Contacts of the helix formed by residues 686 - 699 (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 TYR 686 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200T GLY* 3.5 24.4 + - - -
201T GLU* 2.9 46.2 + - + +
675T ALA* 4.3 11.9 - - + +
676T HIS* 3.9 29.8 - + + -
679T SER* 3.6 11.8 + - - +
685T PRO* 1.3 73.6 - - - +
687T GLU* 1.3 77.7 + - + +
689T ALA* 3.5 12.8 + - - +
690T GLN* 3.7 16.7 - - - +
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Residues in contact with GLU 687 (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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199T ILE* 3.8 23.7 - - - +
200T GLY* 4.0 7.8 + - - -
685T PRO* 4.5 2.5 - - + +
686T TYR* 1.3 94.3 - - + +
688T GLU* 1.3 59.0 + - - +
689T ALA 3.4 0.4 + - - -
690T GLN* 3.3 33.1 + - - +
691T ALA* 4.4 4.5 + - - +
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Residues in contact with GLU 688 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684T ILE* 3.8 31.7 - - + +
685T PRO* 3.5 23.9 + - + +
686T TYR 3.3 0.6 - - - -
687T GLU* 1.3 76.8 - - - +
689T ALA* 1.3 64.2 + - - +
690T GLN 3.3 0.7 - - - -
691T ALA* 3.4 12.6 + - + +
692T PHE* 3.3 36.0 - - + -
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Residues in contact with ALA 689 (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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675T ALA* 3.8 23.3 - - + +
678T LEU* 4.1 13.7 - - + +
679T SER* 4.7 7.2 - - - +
684T ILE* 3.8 11.2 - - + +
685T PRO 3.0 17.8 + - - +
686T TYR 3.7 7.0 - - - +
687T GLU 3.4 0.4 - - - -
688T GLU* 1.3 79.3 - - - +
690T GLN* 1.3 61.0 + - - +
692T PHE* 3.4 17.0 + - - +
693T ILE* 3.5 18.9 - - - +
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Residues in contact with GLN 690 (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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197T LYS 5.5 0.7 - - - +
198T GLY* 3.5 11.7 - - - -
199T ILE* 2.9 29.6 - - - +
200T GLY* 3.1 15.4 + - - -
201T GLU* 3.0 27.9 + - - +
203T THR* 4.6 4.9 - - + +
675T ALA* 4.0 14.8 - - + -
686T TYR* 3.7 15.3 - - - +
687T GLU* 3.3 26.8 - - - +
688T GLU 3.3 0.6 - - - -
689T ALA* 1.3 75.5 - - - +
691T ALA* 1.3 61.8 + - - +
693T ILE* 3.4 12.1 + - + +
694T GLU* 3.3 26.3 + - - +
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Residues in contact with ALA 691 (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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687T GLU 4.4 4.0 + - - +
688T GLU* 3.4 15.3 + - + +
689T ALA 3.3 0.4 - - - -
690T GLN* 1.3 77.6 - - - +
692T PHE* 1.3 64.7 + - + +
694T GLU* 3.3 8.4 + - - +
695T ARG* 3.0 45.9 + - + +
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Residues in contact with PHE 692 (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* 3.4 30.7 - - + +
647T PHE* 4.0 28.0 - + - -
661T ALA* 4.0 29.4 - - + -
665T ILE* 3.7 23.4 - - + +
678T LEU* 4.8 6.3 - - + -
682T LEU* 5.3 5.2 - - + -
684T ILE* 4.1 22.4 - - + -
688T GLU* 3.3 41.7 - - + -
689T ALA* 3.4 12.1 + - - +
690T GLN 3.3 0.6 - - - -
691T ALA* 1.3 84.6 - - + +
693T ILE* 1.3 57.7 + - - +
695T ARG* 4.1 11.2 - - - -
696T TYR* 3.7 8.7 + - - +
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Residues in contact with ILE 693 (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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665T ILE* 5.4 9.2 - - + -
