Contacts of the helix formed by residues 680 - 698 (chain A) in PDB entry 5J3V
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 MET 680 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A LYS* 3.8 30.2 - - + +
639A ASP* 4.1 11.7 - - - +
642A ILE* 3.7 29.2 - - + -
678A ASP* 2.8 14.2 + - - +
679A LYS* 1.3 78.1 - - - +
681A PRO* 1.3 70.5 - - + +
682A GLU* 3.3 28.5 - - + +
683A VAL* 3.2 17.9 + - + +
684A ARG* 3.3 14.0 + - - +
18C LYS* 4.7 4.5 - - - +
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Residues in contact with PRO 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LYS 3.4 7.4 - - - +
680A MET* 1.3 83.3 - - + +
682A GLU* 1.3 76.4 + - - +
684A ARG* 3.1 28.7 + - - +
685A GLN 2.7 31.2 + - - -
721A PHE* 4.3 18.4 - - + -
724A VAL* 3.3 21.1 - - + +
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Residues in contact with GLU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE* 3.6 24.7 - - + -
680A MET* 3.3 23.9 - - + +
681A PRO* 1.3 92.2 - - - +
683A VAL* 1.3 58.1 + - - +
685A GLN* 3.3 21.3 + - - +
686A SER* 2.9 34.5 + - - -
18C LYS* 4.8 19.7 - - + +
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Residues in contact with VAL 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A LYS* 3.9 5.8 - - + -
641A MET* 3.7 34.3 - - + -
642A ILE* 3.7 24.2 - - + -
645A LEU* 4.2 3.7 - - + +
675A CYS* 3.5 28.0 - - + +
678A ASP* 3.8 12.8 - - + +
680A MET* 3.2 28.5 + - + +
681A PRO 3.2 0.6 - - - -
682A GLU* 1.3 77.6 - - - +
684A ARG* 1.3 59.8 + - - +
686A SER* 3.4 4.5 + - - -
687A SER* 3.0 23.9 + - - -
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Residues in contact with ARG 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A CYS 3.8 6.3 - - - +
676A MET* 3.2 26.7 - - - +
677A GLN 4.9 0.4 - - - -
678A ASP 3.2 26.6 + - - +
679A LYS* 4.0 7.8 + - - -
680A MET 3.3 2.0 + - - +
681A PRO* 3.1 37.1 + - - +
683A VAL* 1.3 74.4 - - - +
685A GLN* 1.3 65.0 + - - +
687A SER* 3.0 19.1 + - - -
688A PHE* 3.1 27.0 + - + -
716A ASN* 2.9 24.5 + - - +
721A PHE* 3.6 35.0 - - - -
724A VAL* 4.2 11.2 - - + -
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Residues in contact with GLN 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE* 5.7 1.0 - - - +
681A PRO 2.7 19.3 + - - +
682A GLU* 3.4 29.3 + - - +
684A ARG* 1.3 74.5 - - - +
686A SER* 1.3 67.0 + - - +
688A PHE* 4.9 1.1 - - - -
689A ALA 3.3 7.8 + - - -
723A SER* 3.2 33.6 + - - +
724A VAL* 4.1 17.2 - - + +
727A ASN* 2.8 38.6 + - - +
15C ALA* 4.2 4.1 - - - +
16C PRO 3.8 18.4 - - - +
17C ARG* 5.8 2.0 - - - +
18C LYS* 5.3 11.2 + - - +
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Residues in contact with SER 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE* 3.4 18.6 - - - +
645A LEU* 4.0 21.9 - - - +
646A ASP* 3.0 27.1 + - - +
649A SER* 4.0 4.9 + - - -
682A GLU 2.9 16.8 + - - -
683A VAL 3.4 3.8 + - - -
684A ARG 3.3 0.2 - - - -
685A GLN* 1.3 81.2 + - - +
687A SER* 1.3 60.4 + - - +
689A ALA* 3.5 6.5 + - - +
690A LEU* 3.2 24.9 + - - +
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Residues in contact with SER 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LEU* 4.2 8.5 - - - +
672A MET* 4.3 9.7 - - - +
675A CYS* 3.8 22.0 - - - -
676A MET* 3.6 25.6 - - - +
683A VAL 3.0 14.9 + - - -
684A ARG* 3.0 19.1 + - - -
686A SER* 1.3 77.3 - - - +
688A PHE* 1.3 60.5 + - - +
690A LEU* 3.3 8.1 + - - +
691A LEU* 3.0 26.2 + - - +
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Residues in contact with PHE 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A MET* 3.5 42.0 - - + -
684A ARG* 3.1 20.2 + - + +
685A GLN* 4.0 0.7 - - - +
687A SER* 1.3 78.3 + - - +
689A ALA* 1.3 64.9 + - - +
691A LEU* 3.2 6.3 + - + +
692A GLY* 3.2 18.2 + - - -
712A ILE* 4.0 9.0 - - + -
713A LEU* 3.6 29.2 - - + -
716A ASN* 3.4 47.8 - - + -
724A VAL* 3.8 24.2 - - + -
727A ASN* 3.8 23.9 - - + +
728A ALA* 3.9 5.8 - - + -
730A TRP* 4.6 0.5 - - - -
731A ALA* 4.0 7.8 - - - +
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Residues in contact with ALA 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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646A ASP* 5.8 1.1 - - - +
649A SER* 4.0 6.3 - - - +
685A GLN 3.3 4.6 + - - +
686A SER* 3.6 11.7 - - - +
687A SER 3.2 0.2 - - - -
688A PHE* 1.3 80.7 - - - +
690A LEU* 1.3 60.8 + - - +
692A GLY 3.5 0.7 + - - -
693A ASP* 3.1 30.2 + - - +
727A ASN* 3.4 24.2 - - - +
