Contacts of the helix formed by residues 703 - 707 (chain B) in PDB entry 6A5T
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 THR 703 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701B ALA* 4.5 0.5 - - - +
702B MET* 1.3 96.7 + - + +
704B PRO* 1.3 62.4 - - - +
705B GLU* 2.5 38.8 + - - +
706B ASP* 2.7 22.4 + - - +
707B LEU 4.3 0.5 + - - -
727B LYS* 4.0 16.6 + - - +
741B CYS* 3.8 5.8 - - - -
743B ILE 5.7 0.2 - - - -
744B HIS* 5.6 5.6 - - + -
745B PRO* 4.2 17.7 - - + -
1047B PHE 5.4 6.7 - - - +
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Residues in contact with PRO 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.9 14.6 - - + +
17B CYS* 4.4 18.4 - - - -
631B PHE* 4.9 2.2 - - + -
645B LEU* 3.4 28.2 - - + +
703B THR* 1.3 85.3 - - - +
705B GLU* 1.3 61.6 + - + +
706B ASP 3.3 1.1 + - - -
707B LEU* 3.7 20.1 + - + +
741B CYS* 3.5 21.5 - - - -
742B GLU 4.2 11.4 - - - +
743B ILE 4.5 7.6 - - - +
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Residues in contact with GLU 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 6.5 0.9 - - - -
12B ILE 5.9 3.4 - - - +
14B THR* 5.2 5.7 + - - -
703B THR* 2.5 22.7 + - - +
704B PRO* 1.3 77.9 - - + +
706B ASP* 1.3 62.6 + - - +
707B LEU 3.4 1.0 + - - -
708B GLN* 4.3 9.4 + - - +
710B ARG* 4.6 7.4 - - - +
727B LYS* 5.5 2.8 + - - +
1049B ASP* 4.5 16.8 - - - +
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Residues in contact with ASP 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701B ALA* 4.3 14.6 - - + -
702B MET* 4.6 11.1 + - - +
703B THR* 2.7 12.9 + - - +
705B GLU* 1.3 82.9 - - - +
707B LEU* 1.3 67.0 + - - +
708B GLN 3.4 8.4 - - - +
710B ARG* 3.9 27.2 + - - +
727B LYS* 4.2 29.8 + - - +
728B PRO* 4.9 6.1 - - - +
730B MET* 5.9 4.8 - - + +
738B PHE* 4.4 13.6 - - + -
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Residues in contact with LEU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B VAL* 4.2 20.9 - - + -
643B GLY* 3.3 32.8 - - - +
644B GLU* 4.3 1.3 - - - -
645B LEU* 3.6 39.5 - - + +
701B ALA* 4.6 5.8 - - + -
703B THR 4.3 0.2 + - - -
704B PRO* 3.7 22.0 - - + +
705B GLU 3.4 1.6 - - - -
706B ASP* 1.3 80.7 - - - +
708B GLN* 1.3 71.6 + - + +
709B THR* 3.5 1.7 + - - -
738B PHE* 4.6 24.3 - - + -
741B CYS* 4.6 7.2 - - + -
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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