Contacts of the helix formed by residues 614 - 621 (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 ILE 614 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611T TYR* 3.9 46.0 + - + +
612T SER 3.5 0.8 - - - -
613T GLN* 1.3 73.1 - - - +
615T GLU* 1.3 66.8 + - + +
616T LEU 3.1 2.5 - - - -
617T ARG* 3.1 10.0 + - + +
618T VAL* 3.1 42.9 + - + +
757T ALA* 3.8 32.8 - - + +
760T LEU* 4.0 19.5 - - + -
785T ASP* 3.8 24.0 - - + +
817T LEU* 4.1 15.5 - - + -
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Residues in contact with GLU 615 (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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573T ARG* 3.6 8.0 + - - +
613T GLN 3.4 0.2 - - - -
614T ILE* 1.3 88.5 - - + +
616T LEU* 1.3 61.0 + - + +
618T VAL* 4.3 2.0 + - - +
619T LEU* 3.8 12.6 + - - +
667T PHE* 5.0 7.3 - - - -
670T LEU* 3.5 30.7 - - + +
753T VAL* 3.4 34.6 - - + +
754T GLN* 3.2 36.0 + - - +
757T ALA* 4.6 9.6 - - + -
785T ASP* 4.7 5.7 - - - +
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Residues in contact with LEU 616 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613T GLN* 3.7 22.9 + - + +
614T ILE 3.1 0.2 - - - -
615T GLU* 1.3 79.0 - - + +
617T ARG* 1.3 62.0 + - - +
618T VAL 3.5 0.7 - - - -
619T LEU* 3.6 30.1 - - + +
620T ALA* 3.8 4.7 + - - +
628T LEU* 4.5 7.3 - - + +
632T PHE* 3.6 26.8 - - + -
638T ILE* 3.9 29.6 - - + -
639T HIS* 4.3 14.1 - - + +
666T ASN* 3.3 43.3 - - + +
669T VAL* 4.7 1.1 - - + -
670T LEU* 4.8 4.7 - - + -
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Residues in contact with ARG 617 (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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612T SER* 2.9 24.9 + - - -
613T GLN* 3.0 25.0 + - - +
614T ILE* 3.1 9.6 + - + +
616T LEU* 1.3 76.3 - - - +
618T VAL* 1.3 65.3 + - + +
619T LEU 3.2 1.8 - - - -
620T ALA* 3.2 11.3 + - - +
621T HIS* 3.3 9.0 + - - +
632T PHE* 3.6 46.0 + - + +
813T LEU* 6.0 3.6 - - + -
815T VAL* 3.5 28.4 - - + +
816T PRO 3.0 27.7 + - - -
817T LEU* 3.7 28.0 - - + +
818T GLU* 3.7 21.3 - - - +
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Residues in contact with VAL 618 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614T ILE* 3.1 30.4 + - + +
615T GLU 4.6 3.1 - - - +
616T LEU 3.5 0.2 - - - -
617T ARG* 1.3 74.8 - - + +
619T LEU* 1.3 64.0 + - - +
621T HIS* 3.3 9.7 + - + +
622T LEU* 3.3 34.6 + - + +
752T PRO 3.6 23.1 - - - +
753T VAL* 4.3 10.8 - - + +
756T THR* 4.0 16.6 - - + -
757T ALA* 4.5 16.2 - - + +
760T LEU* 4.6 11.2 - - + -
813T LEU* 5.9 5.2 - - + -
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Residues in contact with LEU 619 (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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615T GLU 3.8 12.9 + - - +
616T LEU* 3.6 21.1 - - + +
618T VAL* 1.3 79.6 - - - +
620T ALA* 1.3 49.3 + - - +
622T LEU* 4.7 1.1 - - - +
623T SER* 2.8 31.5 + - - -
628T LEU* 4.1 18.3 - - + +
669T VAL* 3.9 45.1 - - + +
670T LEU* 5.6 1.3 - - + +
696T TYR* 4.1 11.9 - - - +
703T VAL* 5.0 9.5 - - + +
706T TRP* 3.8 35.0 - - + -
753T VAL* 4.3 16.7 - - + +
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Residues in contact with ALA 620 (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 3.8 5.1 + - - +
617T ARG 3.2 10.0 + - - +
618T VAL 3.1 0.4 - - - -
619T LEU* 1.3 80.0 - - - +
621T HIS* 1.3 58.1 + - - +
622T LEU 3.5 0.2 - - - -
623T SER* 3.3 5.3 + - - -
624T GLY* 3.0 27.2 + - - -
625T ASP 3.9 0.8 + - - +
628T LEU* 3.9 27.1 - - + -
629T ILE* 3.7 30.2 - - + +
632T PHE* 4.5 2.0 - - + -
815T VAL* 4.0 9.6 - - + -
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Residues in contact with HIS 621 (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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617T ARG 3.3 8.8 + - - +
618T VAL* 3.3 13.1 + - + +
620T ALA* 1.3 81.0 - - - +
622T LEU* 1.3 65.3 + - + +
623T SER 3.5 0.3 + - - -
624T GLY* 4.2 5.2 + - - -
723T LEU* 3.8 33.0 - - + +
811T TYR* 5.2 2.4 - - - -
812T PRO 4.8 3.5 + - - -
813T LEU* 3.7 30.5 - - + +
814T ALA* 3.4 39.9 + - + +
815T VAL* 4.7 8.5 - - + +
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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