Contacts of the helix formed by residues 773 - 777 (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 MET 773 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769B TYR* 2.9 32.2 + - + +
770B GLN* 2.5 15.6 + - - +
772B ALA* 1.3 77.5 - - + +
774B GLY* 1.3 54.8 + - - +
775B LYS 2.9 1.8 - - - -
776B GLN* 2.6 39.4 + - - +
979B LYS* 4.9 3.6 - - - +
981B ALA* 3.9 20.0 - - + -
982B SER 5.4 1.3 - - - +
985B GLY* 3.5 34.1 - - - +
987B LYS* 3.7 31.2 - - + -
1093B GLN* 4.8 2.2 - - - +
1095B LEU* 3.6 25.4 - - + +
9P G 6.4 2.0 - - - -
10P G 5.5 1.1 - - - +
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Residues in contact with GLY 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B THR* 4.5 1.0 - - - +
482B SER* 4.0 15.4 - - - -
752B ALA* 6.0 2.0 - - - -
755B ILE* 6.3 2.2 - - - -
770B GLN* 2.9 17.4 + - - +
771B SER* 5.5 1.1 - - - -
773B MET* 1.3 75.4 - - - +
775B LYS* 1.3 56.3 + - - +
776B GLN 3.0 4.9 + - - -
777B ALA* 3.3 17.2 + - - +
1093B GLN* 3.4 26.6 - - - +
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Residues in contact with LYS 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ASN* 5.8 1.2 + - - -
479B TYR* 5.1 2.8 - - - +
480B THR* 4.3 5.4 - - - +
482B SER* 3.8 10.1 - - - +
483B SER* 4.0 28.9 - - - +
486B SER* 3.1 28.7 - - - +
490B ARG* 2.9 32.3 - - - +
519B GLU* 3.8 17.5 + - - +
520B THR 6.1 2.2 - - - -
521B PRO* 6.0 2.6 - - - +
531B ASN* 5.4 0.6 - - - +
752B ALA* 3.8 20.2 - - + -
770B GLN 4.7 0.4 + - - -
771B SER* 3.3 22.7 + - - +
772B ALA* 4.7 6.3 - - - +
773B MET 2.9 2.7 + - - +
774B GLY* 1.3 74.8 - - - +
776B GLN* 1.3 66.8 + - + +
777B ALA 3.7 0.9 - - - -
8P G 5.5 0.4 + - - -
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Residues in contact with GLN 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B TYR* 3.2 28.7 - - + -
480B THR* 5.0 0.7 - - - -
772B ALA 4.1 17.2 + - - +
773B MET* 2.6 20.5 + - - +
775B LYS* 1.3 80.3 - - + +
777B ALA* 1.3 62.8 + - - +
778B MET 3.4 1.7 + - - -
1095B LEU* 3.0 23.2 - - + +
1096B ARG* 3.8 17.8 + - - +
1097B HIS* 2.9 30.5 + - - -
8P G 3.5 35.8 + - - -
9P G 4.1 6.1 + - - +
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Residues in contact with ALA 777 (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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479B TYR 3.4 4.2 - - - +
480B THR* 3.2 26.2 + - - +
774B GLY* 3.3 15.7 + - - +
775B LYS 3.7 0.8 - - - -
776B GLN* 1.3 77.8 - - - +
778B MET* 1.3 63.3 + - - +
779B GLY 3.4 0.3 + - - -
814B PHE* 6.2 0.9 - - + -
819B ALA* 3.8 27.8 - - + +
1093B GLN* 4.2 17.9 - - - +
1094B ARG 3.3 11.7 - - - +
1095B LEU* 3.9 1.5 - - - +
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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