 2.9 - - + -
661A LEU* 3.6 45.5 - - + +
662A ALA* 3.9 7.6 - - + +
665A PHE* 3.8 30.3 - - + -
690A THR* 3.3 10.3 + - + +
691A LEU* 3.0 15.1 + - + +
693A ARG* 1.3 76.7 - - - +
695A THR* 1.3 68.1 + - - +
697A PHE* 3.2 4.5 + - - +
698A HIS* 2.9 26.4 + - + +
703A LEU* 4.4 6.8 - - + +
708A LEU* 3.9 26.9 - - + -
712A ASN* 5.6 5.2 - - - +
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Residues in contact with THR 695 (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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691A LEU* 2.7 40.9 + - - +
692A LYS* 3.7 6.5 - - - -
694A ILE* 1.3 74.5 - - - +
696A ALA* 1.3 63.3 + - - +
697A PHE 3.1 1.2 + - - -
698A HIS* 3.2 14.7 + - + +
699A ASN* 3.3 13.2 + - - +
732A HIS* 4.3 19.4 - - - -
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Residues in contact with ALA 696 (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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626A THR 5.6 0.4 - - - +
629A LEU* 3.8 37.5 - - + +
630A GLU* 4.6 2.9 - - + +
633A SER* 2.7 23.7 + - - -
692A LYS 2.8 21.1 + - - +
693A ARG 3.9 4.9 - - - +
695A THR* 1.3 74.1 - - - +
697A PHE* 1.3 56.8 + - + +
699A ASN* 3.7 13.9 - - - +
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Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A VAL* 3.8 31.9 - - + -
629A LEU* 4.9 3.1 - - + -
632A CYS* 4.2 2.0 - - + -
633A SER* 3.4 23.1 - - - -
636A TYR* 3.8 28.3 - + + -
654A ARG* 5.7 3.8 - - + -
657A LEU* 3.7 19.7 - - + -
658A ILE* 4.0 26.7 - - + -
661A LEU* 4.6 7.6 - - + -
693A ARG* 3.3 23.0 + - - +
694A ILE* 3.2 4.8 + - - +
695A THR 3.1 0.4 - - - -
696A ALA* 1.3 80.8 - - + +
698A HIS* 1.3 58.6 + - - +
699A ASN 3.2 1.8 - - - -
700A ALA 3.4 1.0 + - - -
701A HIS* 2.8 66.5 + + - +
703A LEU* 4.3 2.5 - - + -
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Residues in contact with HIS 698 (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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694A ILE* 2.9 20.6 + - + +
695A THR* 3.2 6.0 + - + +
697A PHE* 1.3 73.6 - - - +
699A ASN* 1.3 65.6 + - - +
701A HIS 3.1 15.3 + - - +
702A ASP 3.4 21.3 - - - -
703A LEU* 3.6 23.5 + - + +
704A SER* 5.4 1.1 - - - -
708A LEU* 3.2 38.4 - - + +
712A ASN* 5.8 3.6 - - - -
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Residues in contact with ASN 699 (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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695A THR 3.3 8.3 + - - +
696A ALA* 3.7 13.5 - - - +
698A HIS* 1.3 82.6 - - - +
700A ALA* 1.3 63.2 + - + +
701A HIS 5.0 0.5 - - - -
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Residues in contact with ALA 700 (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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633A SER* 3.4 29.6 - - - +
634A LYS* 4.9 7.6 - - + +
637A HIS* 3.6 32.9 + - + +
696A ALA 4.6 0.4 - - - +
697A PHE 3.4 2.8 + - - -
699A ASN* 1.3 82.6 - - + +
701A HIS* 1.3 68.2 + - + +
702A ASP 4.4 0.2 + - - -
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Residues in contact with HIS 701 (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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633A SER* 3.0 24.1 + - - -
636A TYR* 3.5 17.2 - - + +
637A HIS* 3.3 39.1 - - + +
654A ARG* 3.0 37.6 + - - +
697A PHE* 2.8 45.2 + + - +
698A HIS* 3.1 18.8 - - - +
699A ASN 3.4 0.8 - - - -
700A ALA* 1.3 81.7 + - - +
702A ASP* 1.3 65.9 - - - +
703A LEU* 3.4 21.8 - - + +
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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