674T SER* 4.7 4.3 - - - -
675T ALA* 4.0 31.0 - - + +
678T LEU* 4.2 15.0 - - + -
689T ALA 3.5 17.7 - - - +
690T GLN* 3.4 9.8 + - - +
691T ALA 3.2 0.6 - - - -
692T PHE* 1.3 75.5 - - - +
694T GLU* 1.3 66.4 + - + +
695T ARG 3.5 0.2 - - - -
696T TYR* 3.5 8.5 - - + +
697T PHE* 3.3 46.6 + - + -
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Residues in contact with GLU 694 (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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196T VAL* 3.5 16.9 + - - +
197T LYS* 3.3 34.5 + - - +
203T THR* 5.3 4.7 - - + +
231T LYS* 5.4 0.5 + - - -
690T GLN 3.3 13.1 + - - +
691T ALA* 3.3 11.9 + - - +
693T ILE* 1.3 76.2 - - + +
695T ARG* 1.3 57.2 + - + +
696T TYR 3.1 5.4 - - - -
697T PHE* 3.1 12.9 + - - +
698T GLN* 3.0 37.6 + - + +
704T ARG* 3.0 28.0 + - - -
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Residues in contact with ARG 695 (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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645T TRP 4.8 1.0 - - - +
646T MET* 3.4 54.0 + - + +
647T PHE* 3.4 38.3 + - - +
691T ALA* 3.0 31.3 + - + +
692T PHE* 5.0 9.0 - - - +
693T ILE 3.5 0.2 - - - -
694T GLU* 1.3 75.9 - - + +
696T TYR* 1.3 57.4 + - - +
698T GLN* 3.9 9.8 - - + +
699T SER* 3.0 24.9 + - - -
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Residues in contact with TYR 696 (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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619T LEU* 4.1 10.2 - - - +
628T LEU* 5.1 5.9 - - - +
642T THR* 4.0 19.3 - - + -
646T MET* 4.5 6.3 - - - +
665T ILE* 3.9 26.9 - - + -
666T ASN* 3.5 26.8 + - - -
669T VAL* 3.8 36.3 - - + +
692T PHE 3.7 13.8 + - - +
693T ILE* 3.5 13.0 - - + +
694T GLU 3.1 0.4 - - - -
695T ARG* 1.3 79.6 - - - +
697T PHE* 1.3 76.6 + + - +
699T SER* 3.0 15.9 + - - -
700T PHE* 3.1 45.9 + + - +
703T VAL* 4.3 14.6 - - + +
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Residues in contact with PHE 697 (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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205T ARG* 5.2 7.9 - - - -
669T VAL* 5.9 0.7 - - + -
693T ILE* 3.3 34.5 + - + -
694T GLU* 3.1 10.8 + - - +
696T TYR* 1.3 100.9 - + - +
698T GLN* 1.3 64.4 + - - +
699T SER 3.4 0.7 - - - -
700T PHE 3.1 20.1 - - - +
701T PRO* 3.6 9.0 - - - +
703T VAL* 4.5 2.7 - - + -
704T ARG* 3.4 66.3 + - + +
707T ILE* 3.9 30.5 - - + -
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Residues in contact with GLN 698 (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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694T GLU* 3.0 24.5 + - + +
695T ARG* 4.1 9.4 - - + +
696T TYR 3.4 0.2 - - - -
697T PHE* 1.3 78.1 + - - +
699T SER* 1.3 61.6 + - - +
700T PHE 4.8 0.2 - - - -
701T PRO* 4.3 9.9 - - - +
704T ARG* 4.3 21.4 - - - +
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Residues in contact with SER 699 (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* 3.5 29.5 - - - +
642T THR 5.4 0.3 + - - -
645T TRP* 4.0 35.1 - - - -
646T MET* 4.8 3.3 - - - +
695T ARG 3.0 13.5 + - - -
696T TYR* 3.0 15.9 + - - -
698T GLN* 1.3 81.0 - - - +
700T PHE* 1.3 73.7 + - - +
701T PRO* 3.5 2.6 - - - +
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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