Contacts of the helix formed by residues 683 - 694 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631B GLU* 5.2 11.0 - - - +
634B PRO* 5.3 11.0 - - + +
681B GLN 4.0 0.8 + - - +
682B ASN* 1.3 77.6 - - - +
684B PHE* 1.3 57.6 + - - +
686B LEU* 4.0 1.6 - - - +
687B SER* 2.9 35.0 + - - -
734B ALA* 3.7 7.6 - - + +
735B LYS* 3.5 42.0 - - + +
736B PRO* 4.5 0.5 - - - +
737B ILE* 4.4 16.0 + - + +
546C SER 5.7 2.6 + - - -
550C GLU* 5.0 17.8 + - - +
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Residues in contact with PHE 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B THR* 4.9 5.6 - - + -
620B LEU* 4.0 22.9 - - + -
633B LEU* 3.3 42.6 - - + -
634B PRO* 3.8 25.5 - - + +
636B LEU* 4.2 6.1 - - + -
637B LEU* 3.8 36.1 - - + -
640B PHE* 4.2 21.8 - + - -
682B ASN* 3.8 12.3 + - - +
683B LYS* 1.3 75.7 - - - +
685B GLY* 1.3 64.3 + - - +
687B SER* 3.6 1.5 - - - -
688B LEU* 2.8 50.4 + - + +
737B ILE* 4.2 8.7 - - - +
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Residues in contact with GLY 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B LEU* 4.0 23.8 - - - -
659B LEU* 4.6 4.0 - - - +
679B VAL* 3.2 17.1 - - - +
682B ASN* 3.0 19.5 + - - -
683B LYS 3.4 0.2 - - - -
684B PHE* 1.3 77.5 - - - +
686B LEU* 1.3 60.7 + - - +
688B LEU* 3.4 3.6 + - - +
689B LEU* 3.1 22.2 + - - +
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Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B VAL 2.9 9.8 + - - +
680B LEU* 4.0 26.5 - - + +
682B ASN 2.8 22.8 + - - +
683B LYS 4.0 1.1 - - - +
685B GLY* 1.3 69.4 - - - -
687B SER* 1.3 65.7 + - - +
689B LEU* 3.3 8.4 + - + +
690B LEU* 3.0 48.4 + - + +
725B LEU* 4.7 4.5 - - + -
733B LEU* 4.5 13.2 - - + -
734B ALA* 3.3 36.6 - - + +
736B PRO* 3.5 21.3 - - + -
763B LEU* 4.9 7.4 - - + -
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Residues in contact with SER 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 4.4 12.1 - - - -
683B LYS 2.9 20.3 + - - -
684B PHE* 3.6 4.5 - - - -
686B LEU* 1.3 76.1 - - - +
688B LEU* 1.3 62.2 + - - +
690B LEU* 3.2 15.8 + - - +
691B ILE* 2.8 27.7 + - - +
736B PRO* 3.5 2.3 - - - +
737B ILE* 2.7 47.0 + - - +
738B SER* 3.8 7.1 + - - -
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Residues in contact with LEU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B LEU* 4.2 22.9 - - + -
616B THR* 5.7 1.3 - - + -
617B ALA* 5.0 5.6 - - + +
620B LEU* 4.5 3.4 - - + -
637B LEU* 4.0 16.3 - - + +
640B PHE* 4.3 18.4 - - + -
644B LEU* 3.9 23.3 - - + -
659B LEU* 4.1 28.9 - - + -
684B PHE* 2.8 40.5 + - + +
685B GLY 3.6 3.6 - - - +
687B SER* 1.3 72.2 - - - +
689B LEU* 1.3 63.6 + - - +
691B ILE* 3.1 15.6 + - - +
692B LEU* 3.2 16.8 + - + +
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Residues in contact with LEU 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B LEU* 3.6 23.8 - - + -
659B LEU* 3.6 18.5 - - + +
