Contacts of the helix formed by residues 235 - 240 (chain A) in PDB entry 1NHX
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 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR* 4.0 13.9 - - + -
84A ASP* 3.5 33.3 + - - +
85A VAL* 3.2 24.7 + - - -
86A ALA* 3.6 15.9 - - - +
165A TYR* 5.1 2.0 - - - -
210A TRP* 4.1 4.7 - + - -
233A SER* 3.1 5.2 + - - +
234A GLY* 1.3 76.9 - - - +
236A GLY* 1.3 81.8 + - - +
237A GLY 3.2 0.3 + - - -
238A ASN* 2.8 21.8 + - - +
239A SER* 3.3 5.4 + - - -
333A PHE* 4.5 9.4 - + - -
358A THR* 4.0 24.2 - - + +
359A ASN* 4.0 5.0 + - - -
401A HIS* 5.4 0.3 + - - -
403A ASN* 2.8 37.7 + - - -
404A SER* 3.9 4.9 - - - -
405A ARG* 3.7 10.1 + - + +
703A PEP 3.3 19.3 - - - -
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Residues in contact with GLY 236 (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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165A TYR* 5.0 6.4 + - - -
234A GLY 3.8 1.4 + - - -
235A TYR* 1.3 72.8 - - - +
237A GLY* 1.3 59.3 + - - -
238A ASN 3.1 0.5 + - - -
239A SER* 3.1 2.9 + - - -
240A LEU* 2.8 46.9 + - - +
243A LYS* 5.7 1.6 - - - -
333A PHE* 3.6 25.2 - - - -
703A PEP 3.4 7.6 - - - -
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.2 15.6 - - - +
219A ILE* 5.1 0.5 - - - +
235A TYR 3.2 0.4 + - - -
236A GLY* 1.3 71.0 - - - -
238A ASN* 1.3 62.9 + - - +
240A LEU 4.7 6.5 - - - +
243A LYS* 5.5 2.7 - - - -
244A LYS* 4.4 16.4 - - - +
245A CYS* 3.9 18.5 - - - -
249A ARG* 5.3 0.9 + - - -
703A PEP 2.7 33.4 + - - +
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Residues in contact with ASN 238 (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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84A ASP* 4.4 0.4 + - - -
86A ALA 2.9 28.5 + - - -
87A ARG* 3.4 9.9 - - - +
88A ILE* 3.1 25.1 + - - +
92A THR* 4.7 1.0 + - - -
219A ILE* 3.5 32.1 - - + +
230A SER* 2.6 27.5 + - - +
233A SER* 2.9 33.4 + - - +
235A TYR* 2.8 8.6 + - - +
237A GLY* 1.3 78.0 - - - +
239A SER* 1.3 58.1 + - - +
241A LEU* 3.2 11.4 - - - +
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Residues in contact with SER 239 (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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159A GLU* 2.7 28.8 - - - +
166A VAL* 3.5 17.6 - - - +
194A HIS* 3.5 27.8 - - - -
233A SER 3.8 0.4 - - - -
234A GLY 2.7 32.8 + - - -
235A TYR 3.3 6.6 + - - -
236A GLY 3.6 1.7 + - - -
238A ASN* 1.3 80.4 - - - +
240A LEU* 1.3 67.3 + - - +
241A LEU* 3.1 6.1 + - - +
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Residues in contact with LEU 240 (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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165A TYR* 5.2 4.7 - - + -
166A VAL* 4.0 20.6 - - + +
169A SER* 3.5 33.2 - - - +
170A MET* 3.9 20.2 - - + +
173A MET* 4.4 15.7 - - + -
236A GLY* 2.8 32.5 + - - +
237A GLY 4.7 4.3 - - - +
239A SER* 1.3 82.3 - - - +
241A LEU* 1.3 63.8 + - - +
242A GLY 3.3 3.9 + - - -
243A LYS* 3.3 25.6 + - + +
244A LYS 4.3 2.8 + - - -
333A PHE* 4.1 23.8 - - + -
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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