Contacts of the helix formed by residues 683 - 698 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B SER* 2.9 30.6 + - - +
547B LEU* 3.9 15.6 + - - +
631C GLU* 5.9 3.4 - - - +
634C PRO* 5.2 9.4 - - + -
681C GLN 4.3 0.4 + - - -
682C ASN* 1.3 78.9 - - - +
684C PHE* 1.3 61.4 + - - +
686C LEU* 4.1 1.6 - - - +
687C SER* 2.8 27.8 + - - -
734C ALA* 3.6 6.8 - - + +
735C LYS* 3.2 54.0 - - - +
736C PRO* 4.5 0.5 - - - +
737C ILE* 4.3 15.1 + - + +
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Residues in contact with PHE 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C THR* 5.0 5.4 - - + -
620C LEU* 4.2 20.0 - - + -
633C LEU* 3.7 41.1 - - + -
634C PRO* 3.8 22.6 - - + +
636C LEU* 4.2 3.8 - - + -
637C LEU* 3.5 49.6 - - + -
640C PHE* 4.1 23.1 - + - -
682C ASN* 3.3 10.8 - - - +
683C LYS* 1.3 76.3 - - - +
685C GLY* 1.3 70.7 + - - +
687C SER* 3.3 5.1 + - - -
688C LEU* 2.9 41.7 + - + +
737C ILE* 4.9 0.7 - - - -
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Residues in contact with GLY 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C LEU* 4.4 11.2 - - - +
624C ILE* 4.7 0.9 - - - -
659C LEU* 5.5 0.7 - - - +
679C VAL* 3.5 31.1 - - - +
682C ASN* 3.3 14.5 + - - -
684C PHE* 1.3 85.7 - - - +
686C LEU* 1.3 62.1 + - - +
688C LEU* 3.3 4.2 + - - +
689C LEU* 3.0 18.4 + - - +
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Residues in contact with LEU 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679C VAL* 3.3 6.8 + - - -
680C LEU* 4.1 30.7 - - + +
682C ASN 2.8 22.4 + - - +
683C LYS 4.1 2.2 - - - +
685C GLY* 1.3 71.2 - - - -
687C SER* 1.3 62.3 + - - +
689C LEU* 3.2 7.5 + - + +
690C LEU* 3.0 47.5 + - + +
725C LEU* 4.7 4.7 - - + -
733C LEU* 4.3 15.5 - - + -
734C ALA* 3.1 39.0 - - + +
736C PRO* 3.6 19.5 - - + -
763C LEU* 4.7 7.4 - - + -
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Residues in contact with SER 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C LEU* 3.3 27.4 - - - -
683C LYS 2.8 20.4 + - - -
684C PHE 3.6 0.9 - - - -
686C LEU* 1.3 78.1 - - - +
688C LEU* 1.3 64.4 + - - +
690C LEU* 3.0 10.3 + - - +
691C ILE* 3.0 28.6 + - - +
736C PRO* 3.6 2.2 - - - +
737C ILE* 2.9 29.8 + - - +
738C SER* 4.1 13.0 + - - -
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Residues in contact with LEU 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C LEU* 4.2 19.3 - - + -
616C THR* 5.8 2.9 - - + -
617C ALA* 5.7 5.4 - - + -
620C LEU* 4.5 15.9 - - + -
637C LEU* 4.8 7.0 - - + +
640C PHE* 4.1 27.4 - - + -
641C SER* 6.1 0.2 - - - -
644C LEU* 4.1 17.2 - - + +
659C LEU* 5.4 7.4 - - + -
684C PHE* 2.9 45.2 + - + +
685C GLY* 3.3 5.6 + - - +
687C SER* 1.3 75.1 - - - +
689C LEU* 1.3 63.6 + - - +
691C ILE* 3.2 9.5 + - + +
692C LEU* 3.0 30.8 + - + +
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Residues in contact with LEU 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C LEU* 3.6 28.5 - - + -
659C LEU* 3.9 20.5 - - + +
660C MET* 5.7 0.4 - - + -
676C LEU* 3.6 25.1 - - + -
679C VAL* 4.7 3.6 - - + -
680C LEU* 3.5 32.3 - - + -
685C GLY 3.0 13.0 + - - +
686C LEU* 3.5 12.1 - - + +
688C LEU* 1.3 76.4 - - - +
690C LEU* 1.3 58.9 + - + +
692C LEU* 3.5 2.4 + - - +
693C LEU* 3.1 46.5 + - + +
721C ALA* 5.0 3.6 - - + -
725C LEU* 4.7 12.3 - - + -
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686C LEU* 3.0 33.3 + - + +
687C SER* 3.0 7.8 + - - +
689C LEU* 1.3 78.6 - - + +
691C ILE* 1.3 66.1 + - - +
693C LEU* 4.0 15.1 - - + +
694C SER* 3.1 24.6 + - - -
725C LEU* 5.0 6.3 - - + -
736C PRO* 4.1 26.5 - - + -
738C SER 4.4 7.2 - - - +
739C ILE* 4.4 16.8 - - + -
740C PRO* 3.6 16.4 - - + +
743C LEU* 3.7 19.6 - - + +
747C PHE* 5.2 0.7 - - + -
763C LEU* 4.7 20.9 - - + -