660B MET* 4.0 24.7 - - + -
676B LEU* 5.2 2.2 - - + -
679B VAL* 4.9 7.4 - - + -
680B LEU* 3.6 31.6 - - + -
685B GLY 3.1 10.6 + - - +
686B LEU* 3.5 13.9 - - + +
688B LEU* 1.3 79.3 - - - +
690B LEU* 1.3 58.9 + - + +
692B LEU* 3.2 3.5 + - - +
693B LEU* 2.9 46.0 + - + +
721B ALA* 5.8 2.0 - - + -
725B LEU* 5.2 5.8 - - + -
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B LEU* 3.0 36.1 + - + +
687B SER* 3.4 8.1 - - - +
688B LEU 3.1 0.4 - - - -
689B LEU* 1.3 78.6 - - + +
691B ILE* 1.3 57.5 + - + +
693B LEU* 3.4 17.0 + - + +
694B SER* 2.8 29.6 + - - -
725B LEU* 5.2 3.6 - - + -
736B PRO* 3.8 17.5 - - + -
738B SER 4.1 2.7 - - - +
739B ILE* 3.5 32.5 - - + -
740B PRO* 3.6 11.2 - - + +
743B LEU* 3.7 24.2 - - + +
747B PHE* 5.1 2.5 - - + -
763B LEU* 4.4 15.9 - - + -
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Residues in contact with ILE 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B LEU* 4.8 5.2 - - + -
641B SER* 3.6 22.7 - - - +
644B LEU* 3.3 35.7 - - + -
645B TYR* 4.0 28.9 - - + +
687B SER* 2.8 29.6 - - - +
688B LEU* 3.1 8.2 + - - +
690B LEU* 1.3 76.0 - - + +
692B LEU* 1.3 63.9 + - - +
694B SER* 3.0 21.1 - - - -
695B ARG* 3.3 8.7 + - - +
738B SER* 4.2 19.5 - - - +
740B PRO* 4.0 13.9 - - + -
556C ASP* 4.4 3.1 - - - +
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Residues in contact with LEU 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B LEU* 6.1 2.0 - - + -
617B ALA* 6.2 1.1 - - + -
644B LEU* 3.4 34.1 - - + -
652B ILE* 3.7 25.4 - - + +
655B LEU* 4.0 19.5 - - + +
656B LEU* 3.3 33.2 - - + +
659B LEU* 3.7 30.3 - - + -
688B LEU* 3.2 14.8 + - + +
689B LEU 3.4 4.0 - - - +
691B ILE* 1.3 76.4 - - - +
693B LEU* 1.3 67.2 + - - +
695B ARG* 2.9 24.4 + - - +
714B TRP* 3.6 6.8 - - - -
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Residues in contact with LEU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B LEU* 3.8 20.4 - - + -
660B MET* 5.2 1.1 - - - -
689B LEU* 2.9 41.5 + - + +
690B LEU* 3.7 10.5 - - + +
692B LEU* 1.3 72.5 - - - +
694B SER* 1.3 53.1 + - - +
696B GLY* 2.6 26.3 + - - -
714B TRP* 3.9 4.6 - - + -
717B VAL 4.7 3.4 - - - +
718B MET* 3.8 23.1 - - - -
721B ALA* 4.0 26.0 - - + -
725B LEU* 4.5 8.1 - - + -
743B LEU* 4.2 3.6 - - + -
746B LEU* 3.0 24.4 - - + +
747B PHE* 4.3 20.4 - - + -
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Residues in contact with SER 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B TYR* 4.3 4.9 - - - -
690B LEU 2.8 15.1 + - - -
691B ILE* 3.0 15.9 + - - -
693B LEU* 1.3 75.1 - - - +
695B ARG* 1.3 51.2 + - - +
696B GLY 2.9 5.9 + - - -
697B GLU* 3.4 6.6 + - - +
740B PRO* 3.5 24.1 - - - +
742B ASN* 3.0 28.7 + - - +
743B LEU* 4.1 8.6 - - - +
746B LEU* 4.4 2.5 - - - +
559C LYS* 2.5 34.0 + - - +
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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