Contacts of the helix formed by residues 170 - 176 (chain B) in PDB entry 7NPA
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 TYR 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLN 5.1 0.7 - - - -
64B ILE* 4.0 35.9 - - + -
67B ARG* 3.6 43.1 + - + +
68B GLU* 2.6 38.9 + - + +
166B ARG* 3.0 21.8 + - - +
167B LYS 3.3 4.0 - - - +
169B GLN* 1.3 92.5 - - + +
171B PHE* 1.3 65.4 + - - +
172B GLN 3.3 2.2 - - - -
173B TYR* 2.9 35.2 + + + +
174B LEU* 3.2 16.3 + - + +
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Residues in contact with PHE 171 (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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49B MET* 3.6 36.6 - - + -
52B GLU* 3.5 32.5 - - + -
53B VAL* 3.7 20.0 - - + -
167B LYS 2.9 11.0 + - - +
168B LEU* 3.3 18.1 + - - +
169B GLN 3.3 1.8 + - - -
170B TYR* 1.3 76.3 - - - +
172B GLN* 1.3 60.9 + - + +
174B LEU* 3.1 2.4 + - + +
175B ALA* 2.8 57.8 + - + +
177B HIS* 3.5 26.0 - + - -
178B ASP 3.7 15.5 - - - -
179B GLY* 3.9 11.2 - - - -
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Residues in contact with GLN 172 (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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170B TYR 3.3 0.8 - - - -
171B PHE* 1.3 81.9 - - + +
173B TYR* 1.3 59.7 + - + +
176B LYS* 3.0 26.9 + - - -
177B HIS 3.6 20.4 - - - +
178B ASP* 2.7 29.5 + - - +
588B LYS 3.7 11.9 + - - +
590B PRO* 3.5 41.6 - - + +
591B GLN* 4.1 0.3 - - - +
592B ARG* 3.5 11.1 + - - -
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Residues in contact with TYR 173 (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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63B GLN* 5.7 3.5 - - + +
67B ARG* 3.3 49.1 + - - +
170B TYR* 2.9 33.2 + + + +
172B GLN* 1.3 81.4 - - + +
174B LEU* 1.3 66.5 + - + +
176B LYS* 4.3 0.2 - - - +
420B PRO* 4.1 12.5 - - + +
457B ALA 3.8 8.7 - - - -
458B PRO* 3.9 17.5 - - + +
584B HIS* 4.3 14.9 - - - -
590B PRO* 3.7 32.5 - - + +
591B GLN* 3.0 31.2 + - + +
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Residues in contact with LEU 174 (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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52B GLU 5.4 3.1 - - - +
60B GLY* 4.0 27.1 - - - +
63B GLN* 4.2 19.7 - - + -
64B ILE* 4.1 14.6 - - + -
167B LYS* 3.8 57.7 - - + +
170B TYR* 3.2 13.0 + - + +
171B PHE* 3.1 4.2 + - + +
173B TYR* 1.3 84.7 - - + +
175B ALA* 1.3 62.6 + - - +
176B LYS* 3.8 12.5 + - - +
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Residues in contact with ALA 175 (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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52B GLU* 3.9 17.0 - - + +
171B PHE* 2.8 58.2 + - + +
174B LEU* 1.3 72.4 - - - +
176B LYS* 1.3 66.7 + - - +
177B HIS* 3.1 26.1 - - - +
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Residues in contact with LYS 176 (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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503A GLU 4.6 2.8 - - - +
506A LYS* 4.1 30.5 - - - +
529A LYS* 6.1 1.3 - - - +
172B GLN 3.0 19.5 + - - -
173B TYR 4.3 0.2 - - - +
174B LEU 3.9 9.6 - - - +
175B ALA* 1.3 82.8 - - - +
177B HIS* 1.3 60.3 + - - +
590B PRO 4.5 1.6 - - - -
591B GLN* 3.7 43.1 + - + +
592B ARG* 3.5 22.7 + - - +
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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