Contacts of the helix formed by residues 628 - 634 (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 LEU 628 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616T LEU* 4.5 6.1 - - + +
619T LEU* 4.1 18.6 - - + -
620T ALA* 3.9 31.4 - - + +
625T ASP* 3.0 20.2 + - + +
627T ASN* 1.3 75.5 - - - +
629T ILE* 1.3 63.8 + - - +
630T ARG 3.2 1.7 + - - -
631T VAL* 3.6 9.7 + - - +
632T PHE* 3.3 26.5 - - + -
638T ILE* 3.8 25.4 - - + -
666T ASN* 5.6 1.6 - - - +
696T TYR* 5.1 6.7 - - - +
700T PHE* 3.8 27.1 - - + -
703T VAL* 3.9 23.8 - - + -
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Residues in contact with ILE 629 (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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620T ALA* 3.7 33.2 - - + +
624T GLY* 4.2 7.6 - - - -
625T ASP 3.1 27.0 + - - +
626T GLU* 4.9 4.5 - - - +
628T LEU* 1.3 75.7 - - - +
630T ARG* 1.3 62.9 + - - +
632T PHE* 3.3 4.0 + - - +
633T GLN* 3.0 33.8 + - + +
814T ALA* 3.7 35.9 - - + +
815T VAL* 3.9 15.7 - - + -
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Residues in contact with ARG 630 (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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626T GLU 3.4 20.5 + - - +
627T ASN* 3.5 24.0 - - - +
628T LEU 3.2 0.2 - - - -
629T ILE* 1.3 78.9 - - - +
631T VAL* 1.3 61.8 + - + +
633T GLN* 3.7 5.9 + - - +
634T GLU* 3.3 47.7 + - + +
645T TRP* 3.9 32.5 - - + +
651T ARG* 5.8 3.2 - - - +
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Residues in contact with VAL 631 (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 18.4 - - - +
628T LEU* 3.9 9.2 - - - +
629T ILE 3.3 0.4 - - - -
630T ARG* 1.3 76.5 - - - +
632T PHE* 1.3 63.3 + - + +
634T GLU* 3.7 2.8 + - - +
635T GLY 3.3 3.6 + - - -
636T ARG* 3.2 43.1 + - + +
637T ASP 3.8 22.7 - - - +
638T ILE* 4.0 27.6 - - + +
641T GLU* 3.9 18.6 - - + +
645T TRP* 4.0 21.1 - - + -
700T PHE* 5.2 1.1 - - + -
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Residues in contact with PHE 632 (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* 4.7 4.5 - - - -
616T LEU* 3.6 40.8 - - + -
617T ARG* 3.6 45.2 + - + +
620T ALA* 4.5 4.7 - - + -
628T LEU* 3.3 26.9 - - + -
629T ILE 3.3 4.9 + - - +
631T VAL* 1.3 77.4 - - + +
633T GLN* 1.3 63.5 + - - +
634T GLU 3.2 2.2 - - - -
635T GLY* 3.3 13.5 + - - +
636T ARG 5.2 5.2 - - - +
638T ILE* 4.2 32.8 - - + -
815T VAL* 3.9 28.3 - - + -
816T PRO* 3.3 22.6 - - + +
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Residues in contact with GLN 633 (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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629T ILE* 3.0 30.6 + - + +
630T ARG* 4.0 7.2 - - - +
631T VAL 3.5 0.2 - - - -
632T PHE* 1.3 76.2 - - - +
634T GLU* 1.3 63.5 + - + +
814T ALA 3.0 26.7 + - - -
816T PRO* 3.3 21.4 - - + +
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Residues in contact with GLU 634 (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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630T ARG* 3.3 42.2 + - + +
631T VAL* 3.7 1.0 + - - +
632T PHE 3.2 0.4 - - - -
633T GLN* 1.3 82.5 - - + +
635T GLY* 1.3 60.0 + - - +
636T ARG* 3.0 52.2 + - + +
641T GLU* 5.4 1.4 - - - +
651T ARG* 5.2 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