Contacts of the helix formed by residues 658 - 668 (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 MET 658 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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643T ALA* 3.6 22.3 - - + +
647T PHE* 3.6 50.6 - - + -
649T VAL* 4.2 26.2 - - + -
653T ALA 4.2 14.1 - - - +
654T VAL* 4.3 5.6 - - + -
655T ASP* 3.3 26.6 + - - +
657T LEU* 1.3 80.5 - - + +
659T ARG* 1.3 63.3 + - - +
660T ARG 3.2 0.7 - - - -
661T ALA* 3.4 7.4 + - - +
662T ALA* 3.2 17.3 + - - +
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Residues in contact with ARG 659 (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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637T ASP* 2.9 32.0 + - - -
639T HIS* 3.6 40.5 + - - +
640T THR* 3.4 20.1 + - - +
643T ALA* 4.7 0.2 - - - -
654T VAL* 4.2 11.1 - - + +
655T ASP 3.3 15.1 + - - +
656T PRO* 4.5 8.5 - - + -
657T LEU 3.4 0.2 - - - -
658T MET* 1.3 77.7 - - - +
660T ARG* 1.3 58.3 + - - +
662T ALA* 3.9 2.0 - - - +
663T LYS* 3.2 42.1 + - - +
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Residues in contact with ARG 660 (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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656T PRO 3.4 19.9 + - - +
657T LEU* 3.5 20.5 + - - +
658T MET 3.2 0.2 - - - -
659T ARG* 1.3 77.8 - - - +
661T ALA* 1.3 64.5 + - - +
662T ALA 3.2 0.2 - - - -
663T LYS* 3.3 16.9 + - - +
664T THR* 3.3 19.4 + - + +
681T GLU 4.5 12.5 + - - -
682T LEU* 4.2 23.0 - - + +
683T ALA* 5.8 5.7 - - - +
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Residues in contact with ALA 661 (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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646T MET* 5.9 1.8 - - + -
647T PHE* 5.2 6.1 - - + -
657T LEU* 3.4 12.7 + - + +
658T MET* 3.7 11.0 - - - +
659T ARG 3.4 0.2 - - - -
660T ARG* 1.3 80.7 - - - +
662T ALA* 1.3 57.2 + - - +
663T LYS 3.4 0.2 - - - -
664T THR* 3.0 18.6 + - - -
665T ILE* 3.3 19.8 - - - +
682T LEU* 4.2 13.4 - - + +
684T ILE* 5.2 4.7 - - + -
692T PHE* 4.0 28.3 - - + -
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Residues in contact with ALA 662 (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* 3.7 22.2 - - - +
642T THR* 4.1 13.5 - - + +
643T ALA* 4.0 19.3 - - + +
646T MET* 4.9 3.8 - - - -
647T PHE* 6.4 0.2 - - + -
658T MET 3.2 16.2 + - - +
659T ARG 4.0 0.7 - - - +
660T ARG 3.2 0.4 - - - -
661T ALA* 1.3 76.2 - - - +
663T LYS* 1.3 60.2 + - - +
664T THR 3.3 0.4 - - - -
665T ILE* 3.4 9.7 + - - +
666T ASN* 2.8 35.1 + - - +
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Residues in contact with LYS 663 (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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587T ARG* 5.9 5.7 - - - +
639T HIS* 3.8 41.8 + - + +
659T ARG* 3.2 31.9 + - - +
660T ARG* 3.3 10.0 + - + +
662T ALA* 1.3 78.4 - - - +
664T THR* 1.3 61.5 + - + +
666T ASN* 4.0 1.3 - - - +
667T PHE* 3.2 27.2 + - + +
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Residues in contact with THR 664 (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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660T ARG* 3.5 14.1 - - + +
661T ALA 3.0 19.2 + - - -
663T LYS* 1.3 79.1 - - + +
665T ILE* 1.3 58.7 + - - +
667T PHE* 4.2 3.5 - - - +
668T GLY* 3.2 20.3 + - - -
673T MET* 3.9 15.4 - - - +
678T LEU* 3.8 14.0 - - - +
681T GLU* 5.1 11.2 - - + -
682T LEU* 3.5 33.6 - - + +
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Residues in contact with ILE 665 (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* 6.0 0.2 - - + -
646T MET* 3.9 19.1 - - + -
661T ALA 3.3 20.6 - - - +
662T ALA* 3.4 7.5 + - - +
663T LYS 3.3 0.2 - - - -
664T THR* 1.3 77.6 - - - +
666T ASN* 1.3 61.4 + - - +
667T PHE 3.2 1.8 - - - -
668T GLY* 3.7 1.5 - - - -
669T VAL* 2.9 31.4 + - + +
673T MET* 5.6 0.9 - - - -
678T LEU* 4.3 18.8 - - + -
692T PHE* 3.7 35.7 - - + +
693T ILE* 5.5 8.1 - - + -
696T TYR* 3.9 35.2 - - + -
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Residues in contact with ASN 666 (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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616T LEU* 3.3 29.3 - - + +
628T LEU* 5.6 2.1 - - - +
638T ILE* 4.2 8.7 + - - +
639T HIS* 3.7 32.4 - - + +
642T THR* 3.4 28.1 + - - +
662T ALA 2.8 28.4 + - - +
663T LYS 4.0 1.6 - - - +
664T THR 3.5 0.2 - - - -
665T ILE* 1.3 77.2 - - - +
667T PHE* 1.3 55.4 + - - +
669T VAL* 3.4 7.5 - - - +
670T LEU* 3.3 18.9 - - - +
696T TYR* 3.5 23.6 + - - -
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Residues in contact with PHE 667 (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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587T ARG* 6.0 4.9 - - - -
615T GLU* 5.0 6.5 - - - -
663T LYS* 3.2 17.7 + - + +
664T THR* 4.5 3.6 - - - +
666T ASN* 1.3 76.5 - - - +
668T GLY* 1.3 64.1 + - - +
669T VAL 3.4 0.7 - - - -
670T LEU* 3.6 32.8 - - + +
671T TYR* 3.4 33.0 - + - -
673T MET* 6.3 0.2 - - + -
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Residues in contact with GLY 668 (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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664T THR 3.2 17.1 + - - -
665T ILE* 3.2 5.2 + - - -
667T PHE* 1.3 75.5 - - - +
669T VAL* 1.3 55.7 - - - +
670T LEU 3.1 6.1 + - - -
671T TYR* 3.3 19.3 + - - -
672T GLY 2.9 33.3 + - - -
673T MET* 3.6 15.0 + - - +
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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