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Residues in contact with ILE 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ASP* 3.2 25.4 - - - +
559B LYS* 5.2 0.3 + - - -
637C LEU* 5.0 6.5 - - + -
641C SER* 4.6 18.4 - - - +
644C LEU* 3.5 29.4 - - + -
645C TYR* 4.3 20.0 - - + -
687C SER 3.0 19.2 + - - +
688C LEU* 3.6 9.0 - - + +
690C LEU* 1.3 75.3 - - - +
692C LEU* 1.3 58.1 + - - +
694C SER* 3.4 3.3 + - - -
695C ARG* 3.0 27.2 + - - +
738C SER* 4.0 14.4 - - - +
740C PRO* 4.1 17.0 - - + -
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Residues in contact with LEU 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644C LEU* 3.5 33.0 - - + -
652C ILE* 3.8 24.3 - - + +
655C LEU* 3.7 30.7 - - + -
656C LEU* 4.0 18.8 - - + +
659C LEU* 3.8 30.1 - - + -
688C LEU* 3.0 22.0 + - + +
689C LEU 3.5 8.3 - - - +
690C LEU 3.2 0.2 - - - -
691C ILE* 1.3 74.4 - - - +
693C LEU* 1.3 67.0 + - - +
695C ARG* 3.0 15.4 + - - +
696C GLY* 3.1 9.9 + - - -
714C TRP* 4.1 2.1 - - - -
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Residues in contact with LEU 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C LEU* 3.6 30.1 - - + -
689C LEU* 3.1 24.3 + - + +
690C LEU* 4.0 9.9 - - + +
691C ILE 3.5 0.2 - - - -
692C LEU* 1.3 78.1 - - - +
694C SER* 1.3 63.1 + - - +
696C GLY* 3.3 3.3 + - - -
697C GLU 3.2 15.6 + - - -
714C TRP* 4.2 5.1 - - - -
718C MET* 3.7 16.4 - - + -
721C ALA* 4.2 17.7 - - + -
725C LEU* 4.2 12.6 - - + -
743C LEU* 4.1 4.0 - - + -
746C LEU* 3.3 25.0 - - + +
747C PHE* 3.8 32.3 - - + -
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Residues in contact with SER 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559B LYS* 3.4 17.3 + - - -
690C LEU 3.1 19.1 + - - -
691C ILE* 3.5 6.1 - - - -
693C LEU* 1.3 75.8 - - - +
695C ARG* 1.3 65.2 + - - +
697C GLU* 3.1 19.8 + - - +
698C ASP* 3.4 5.7 - - - +
740C PRO* 3.4 24.7 - - - +
742C ASN* 2.8 24.7 + - - -
743C LEU* 4.1 6.9 - - - +
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Residues in contact with ARG 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559B LYS* 3.5 18.6 - - - +
644C LEU* 3.4 21.7 + - + +
645C TYR* 3.0 27.4 + - + +
646C HIS* 4.3 2.4 - - - +
647C LEU 2.9 30.1 + - - +
648C PRO* 5.1 0.6 - - - +
652C ILE* 3.4 29.4 - - + -
691C ILE* 3.0 14.0 + - + +
692C LEU* 3.0 9.4 + - - +
694C SER* 1.3 76.0 - - - +
696C GLY* 1.3 60.8 + - - +
697C GLU 3.1 1.3 + - - -
698C ASP* 3.3 26.9 + - - +
699C LEU* 3.5 38.5 - - + +
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Residues in contact with GLY 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C ILE* 4.4 4.9 - - - +
692C LEU 3.1 9.7 + - - -
693C LEU 3.3 0.4 + - - -
694C SER 3.2 0.2 - - - -
695C ARG* 1.3 73.9 - - - +
697C GLU* 1.3 60.3 + - - +
698C ASP 3.5 0.2 - - - -
699C LEU* 4.1 9.2 - - - -
700C GLN* 3.1 31.6 + - - +
714C TRP* 3.3 36.5 + - - -
746C LEU* 4.9 0.5 - - - +
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Residues in contact with GLU 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693C LEU 3.2 9.7 + - - +
694C SER* 3.1 14.3 + - - +
695C ARG 3.1 0.6 - - - -
696C GLY* 1.3 76.8 - - - +
698C ASP* 1.3 66.0 + - - +
700C GLN* 3.5 14.8 + - - +
742C ASN* 3.3 40.8 + - - +
745C SER* 3.7 11.8 + - - -
746C LEU* 3.7 25.1 - - + +
749C ARG* 2.8 40.3 + - - -
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Residues in contact with ASP 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS* 2.5 44.6 + - - +
694C SER 3.4 1.9 - - - +
695C ARG* 3.3 19.0 + - - +
697C GLU* 1.3 79.6 - - - +
699C LEU* 1.3 64.2 + - + +
700C GLN 3.2 5.1 + - - -
742C ASN* 3.1 25.8 + - - -
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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