730A TRP* 3.7 11.6 - - - -
14C LYS* 3.7 21.8 - - + -
15C ALA 5.8 0.2 - - - +
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Residues in contact with LEU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LEU* 3.9 27.4 - - + +
648A LEU* 3.6 41.3 - - + +
649A SER* 3.5 14.7 + - - +
652A ALA* 4.5 3.1 - - + -
668A ILE* 3.8 19.7 - - + -
672A MET* 3.6 23.3 - - + -
686A SER 3.2 9.7 + - - +
687A SER 3.5 9.2 - - - +
688A PHE 3.3 0.2 - - - -
689A ALA* 1.3 75.8 - - - +
691A LEU* 1.3 65.2 + - - +
693A ASP* 3.9 0.8 - - - -
694A LEU* 3.0 46.5 + - + +
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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
----------------------------------------------------------
672A MET* 4.3 10.0 - - + -
676A MET* 3.7 20.9 - - + -
687A SER 3.0 13.6 + - - +
688A PHE* 3.4 9.0 - - + +
689A ALA 3.2 0.4 - - - -
690A LEU* 1.3 76.1 - - - +
692A GLY* 1.3 52.2 + - - +
694A LEU* 3.4 4.3 + - + +
695A THR* 2.6 39.6 + - - +
702A VAL* 3.8 18.1 - - + +
709A PHE* 3.8 33.9 - - + -
713A LEU* 3.8 38.8 - - + -
731A ALA* 4.1 8.7 - - + -
735A ILE* 4.3 6.1 - - + -
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Residues in contact with GLY 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 PHE 3.2 8.6 + - - -
689A ALA 3.5 0.4 + - - -
690A LEU 3.4 0.2 - - - -
691A LEU* 1.3 79.2 - - - +
693A ASP* 1.3 62.6 + - - +
695A THR* 3.1 18.7 + - - -
696A LYS* 3.3 18.7 + - - +
730A TRP* 3.5 26.4 - - - -
731A ALA* 4.4 11.4 - - - +
734A GLU* 4.4 3.5 - - - +
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Residues in contact with ASP 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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649A SER* 3.6 19.2 - - - +
652A ALA* 3.7 26.8 - - + +
653A GLU* 4.3 11.2 - - - +
689A ALA 3.1 18.3 + - - +
690A LEU* 4.0 4.5 - - - +
692A GLY* 1.3 75.7 - - - +
694A LEU* 1.3 57.2 + - - +
696A LYS* 3.8 10.2 + - - +
697A ALA* 3.3 25.1 + - - +
730A TRP* 3.2 13.5 - - - -
14C LYS* 3.1 37.6 + - - -
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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
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652A ALA* 3.7 21.5 - - + -
659A ILE* 4.2 10.5 - - + -
663A VAL* 3.7 34.8 - - + -
668A ILE* 4.1 12.3 - - + -
669A LEU* 5.1 1.6 - - + -
672A MET* 3.7 29.4 - - + -
690A LEU* 3.0 34.9 + - + +
691A LEU* 3.9 4.7 - - + +
693A ASP* 1.3 74.6 - - - +
695A THR* 1.3 60.3 + - - +
696A LYS 3.3 0.7 - - - -
697A ALA* 3.8 2.5 - - + -
698A CYS* 3.0 38.7 + - - +
702A VAL* 3.6 12.9 - - + +
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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* 2.6 29.0 + - - +
692A GLY* 3.1 13.3 + - - -
694A LEU* 1.3 78.3 - - - +
696A LYS* 1.3 61.6 + - - +
699A PHE* 3.4 45.8 + - + +
702A VAL* 4.5 5.4 - - - +
734A GLU* 3.3 37.0 - - + +
735A ILE* 3.7 18.4 - - - +
738A GLN* 3.6 7.6 + - + -
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Residues in contact with LYS 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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692A GLY 3.3 14.7 + - - +
693A ASP* 3.8 8.0 + - - +
695A THR* 1.3 79.2 - - + +
697A ALA* 1.3 62.9 + - - +
699A PHE 5.3 0.2 + - - -
730A TRP* 4.4 11.7 - - + -
734A GLU* 3.2 37.7 + - + +
738A GLN* 4.1 14.1 + - - +
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Residues in contact with ALA 697 (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 ALA 4.2 4.9 - - - +
656A GLY* 3.2 37.2 - - - +
657A GLY* 3.9 13.7 - - - +
659A ILE* 4.3 11.4 - - + -
660A GLU* 5.5 0.5 - - - +
693A ASP 3.3 17.2 + - - +
694A LEU* 4.1 6.5 - - + +
695A THR 3.4 0.2 - - - -
696A LYS* 1.3 82.8 - - - +
698A CYS* 1.3 61.6 + - - +
699A PHE 4.1 0.2 - - - -
700A GLN* 4.9 1.2 + - - +
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Residues in contact with CYS 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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659A ILE* 4.4 0.9 - - - -
660A GLU* 4.1 15.5 - - + -
663A VAL* 3.6 40.2 - - - -
694A LEU* 3.0 27.6 + - - +
697A ALA* 1.3 82.6 - - - +
699A PHE* 1.3 63.7 + - - +
700A GLN* 3.2 27.7 + - - +
701A HIS* 3.6 11.7 + - + +
702A VAL* 3.2 10.6 - - - +
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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) + - + + + + + -
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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