Contacts of the helix formed by residues 638 - 647 (chain T) in PDB entry 1BGX
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 ILE 638 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613T GLN* 3.3 34.8 + - - +
616T LEU* 3.9 21.3 - - + -
628T LEU* 3.8 28.5 - - + -
631T VAL* 4.0 26.7 - - + -
632T PHE* 4.2 24.2 - - + -
636T ARG 3.7 3.0 + - - -
637T ASP* 1.3 71.1 - - - +
639T HIS* 1.3 68.6 + - + +
640T THR 3.2 0.2 - - - -
641T GLU* 4.1 0.4 - - + -
642T THR* 2.8 44.3 + - - +
666T ASN* 4.3 11.7 - - - +
700T PHE* 5.2 1.6 - - + -
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Residues in contact with HIS 639 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613T GLN* 3.3 29.4 + - + -
616T LEU* 4.3 7.7 - - + +
637T ASP* 3.1 11.2 + - - +
638T ILE* 1.3 80.0 - - + +
640T THR* 1.3 60.1 + - - +
642T THR 4.4 0.9 - - - -
643T ALA* 4.2 2.6 + - - +
659T ARG* 3.6 42.4 + - + +
662T ALA* 3.7 18.8 - - - +
663T LYS* 3.8 39.8 + - + +
666T ASN* 3.7 34.3 - - + +
667T PHE* 5.9 0.4 + - - +
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Residues in contact with THR 640 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637T ASP* 3.2 27.1 + - - +
638T ILE 3.2 0.4 - - - -
639T HIS* 1.3 76.5 - - - +
641T GLU* 1.3 62.7 - - - +
642T THR 3.2 1.9 + - - -
643T ALA* 3.4 5.5 + - - +
644T SER* 2.9 24.4 + - - -
651T ARG* 3.5 31.6 - - + +
654T VAL* 4.2 16.7 - - + +
659T ARG* 3.4 18.8 + - - +
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Residues in contact with GLU 641 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631T VAL* 3.9 30.9 - - + +
634T GLU* 5.4 1.6 - - - +
636T ARG* 4.0 15.1 - - + -
637T ASP 3.3 19.0 + - - +
638T ILE* 4.3 1.6 - - + +
640T THR* 1.3 76.1 - - - +
642T THR* 1.3 64.2 + - - +
644T SER* 3.6 14.3 + - - -
645T TRP* 3.5 45.5 + - + -
651T ARG* 2.9 58.0 + - - +
700T PHE* 5.6 0.7 - - + -
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Residues in contact with THR 642 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638T ILE* 2.8 26.9 + - - +
639T HIS 4.6 0.2 - - - -
640T THR 3.2 0.2 - - - -
641T GLU* 1.3 77.4 - - - +
643T ALA* 1.3 61.3 + - - +
644T SER 3.1 1.7 + - - -
645T TRP* 3.4 4.7 + - - +
646T MET* 3.3 44.0 + - + +
662T ALA* 4.1 10.1 - - + +
665T ILE* 6.0 0.4 - - + -
666T ASN* 3.4 27.0 + - - +
696T TYR* 4.0 21.5 - - + -
699T SER* 5.4 1.0 + - - -
700T PHE* 4.2 21.7 - - + -
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Residues in contact with ALA 643 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639T HIS 4.2 4.5 - - - +
640T THR 3.4 9.2 + - - +
642T THR* 1.3 78.1 - - - +
644T SER* 1.3 60.3 + - - +
645T TRP 3.5 0.2 - - - -
646T MET* 4.0 8.5 - - - -
647T PHE* 3.4 29.6 + - + +
649T VAL* 4.0 6.3 - - - +
654T VAL* 4.2 12.6 - - + -
658T MET* 3.6 35.3 - - + +
662T ALA* 4.0 11.1 - - + +
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Residues in contact with SER 644 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640T THR 2.9 16.1 + - - -
641T GLU* 3.6 17.0 - - - -
642T THR 3.1 0.8 - - - -
643T ALA* 1.3 78.7 - - - +
645T TRP* 1.3 67.1 + - - +
648T GLY* 3.2 20.6 + - - -
649T VAL* 3.2 30.9 + - - +
651T ARG* 3.5 27.1 - - - +
654T VAL* 3.7 4.2 - - - +
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Residues in contact with TRP 645 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627T ASN* 3.6 36.1 - - + -
630T ARG* 3.9 35.9 - - + +
631T VAL* 4.0 14.8 - - + -
641T GLU* 3.5 41.6 + - + +
642T THR* 3.4 4.4 + - - +
644T SER* 1.3 82.8 - - - +
646T MET* 1.3 62.3 + - - +
648T GLY* 4.4 4.0 + - - -
651T ARG* 5.4 2.9 - - - +
695T ARG 4.8 0.9 - - - +
699T SER* 4.0 25.7 - - - -
700T PHE* 3.9 24.9 - + - -
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Residues in contact with MET 646 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642T THR* 3.3 39.2 + - + +
643T ALA* 4.1 4.7 - - - +
644T SER 3.3 0.4 - - - -
645T TRP* 1.3 81.8 - - - +
647T PHE* 1.3 83.6 + - + +
661T ALA* 5.5 1.6 - - + +
662T ALA* 4.9 5.4 - - - -
665T ILE* 3.9 19.3 - - + -
692T PHE* 3.4 39.7 - - + +
695T ARG* 3.4 54.0 + - + +
696T TYR* 4.5 6.3 - - - +
699T SER* 4.8 2.5 - - - +
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Residues in contact with PHE 647 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643T ALA* 3.4 24.4 + - + +
646T MET* 1.3 95.6 - - + +
648T GLY* 1.3 60.1 + - - +
649T VAL* 4.2 11.2 - - + +
658T MET* 3.6 47.1 - - + -
661T ALA* 5.2 4.0 - - + -
662T ALA* 6.4 0.2 - - + -
692T PHE* 4.0 34.5 - + - -
695T ARG* 3.4 24.1 + - - +
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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