Contacts of the helix formed by residues 660 - 666 (chain A) in PDB entry 4HBN
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 GLU 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A MET* 3.9 28.3 - - + -
657A TYR* 3.6 17.5 - - + -
658A PHE* 3.1 6.9 + - - -
659A GLY* 1.3 75.6 + - - +
661A ILE* 1.3 70.6 + - - +
662A CYS 3.4 0.9 - - - -
663A LEU* 3.1 8.4 + - + +
664A LEU* 3.0 36.1 + - + +
689A PHE* 5.0 2.0 - - + -
703A PHE* 4.4 22.7 - - + +
706A VAL* 4.3 0.2 - - - +
707A ALA* 3.9 6.3 + - + -
710A ARG* 2.9 32.6 + - - -
801A CMP 2.8 16.8 + - - -
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Residues in contact with ILE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A GLY 3.3 0.8 - - - -
660A GLU* 1.3 93.6 - - - +
662A CYS* 1.3 57.4 + - - +
664A LEU* 3.6 6.0 + - - +
665A THR* 2.7 50.6 + - + +
668A ARG 5.5 0.2 - - - +
670A THR* 3.5 32.3 - - + +
707A ALA* 4.0 11.7 - - + +
710A ARG* 4.5 4.3 - - + -
711A LEU* 3.7 32.3 - - + +
714A ILE* 5.7 0.2 - - + -
801A CMP 3.3 44.6 - - + +
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Residues in contact with CYS 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A GLY* 3.4 27.8 - - - +
659A GLY 4.2 0.2 + - - -
660A GLU 3.4 0.4 - - - -
661A ILE* 1.3 76.2 - - - +
663A LEU* 1.3 61.6 + - + +
665A THR* 4.1 5.6 - - - -
666A ARG* 2.8 28.5 + - - +
667A GLY 3.3 24.0 - - - +
668A ARG 3.3 26.9 - - - -
669A ARG* 3.4 30.1 - - - +
686A VAL* 5.0 1.0 - - - +
801A CMP 3.5 5.9 + - - -
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A GLY 4.4 3.1 - - - +
630A LYS 4.0 4.0 - - - -
631A LYS 3.5 37.2 - - - +
632A MET* 3.5 34.8 - - + -
659A GLY 3.7 4.9 - - - +
660A GLU 3.1 10.0 + - - +
662A CYS* 1.3 80.6 - - + +
664A LEU* 1.3 65.3 + - - +
666A ARG* 4.3 6.4 + - - +
684A LEU 4.0 7.9 - - - +
686A VAL* 3.8 32.5 - - + +
689A PHE* 3.6 39.9 - - + -
690A ASN* 4.3 8.3 + - - +
700A ARG* 5.4 0.5 + - - -
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A GLU* 3.0 19.6 + - + +
661A ILE* 4.0 3.8 - - - +
663A LEU* 1.3 80.5 - - - +
665A THR* 1.3 65.8 + - + +
666A ARG* 4.7 2.8 - - - +
689A PHE* 4.0 17.3 - - + -
700A ARG* 3.4 30.4 + - + +
703A PHE* 3.8 19.3 - - + +
704A GLU* 4.2 21.1 - - + +
707A ALA* 3.6 31.0 - - + -
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Residues in contact with THR 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A ILE* 2.7 41.6 + - + +
662A CYS* 4.1 1.9 - - - -
664A LEU* 1.3 84.4 - - + +
666A ARG* 1.3 70.9 + - - +
667A GLY* 3.2 18.0 + - - -
668A ARG 4.9 0.9 + - - -
707A ALA* 6.5 0.2 - - + -
711A LEU* 5.8 2.0 - - + -
718A ASN* 4.3 26.5 - - + -
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Residues in contact with ARG 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A ILE* 5.5 4.8 - - - +
629A GLY 5.4 1.8 - - - -
662A CYS 2.8 26.6 + - - +
663A LEU 4.3 9.2 + - - +
664A LEU 4.7 2.7 - - - +
665A THR* 1.3 77.0 + - - +
667A GLY* 1.3 58.4 + - - +
686A VAL* 4.5 21.9 - - + +
690A ASN* 4.1 18.8 - - - +
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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