Contacts of the helix formed by residues 701 - 710 (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 PRO 701 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625T ASP* 3.7 5.2 - - - +
626T GLU* 4.3 6.3 - - - +
627T ASN* 4.0 12.3 - - - +
697T PHE 3.6 9.0 - - - +
698T GLN* 4.3 11.9 - - - +
699T SER 3.5 10.1 - - - +
700T PHE* 1.4 78.6 - - - +
702T LYS* 1.3 66.7 + - + +
703T VAL 3.2 5.6 + - - -
704T ARG* 3.3 15.8 + - + +
705T ALA* 3.5 9.9 + - - +
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Residues in contact with LYS 702 (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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623T SER* 3.9 19.7 + - - +
624T GLY* 3.0 26.9 + - - +
625T ASP* 3.0 21.7 + - + +
626T GLU* 3.7 27.7 + - - +
701T PRO* 1.3 75.5 - - + +
703T VAL* 1.3 59.5 + - - +
704T ARG 3.4 0.2 - - - -
705T ALA* 3.5 13.5 + - + +
706T TRP* 3.0 26.7 + - - +
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Residues in contact with VAL 703 (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* 5.0 11.4 - - + +
623T SER* 4.5 7.9 - - - +
625T ASP* 3.6 16.8 + - + +
628T LEU* 3.9 25.1 - - + -
669T VAL* 4.7 9.0 - - + -
696T TYR* 4.3 22.7 - - + +
697T PHE* 4.5 7.9 - - + -
700T PHE* 3.9 22.4 - - + +
701T PRO 3.2 0.8 - - - -
702T LYS* 1.3 74.9 - - - +
704T ARG* 1.3 65.6 + - - +
706T TRP* 3.3 10.2 + - + +
707T ILE* 3.2 29.9 + - + +
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Residues in contact with ARG 704 (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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194T PRO* 5.2 6.3 - - - +
195T GLY* 4.6 14.1 - - - +
196T VAL* 3.8 22.1 - - - +
205T ARG* 3.6 19.7 + - - +
694T GLU* 3.0 37.0 + - - -
697T PHE* 3.4 54.0 - - + +
698T GLN* 4.3 18.4 - - - +
700T PHE 4.1 1.4 + - - -
701T PRO 3.3 10.8 + - - +
703T VAL* 1.3 78.0 - - - +
705T ALA* 1.3 62.3 + - - +
707T ILE* 3.3 4.9 + - - +
708T GLU* 3.3 32.6 + - - +
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Residues in contact with ALA 705 (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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189T GLU* 3.0 27.8 - - - +
701T PRO 3.5 9.8 + - - +
702T LYS* 3.7 18.8 - - + +
703T VAL 3.3 0.2 - - - -
704T ARG* 1.3 80.4 - - - +
706T TRP* 1.3 55.8 + - - +
707T ILE 3.4 0.2 - - - -
708T GLU* 3.5 10.9 + - - +
709T LYS* 3.0 23.6 + - - +
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Residues in contact with TRP 706 (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* 3.8 31.0 - - + -
622T LEU* 3.3 58.4 + - + +
623T SER* 3.9 14.6 - - - -
669T VAL 5.8 2.0 - - - -
702T LYS 3.0 17.9 + - - +
703T VAL* 3.5 9.2 - - + +
704T ARG 3.2 0.4 - - - -
705T ALA* 1.3 75.0 - - - +
707T ILE* 1.3 71.1 + - + +
708T GLU 3.2 0.4 - - - -
709T LYS* 3.2 12.6 + - + +
710T THR* 2.8 49.1 + - - -
749T PHE* 4.6 13.0 - - + -
752T PRO* 4.1 16.2 - - + -
753T VAL* 3.9 24.0 - - + -
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Residues in contact with ILE 707 (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* 3.8 20.6 - - - +
669T VAL* 5.0 12.8 - - + +
672T GLY* 6.1 4.9 - - - -
697T PHE* 3.9 31.6 - - + -
703T VAL* 3.2 22.1 + - + +
704T ARG* 3.3 6.7 + - - +
706T TRP* 1.3 88.8 - - + +
708T GLU* 1.3 57.9 + - - +
710T THR* 3.9 5.7 - - - +
711T LEU* 2.9 31.2 + - + +
749T PHE* 4.0 29.2 - - + -
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Residues in contact with GLU 708 (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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186T THR* 4.4 9.9 - - - +
187T GLY* 4.4 3.6 - - - -
188T ASP* 3.1 53.6 + - - +
189T GLU* 3.9 5.0 - - - +
205T ARG* 3.4 27.1 - - - +
704T ARG* 3.3 28.2 + - - +
705T ALA* 3.6 16.8 - - - +
706T TRP 3.2 0.4 - - - -
707T ILE* 1.3 77.0 - - - +
709T LYS* 1.3 56.7 + - - +
710T THR 3.4 0.2 - - - -
711T LEU* 3.9 5.1 - - - +
712T GLU* 3.2 24.3 + - - +
715T ARG* 5.4 0.2 + - - -
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Residues in contact with LYS 709 (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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25T ARG* 5.4 7.4 - - - +
189T GLU* 3.3 27.6 + - + +
705T ALA 3.0 17.2 + - - +
706T TRP* 3.2 17.2 + - + +
708T GLU* 1.3 76.6 - - - +
710T THR* 1.3 59.6 + - - +
712T GLU* 3.0 32.3 + - - +
713T GLU* 2.9 52.5 + - - +
716T ARG* 4.7 3.0 - - - +
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Residues in contact with THR 710 (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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706T TRP* 2.8 46.3 + - - -
707T ILE* 4.1 4.0 - - - -
708T GLU 3.4 0.2 - - - -
709T LYS* 1.3 74.2 - - - +
711T LEU* 1.3 64.3 + - - +
712T GLU 3.1 1.3 - - - -
713T GLU* 3.2 20.8 - - + +
714T GLY* 3.4 5.7 + - - -
720T VAL* 4.1 19.7 - - + +
748T ALA* 4.2 4.6 - - + +
749T PHE* 4.0 37.2 - - + +
752T PRO* 4.6 8.3 - - + -
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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