Contacts of the helix formed by residues 683 - 701 (chain A) in PDB entry 2XER
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 LYS 683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A GLU* 4.0 22.7 + - - +
634A PRO* 4.7 17.0 - - + +
682A ASN* 1.3 75.4 - - - +
684A PHE* 1.3 56.9 + - - +
686A LEU* 4.0 0.7 - - - +
687A SER* 2.6 38.4 + - - -
734A ALA* 3.3 8.5 - - + +
735A LYS* 3.3 41.2 - - + +
737A ILE* 4.0 13.9 - - + -
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Residues in contact with PHE 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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616A THR* 4.5 9.4 - - + -
620A LEU* 4.2 22.7 - - + -
633A LEU* 3.6 37.0 - - + -
634A PRO* 4.1 14.0 - - + +
636A LEU* 3.9 12.1 - - + -
637A LEU* 3.6 38.1 - - + -
640A PHE* 3.7 28.7 - + - -
682A ASN* 3.3 8.0 + - - +
683A LYS* 1.3 76.1 - - - +
685A GLY* 1.3 59.4 + - - +
687A SER* 4.3 3.1 - - - -
688A LEU* 2.7 63.9 + - + +
737A ILE* 4.7 1.8 - - - +
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Residues in contact with GLY 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU* 3.9 18.8 - - - -
659A LEU* 4.7 1.2 - - - +
679A VAL* 3.2 35.1 - - - +
682A ASN* 2.8 18.0 + - - -
684A PHE* 1.3 72.6 - - - +
686A LEU* 1.3 57.6 + - - +
688A LEU* 3.6 2.8 - - - +
689A LEU* 3.0 23.0 + - - +
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Residues in contact with LEU 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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679A VAL* 3.0 10.7 + - - +
680A LEU* 3.4 37.2 - - + +
682A ASN 2.8 21.2 + - - +
683A LYS 4.0 2.0 - - - +
685A GLY* 1.3 71.6 - - - +
687A SER* 1.3 62.6 + - - +
689A LEU* 3.3 5.7 + - + +
690A LEU* 3.1 43.9 + - + +
725A LEU* 4.8 4.7 - - + -
733A LEU* 4.1 11.9 - - + -
734A ALA* 3.2 33.4 - - + +
736A PRO* 3.7 21.3 - - + -
763A LEU* 4.9 7.2 - - + -
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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
----------------------------------------------------------
637A LEU* 4.0 19.1 - - - -
683A LYS 2.6 25.2 + - - -
684A PHE* 3.7 3.8 - - - -
686A LEU* 1.3 77.5 - - - +
688A LEU* 1.3 59.5 + - - +
690A LEU* 3.4 7.4 + - - +
691A ILE* 2.9 33.0 + - - +
736A PRO* 3.3 6.3 - - - +
737A ILE* 2.8 38.7 + - - +
738A SER 5.0 3.6 - - - -
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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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613A LEU* 4.2 26.7 - - + -
616A THR* 5.6 1.3 - - + -
617A ALA* 5.1 7.9 - - + -
620A LEU* 4.7 12.8 - - + -
637A LEU* 4.4 4.9 - - + +
640A PHE* 4.9 12.6 - - + -
644A LEU* 5.3 2.5 - - + -
659A LEU* 4.7 9.6 - - + -
684A PHE* 2.7 52.0 + - + +
685A GLY 3.6 4.7 - - - +
687A SER* 1.3 71.6 - - - +
689A LEU* 1.3 66.5 + - - +
691A ILE* 3.2 9.6 + - + +
692A LEU* 3.0 46.7 + - + +
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Residues in contact with LEU 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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656A LEU* 3.5 25.4 - - + -
659A LEU* 3.6 20.6 - - + +
660A MET* 3.8 21.5 - - + -
676A LEU* 4.6 11.7 - - + -
679A VAL* 4.8 2.9 - - + -
680A LEU* 3.6 30.1 - - + -
685A GLY 3.0 14.1 + - - +
686A LEU* 3.4 12.3 - - + +
688A LEU* 1.3 76.5 - - - +
690A LEU* 1.3 59.5 + - + +
692A LEU* 3.3 2.9 + - - +
693A LEU* 2.9 49.8 + - + +
721A ALA* 5.6 1.8 - - + -
725A LEU* 4.7 11.4 - - + -
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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
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686A LEU* 3.1 29.2 + - + +
687A SER* 3.7 5.8 - - - +
688A LEU 3.1 0.2 - - - -
689A LEU* 1.3 80.3 - - + +
691A ILE* 1.3 62.0 + - + +
693A LEU* 3.9 14.7 - - + +
694A SER* 2.9 30.7 + - - -
725A LEU* 5.2 4.7 - - + -
736A PRO* 4.0 33.0 - - + -
738A SER 4.8 1.6 - - - +
739A ILE* 4.0 22.0 - - + -
740A PRO* 3.8 11.2 - - + +
743A LEU* 3.8 21.4 - - + +
747A PHE* 5.3 0.7 - - + -
763A LEU* 4.7 18.4 - - + -
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Residues in contact with ILE 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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637A LEU* 3.9 19.1 - - + -
641A SER* 4.3 22.2 - - - +
644A LEU* 3.4 22.2 - - + +
645A TYR* 5.7 5.6 - - + +
687A SER 2.9 17.1 + - - +
688A LEU* 3.2 7.4 + - + +
690A LEU* 1.3 76.5 - - - +
692A LEU* 1.3 58.2 + - - +
694A SER* 3.5 4.6 - - - -
695A ARG* 3.0 28.0 + - + +
738A SER* 3.6 35.2 - - - +
740A PRO* 3.8 13.5 - - + -
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Residues in contact with LEU 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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613A LEU* 4.8 2.7 - - + -
