Contacts of the strand formed by residues 778 - 783 (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 ARG 778 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447T THR* 3.8 35.6 + - - +
559T ARG* 3.9 13.3 - - - +
601T GLU* 4.8 3.6 + - - +
604T TRP* 3.6 31.0 - - + -
772T LEU* 4.3 9.4 - - - -
773T GLU* 6.0 0.4 - - - -
777T ALA* 1.3 78.1 - - - +
779T MET* 1.3 62.1 + - - +
780T LEU* 4.3 9.2 - - + -
789T LEU* 3.6 6.2 - - - +
790T GLU* 3.1 67.6 + - + +
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Residues in contact with MET 779 (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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440T VAL* 3.7 16.4 - - + -
443T HIS 4.9 1.6 - - - +
444T MET* 3.5 30.8 + - + +
447T THR* 5.8 1.2 - - - -
765T MET* 3.6 53.4 - - + +
768T LEU* 4.0 18.6 - - + -
769T PHE* 5.2 4.6 - - + +
772T LEU* 4.1 18.1 - - + +
778T ARG* 1.3 79.1 - - - +
780T LEU* 1.3 70.7 + - - +
787T LEU* 3.7 31.0 - - + -
788T VAL 4.5 0.2 - - - +
789T LEU* 3.9 13.9 - - + -
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Residues in contact with LEU 780 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444T MET* 3.1 30.4 - - - +
447T THR* 5.4 1.3 - - + -
448T GLY* 3.4 31.0 - - - +
449T VAL* 3.9 20.8 - - + +
559T ARG* 4.3 5.6 - - - +
564T PHE* 3.6 8.8 - - - -
606T LEU* 3.8 16.4 - - + -
778T ARG* 4.3 14.4 - - - -
779T MET* 1.3 82.4 - - - +
781T LEU* 1.3 76.3 + - + +
788T VAL* 3.1 16.8 + - + +
789T LEU 4.6 2.2 - - - +
790T GLU* 3.6 36.1 - - + +
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Residues in contact with LEU 781 (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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444T MET* 4.7 2.7 - - - +
449T VAL* 3.9 32.1 - - + -
562T THR* 4.6 9.2 - - - +
564T PHE* 3.9 17.9 - - + -
581T LEU* 3.9 26.7 - - + -
598T PHE* 5.1 6.5 - - + -
780T LEU* 1.3 92.0 - - + +
782T GLN* 1.3 61.4 + - - +
783T VAL* 4.2 9.4 - - + -
786T GLU 4.5 0.2 - - - -
787T LEU* 3.4 14.0 - - - +
788T VAL* 3.3 50.8 + - + +
827T TRP* 4.8 14.6 - - + -
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Residues in contact with GLN 782 (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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444T MET* 4.8 3.6 - - + -
564T PHE* 4.0 20.0 - - + -
573T ARG* 5.2 2.8 - - - +
574T LEU* 3.5 63.4 + - + +
576T SER* 5.5 1.2 + - - -
582T GLN* 4.7 3.1 + - - +
758T ALA* 6.3 0.4 - - - +
761T MET* 3.5 31.5 - - + +
765T MET* 4.1 11.0 - - + -
781T LEU* 1.3 77.0 - - - +
783T VAL* 1.3 61.9 + - - +
784T HIS 3.9 19.0 + - - +
786T GLU 3.4 7.8 + - - +
787T LEU* 4.0 20.6 - - + -
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Residues in contact with VAL 783 (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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564T PHE* 5.9 1.3 - - + -
576T SER* 5.6 0.9 - - - +
581T LEU* 3.2 46.9 - - + +
582T GLN* 4.8 2.9 - - - +
584T ILE* 5.0 2.2 - - + -
781T LEU* 4.7 2.2 - - + -
782T GLN* 1.3 80.8 - - - +
784T HIS* 1.3 64.4 + - + +
785T ASP 2.7 18.0 + - - -
786T GLU* 2.8 48.4 + - + +
788T VAL* 5.3 1.6 - - + -
827T TRP* 4.0 22.4 - - + -
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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