Contacts of the helix formed by residues 637 - 645 (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 LEU 637 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543B TYR* 5.8 9.9 - - + -
558B ARG* 5.7 0.2 - - - +
634C PRO 3.1 15.5 + - - +
636C LEU* 1.3 79.2 - - - +
638C SER* 1.3 54.6 + - - +
640C PHE* 3.3 4.4 + - - +
641C SER* 2.6 65.1 + - - +
684C PHE* 3.5 28.5 - - + +
687C SER* 3.3 33.2 - - - -
688C LEU* 5.1 6.7 - - + +
691C ILE* 5.0 8.7 - - + -
737C ILE* 3.5 30.1 - - + -
738C SER* 4.8 11.0 - - - +
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Residues in contact with SER 638 (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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540B GLU* 3.3 36.2 + - - +
543B TYR* 4.6 9.2 - - - -
558B ARG* 4.1 8.8 + - - +
634C PRO 4.3 1.6 + - - -
635C CYS 4.4 4.0 + - - -
637C LEU* 1.3 79.2 - - - +
639C PRO* 1.3 70.7 - - - +
641C SER* 3.1 22.4 + - - -
642C LEU* 3.4 13.0 + - - +
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Residues in contact with PRO 639 (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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598C ALA 4.0 14.6 - - - +
601C LEU* 3.8 35.2 - - + -
602C PRO* 4.4 8.1 - - + -
635C CYS 3.8 7.4 - - - +
636C LEU* 2.9 26.2 - - - +
638C SER* 1.3 96.1 - - - +
640C PHE* 1.3 59.2 + - - +
641C SER 3.3 0.2 + - - -
642C LEU* 3.4 11.9 + - + +
643C LEU* 3.2 20.1 + - - +
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Residues in contact with PHE 640 (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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601C LEU* 3.6 21.1 - - + -
609C ALA 4.3 2.7 - - - -
612C ILE* 3.6 23.6 - - + -
613C LEU* 3.5 51.5 - - + +
616C THR* 4.1 13.7 - - + -
636C LEU* 3.4 37.7 - - + +
637C LEU* 3.3 4.2 + - - +
638C SER 3.3 0.6 - - - -
639C PRO* 1.3 79.1 - - - +
641C SER* 1.3 64.0 + - - +
643C LEU* 3.5 12.1 - - + +
644C LEU* 3.0 30.2 + - - +
684C PHE* 4.1 18.4 - + - -
688C LEU* 4.1 15.3 - - + -
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Residues in contact with SER 641 (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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543B TYR* 5.6 0.2 - - - -
556B ASP* 5.6 0.2 - - - -
558B ARG* 2.8 31.7 + - - -
637C LEU* 2.6 43.3 + - - +
638C SER* 3.1 5.7 + - - -
640C PHE* 1.3 76.1 - - - +
642C LEU* 1.3 65.5 + - - +
644C LEU* 3.5 2.7 + - - +
645C TYR* 3.1 35.2 + - - -
688C LEU* 6.1 0.4 - - - -
691C ILE* 4.7 16.0 - - - +
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Residues in contact with LEU 642 (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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540B GLU* 5.9 2.5 - - - +
558B ARG* 3.2 35.7 - - + +
562B ILE* 6.1 1.3 - - + -
602B PRO* 4.3 15.9 - - + +
603B PHE* 4.2 33.0 - - + +
638C SER* 3.4 11.9 + - - +
639C PRO* 3.9 9.6 - - + +
640C PHE 3.4 0.2 - - - -
641C SER* 1.3 74.0 - - - +
643C LEU* 1.3 68.6 + - - +
645C TYR* 3.1 30.5 + - + +
646C HIS* 3.4 18.5 - - + +
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Residues in contact with LEU 643 (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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606C THR* 4.0 28.0 - - + +
609C ALA* 3.5 49.4 - - + +
610C ALA* 3.6 7.6 - - + +
613C LEU* 3.8 20.9 - - + -
639C PRO 3.2 12.6 + - - +
640C PHE* 3.5 17.5 - - + +
641C SER 3.2 0.2 - - - -
642C LEU* 1.3 79.2 - - - +
644C LEU* 1.3 62.3 + - - +
646C HIS* 3.3 10.5 + - - +
647C LEU* 3.2 29.6 + - + +
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Residues in contact with LEU 644 (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* 3.6 12.8 - - + -
640C PHE 3.0 20.5 + - - +
641C SER* 3.8 4.7 - - - +
642C LEU 3.3 0.2 - - - -
643C LEU* 1.3 76.8 - - - +
645C TYR* 1.3 64.4 + - - +
646C HIS 3.0 1.4 + - - -
647C LEU* 3.3 15.5 + - + +
652C ILE* 3.8 7.6 - - + -
655C LEU* 3.5 20.4 - - + -
688C LEU* 4.1 17.0 - - + -
691C ILE* 3.5 36.1 - - + -
692C LEU* 3.5 38.6 - - + +
695C ARG* 3.4 21.8 + - + +
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Residues in contact with TYR 645 (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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556B ASP* 2.8 35.4 + - - -
558B ARG* 3.6 31.3 + - + +
559B LYS* 3.6 52.2 - - + +
562B ILE* 5.1 6.5 - - + -
603B PHE 5.9 0.2 - - - -
641C SER* 3.1 26.2 - - - -
642C LEU* 3.1 23.6 + - + +
644C LEU* 1.3 78.0 - - - +
646C HIS* 1.3 78.8 + - + +
647C LEU 3.6 0.2 - - - -
691C ILE* 4.3 16.3 - - + +
695C ARG* 3.0 31.4 + - + +
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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