617A ALA* 6.2 0.9 - - + -
644A LEU* 3.5 32.1 - - + -
652A ILE* 3.5 18.1 - - + +
655A LEU* 3.9 31.9 - - + +
656A LEU* 3.5 37.2 - - + +
659A LEU* 4.2 11.4 - - + -
688A LEU* 3.0 43.6 + - + +
689A LEU 3.6 0.2 - - - +
691A ILE* 1.3 73.6 - - - +
693A LEU* 1.3 66.3 + - - +
694A SER 3.0 1.1 - - - -
695A ARG* 3.2 1.2 + - - -
696A GLY* 2.9 20.3 + - - -
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Residues in contact with LEU 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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656A LEU* 3.5 29.4 - - + -
660A MET* 4.7 2.0 - - + -
689A LEU* 2.9 36.0 + - + +
690A LEU* 4.0 8.7 - - + +
692A LEU* 1.3 75.6 - - - +
694A SER* 1.3 60.2 + - - +
696A GLY* 3.5 1.6 + - - -
697A GLU* 3.1 16.3 + - - +
714A TRP* 4.3 3.1 - - - -
717A VAL 4.8 0.9 - - - +
718A MET* 3.8 23.1 - - - -
721A ALA* 4.0 22.4 - - + -
725A LEU* 4.5 4.9 - - + -
743A LEU* 4.0 4.3 - - + -
746A LEU* 3.3 24.3 - - + +
747A PHE* 3.9 26.0 - - + -
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Residues in contact with SER 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 LEU 2.9 20.0 + - - -
691A ILE* 3.5 6.7 - - - -
692A LEU 3.0 0.2 - - - -
693A LEU* 1.3 73.4 - - - +
695A ARG* 1.3 61.3 + - - +
697A GLU* 2.9 26.1 + - - +
698A ASP* 3.2 8.6 + - - -
740A PRO* 3.2 27.1 - - - +
742A ASN* 3.0 26.8 + - - -
743A LEU* 3.9 4.9 - - - +
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Residues in contact with ARG 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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644A LEU* 3.0 34.1 + - + +
645A TYR* 3.6 46.2 + - + +
647A LEU 3.7 13.9 + - - +
652A ILE* 3.7 22.7 - - + -
691A ILE* 3.0 18.0 + - + +
692A LEU 3.2 3.3 + - - +
694A SER* 1.3 75.6 + - - +
696A GLY* 1.3 61.5 + - - +
698A ASP* 3.1 39.8 + - - +
699A LEU* 3.2 38.8 + - + +
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Residues in contact with GLY 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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649A SER* 6.4 0.9 - - - -
652A ILE* 4.0 12.2 - - - +
692A LEU 2.9 12.1 + - - -
693A LEU 3.8 0.9 - - - -
695A ARG* 1.3 77.2 - - - +
697A GLU* 1.3 56.2 + - - +
699A LEU* 3.6 4.3 + - - +
700A GLN* 2.8 40.1 + - - +
714A TRP* 3.7 25.8 - - - -
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Residues in contact with GLU 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 LEU 3.1 11.8 + - - +
694A SER* 2.9 13.7 + - - +
696A GLY* 1.3 74.8 - - - +
698A ASP* 1.3 62.8 + - - +
700A GLN* 4.6 3.7 - - - +
701A SER* 2.8 38.8 + - - +
714A TRP* 4.6 0.2 - - - -
742A ASN* 3.1 29.0 - - + +
745A SER* 2.9 20.3 + - - -
746A LEU* 3.4 36.2 - - + +
749A ARG* 2.6 36.8 + - - -
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Residues in contact with ASP 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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645A TYR* 4.5 9.2 - - - -
694A SER* 3.2 9.1 + - - +
695A ARG* 3.1 42.4 + - - +
697A GLU* 1.3 78.3 - - - +
699A LEU* 1.3 62.2 + - + +
701A SER* 4.1 3.8 - - - -
702A SER* 3.1 24.4 + - - -
742A ASN* 3.0 21.2 + - - -
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Residues in contact with LEU 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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647A LEU 3.5 12.6 - - - +
648A PRO* 3.5 11.4 - - + +
649A SER* 3.4 42.4 - - - +
652A ILE* 4.4 6.3 - - + -
695A ARG* 3.2 43.2 + - - +
696A GLY* 4.2 3.6 - - - +
697A GLU 3.1 0.4 - - - -
698A ASP* 1.3 77.9 - - + +
700A GLN* 1.3 62.3 + - - +
701A SER 3.2 5.3 + - - -
702A SER* 3.7 13.8 + - - +
703A ASP* 3.3 14.0 - - - +
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Residues in contact with GLN 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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649A SER* 2.3 34.2 + - - -
696A GLY* 2.8 26.9 + - - +
697A GLU* 3.3 7.4 + - - +
699A LEU* 1.3 77.9 + - - +
701A SER* 1.3 59.4 + - - +
703A ASP* 3.0 35.0 - - - +
710A GLN* 3.6 10.7 + - - +
711A ASN* 5.1 5.7 - - - +
714A TRP* 3.4 43.3 - - + +
746A LEU* 6.1 0.7 - - + -
749A ARG* 5.3 8.0 + - - +
750A TYR* 5.8 0.4 - - - +
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Residues in contact with SER 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 GLU* 2.8 26.2 + - - +
698A ASP* 4.1 5.2 - - - -
700A GLN* 1.3 78.4 - - - +
702A SER* 1.3 56.3 + - - +
703A ASP* 2.9 13.4 + - - +
749A ARG* 3.4 29.6 + - - +
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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
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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