Contacts of the helix formed by residues 685 - 702 (chain A) in PDB entry 5XA0
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 ASN 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A PHE 3.6 10.5 - - - +
678A GLU* 3.1 8.9 - - - +
680A VAL* 2.9 42.8 - - + +
683A GLY 2.7 9.0 + - - +
684A GLU* 1.3 76.9 - - - +
686A ALA* 1.3 70.4 + - - +
687A LEU 3.1 2.8 + - - +
688A GLU* 3.3 3.6 + - - +
689A ALA* 3.1 23.0 + - - +
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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
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678A GLU* 2.6 19.4 + - - +
679A GLY* 4.1 6.7 - - - +
680A VAL 2.6 24.8 + - - +
681A SER* 4.5 6.5 - - - +
683A GLY 5.2 0.2 - - - -
685A ASN* 1.3 71.4 - - - +
687A LEU* 1.3 57.5 + - - +
689A ALA* 3.6 1.0 + - - +
690A GLY* 3.0 27.9 + - - -
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Residues in contact with LEU 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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680A VAL 4.6 0.2 + - - -
681A SER 5.9 1.3 + - - +
683A GLY* 5.6 5.3 - - - -
684A GLU 5.4 5.4 - - - +
685A ASN 3.1 3.1 - - - +
686A ALA* 1.3 79.8 - - - +
688A GLU* 1.3 64.4 + - - +
690A GLY* 3.2 9.8 + - - -
691A GLU* 3.7 9.7 + - - +
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Residues in contact with GLU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLU* 4.7 9.8 - - - +
685A ASN 3.3 14.7 + - - +
687A LEU* 1.3 79.7 - - - +
689A ALA* 1.3 62.9 + - - +
691A GLU* 3.8 12.2 + - - +
692A ASP* 4.5 2.8 + - - +
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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
----------------------------------------------------------
678A GLU* 3.5 31.9 - - + -
685A ASN 3.1 9.3 + - - +
686A ALA 4.3 1.6 - - - +
688A GLU* 1.3 76.2 - - - +
690A GLY* 1.3 67.7 + - - +
691A GLU 3.2 0.7 + - - -
692A ASP* 3.2 10.1 + - - +
693A GLU* 3.1 19.1 + - + +
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Residues in contact with GLY 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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686A ALA 3.0 19.3 + - - -
687A LEU* 3.2 3.9 + - - -
689A ALA* 1.3 76.0 - - - +
691A GLU* 1.3 65.2 + - - +
693A GLU* 2.7 18.8 + - - -
694A GLU* 2.9 16.9 + - - +
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Residues in contact with GLU 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A LEU 3.7 7.6 + - - +
688A GLU* 4.2 9.2 - - - +
689A ALA 3.2 0.8 + - - -
690A GLY* 1.3 75.4 - - - +
692A ASP* 1.3 65.8 + - - +
693A GLU 3.1 0.2 + - - -
694A GLU* 4.3 2.3 - - - +
695A GLU* 3.2 24.0 + - - +
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Residues in contact with ASP 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A GLU 4.5 3.2 + - - +
689A ALA* 3.2 10.4 + - - +
691A GLU* 1.3 78.6 - - - +
693A GLU* 1.3 57.7 + - - +
695A GLU* 3.7 3.9 - - - +
696A VAL* 2.9 35.1 + - + +
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Residues in contact with GLU 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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689A ALA* 3.1 12.1 + - + +
690A GLY* 2.7 20.1 + - - +
692A ASP* 1.3 70.9 - - - +
694A GLU* 1.3 69.1 + - - +
695A GLU 3.1 0.7 + - - -
696A VAL* 4.0 2.4 - - - +
697A TRP* 3.1 23.6 + - - +
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Residues in contact with GLU 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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690A GLY 2.9 15.9 + - - +
691A GLU* 4.4 1.8 - - - +
693A GLU* 1.3 75.6 - - - +
695A GLU* 1.4 61.3 + - - +
697A TRP* 3.6 5.0 - - - +
698A LEU* 3.2 24.4 + - - +
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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
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632A ASP* 6.0 7.0 - - + -
691A GLU 3.2 19.5 + - - +
692A ASP* 3.7 4.3 - - - +
693A GLU 3.1 1.0 - - - -
694A GLU* 1.4 76.3 - - - +
696A VAL* 1.3 65.8 + - - +
698A LEU* 4.6 1.5 - - - +
699A PHE* 3.1 31.6 + - + +
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Residues in contact with VAL 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 ASP* 2.9 22.0 + - + +
693A GLU* 4.3 2.0 - - - +
695A GLU* 1.3 74.0 - - - +
697A TRP* 1.4 53.6 + - - +
699A PHE* 4.8 1.6 - - - -
700A TRP* 2.7 41.4 + - + +
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Residues in contact with TRP 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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693A GLU 3.1 17.7 + - - +
694A GLU* 3.6 6.3 - - - +
696A VAL* 1.4 74.7 - - - +
698A LEU* 1.3 70.7 + - - +
700A TRP* 4.0 0.8 - - - +
701A ARG* 3.0 21.3 + - - +
724A LYS* 5.5 6.5 - - + +
726A ASP* 3.0 36.2 - - + +
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Residues in contact with LEU 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 GLU 3.2 12.7 + - - +
695A GLU* 4.6 1.3 - - - +
697A TRP* 1.3 81.0 - - - +
699A PHE* 1.3 65.4 + - - +
701A ARG* 3.1 14.4 + - - +
702A ASP* 3.2 8.1 + - - -
726A ASP* 5.7 2.0 - - - +
729A ILE* 6.2 0.7 - - - -
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Residues in contact with PHE 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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635A SER* 3.9 29.8 - - - -
695A GLU* 3.1 19.9 + - + +
696A VAL* 4.6 1.8 - - - +
698A LEU* 1.3 76.9 - - - +
700A TRP* 1.3 54.5 + - - +
702A ASP* 2.5 39.1 + - - +
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Residues in contact with TRP 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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696A VAL* 2.7 27.3 + - + +
697A TRP* 4.0 1.1 - - - +
699A PHE* 1.3 76.7 - - - +
701A ARG* 1.3 66.3 + - - +
702A ASP* 3.2 4.4 + - - +
703A SER 4.6 0.3 + - - -
710A LYS* 5.5 4.0 - - - +
730A LEU* 5.8 0.7 - - - -
733A TYR* 5.5 0.3 - - - +
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Residues in contact with ARG 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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697A TRP 3.0 13.1 + - - +
698A LEU* 3.1 12.5 + - - +
700A TRP* 1.3 78.5 - - - +
702A ASP* 1.3 68.3 + - - +
703A SER 3.0 2.6 + - - -
704A ASN* 4.6 0.3 - - - -
710A LYS* 5.0 0.5 - - - +
726A ASP* 4.2 3.6 - - - +
729A ILE* 3.3 35.1 - - + +
730A LEU* 3.6 20.8 - - + +
733A TYR* 3.6 19.8 - - - +
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Residues in contact with ASP 702 (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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698A LEU 3.2 5.1 + - - -
699A PHE* 2.5 24.1 + - - +
700A TRP* 3.8 3.6 - - - +
701A ARG* 1.3 75.5 - - - +
703A SER* 1.3 57.0 + - - +
704A ASN* 2.7 24.3 + - - +
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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
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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