Contacts of the helix formed by residues 163 - 174 (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 SER 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A TYR* 4.3 2.7 - - - -
161A THR* 3.0 17.0 + - - +
162A ASP* 1.3 79.2 - - - +
164A PRO* 1.3 64.8 - - - +
165A TYR* 3.5 12.6 + - - +
166A VAL* 3.1 36.5 + - - +
167A VAL* 3.2 14.9 + - - +
194A HIS* 4.1 9.9 - - - -
196A VAL* 4.1 13.6 - - - +
234A GLY* 5.3 2.5 + - - -
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Residues in contact with PRO 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 5.1 10.2 - - + +
60A MET* 3.5 38.5 - - + +
65A ILE* 4.0 16.6 - - + -
140A TYR* 4.1 25.1 - - + +
162A ASP 3.6 8.7 - - - +
163A SER* 1.3 82.6 - - - +
165A TYR* 1.3 61.6 + - + +
167A VAL* 3.3 11.4 + - + +
168A ALA 3.0 23.7 + - - -
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 3.5 14.2 - - - -
65A ILE* 4.7 9.4 - - + -
66A LEU* 4.8 6.1 - - + -
78A ALA* 3.7 24.0 - - + -
163A SER* 3.2 10.9 + - - +
164A PRO* 1.3 78.6 - - + +
166A VAL* 1.3 62.3 + - - +
168A ALA* 3.5 2.6 + - - +
169A SER* 2.9 52.4 + - - -
210A TRP* 3.5 36.0 - + + -
234A GLY 3.6 15.5 - - - -
235A TYR* 5.3 1.9 - - - -
236A GLY* 5.0 8.3 + - - -
239A SER* 5.1 1.1 - - - -
240A LEU* 5.2 2.9 - - + -
333A PHE* 4.7 14.0 - - - -
356A ILE* 4.1 14.2 - - + +
358A THR* 2.6 35.2 + - - +
407A CYS* 6.1 0.7 - - - +
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Residues in contact with VAL 166 (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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142A ILE* 4.0 2.0 - - + -
159A GLU* 3.5 22.7 - - - +
161A THR* 3.9 15.9 - - + +
163A SER* 3.1 25.8 + - - +
165A TYR* 1.3 75.8 - - + +
167A VAL* 1.3 56.3 + - - +
169A SER* 3.6 0.5 - - - -
170A MET* 2.7 52.0 + - + +
194A HIS* 4.0 5.6 - - + -
234A GLY 4.2 6.1 - - - +
239A SER* 3.5 37.7 - - - +
240A LEU* 4.0 9.0 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A CYS* 3.7 18.4 - - - -
52A GLU* 5.1 0.4 - - - +
56A LEU* 3.7 23.1 - - + -
140A TYR* 3.5 37.9 - - + -
142A ILE* 3.7 20.2 - - + -
161A THR* 3.8 0.9 - - + -
163A SER 3.2 13.3 + - - +
164A PRO* 3.3 9.1 + - + +
166A VAL* 1.3 78.3 - - - +
168A ALA* 1.3 58.9 + - - +
170A MET* 3.2 2.1 + - - +
171A ARG* 3.0 27.0 + - - +
176A MET* 4.0 15.5 - - + +
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Residues in contact with ALA 168 (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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53A ASN* 4.0 20.6 - - - +
56A LEU* 5.4 3.8 - - + +
57A LEU* 4.5 5.6 - - + -
60A MET* 3.9 17.7 - - + -
164A PRO 3.0 16.1 + - - +
165A TYR* 4.0 2.7 - - - +
167A VAL* 1.3 77.3 - - - +
169A SER* 1.3 62.4 + - - +
171A ARG* 3.5 15.7 + - - +
172A ILE* 3.6 14.6 + - - +
356A ILE* 3.8 19.0 - - + +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 2.9 44.6 + - - -
168A ALA* 1.3 74.8 - - - +
170A MET* 1.3 60.6 + - - +
172A ILE* 3.2 4.3 + - - +
173A MET* 2.9 34.0 + - - +
240A LEU* 3.5 29.8 - - - -
333A PHE* 5.8 0.5 - - - -
356A ILE* 4.2 9.3 - - - +
407A CYS* 4.2 16.7 - - - +
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Residues in contact with MET 170 (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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142A ILE* 4.0 20.0 - - + -
144A PHE* 3.5 44.2 - - + -
159A GLU* 3.4 22.9 - - + +
166A VAL* 2.7 42.7 + - + +
167A VAL 3.6 4.3 - - - +
169A SER* 1.3 70.6 - - - +
171A ARG* 1.3 58.5 + - - +
173A MET* 4.4 4.0 - - - +
174A THR* 2.6 54.3 + - + +
176A MET* 4.6 1.1 - - - -
240A LEU* 3.9 25.8 - - + -
241A LEU 4.1 0.9 - - - -
242A GLY 4.2 4.7 - - - +
243A LYS 5.9 0.2 - - - -
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Residues in contact with ARG 171 (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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48A GLY 3.1 28.2 + - - +
49A SER* 3.7 8.5 + - - +
50A GLU* 3.4 34.1 - - - +
52A GLU* 5.9 0.7 - - - -
53A ASN* 3.5 38.8 - - - +
167A VAL 3.0 8.6 + - - +
168A ALA* 3.5 12.6 - - - +
169A SER 3.3 0.2 - - - -
170A MET* 1.3 76.0 - - - +
172A ILE* 1.3 61.8 + - + +
174A THR 2.9 15.9 - - - +
176A MET* 3.7 34.8 + - + +
330A ASN* 3.8 5.7 + - - -
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Residues in contact with ILE 172 (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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53A ASN* 6.4 0.2 - - - +
168A ALA 3.6 15.2 + - - +
169A SER 3.2 6.5 + - - +
170A MET 3.2 0.4 - - - -
171A ARG* 1.3 82.8 - - + +
173A MET* 1.3 64.2 + - - +
174A THR 3.3 0.4 - - - -
330A ASN* 3.2 32.3 + - - +
354A ASN 4.1 13.0 - - - +
356A ILE* 3.9 20.6 - - + -
407A CYS* 3.6 25.1 - - - +
408A THR 3.3 40.6 - - - +
409A PRO* 3.5 16.4 - - + +
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A MET* 4.9 0.9 - - - +
169A SER 2.9 19.7 + - - +
170A MET* 4.4 5.2 - - - +
172A ILE* 1.3 77.7 - - - +
174A THR* 1.3 67.4 + - + +
240A LEU* 4.4 17.7 - - + -
243A LYS* 4.2 4.5 - - + +
329A GLU* 3.2 41.2 - - - +
330A ASN* 2.9 19.0 + - - -
331A GLY* 3.3 29.8 - - - +
332A PHE 3.7 21.5 - - - +
333A PHE* 3.7 22.7 - - + +
407A CYS* 3.7 19.7 - - - -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.4 24.0 - - + +
145A SER 3.9 8.5 - - - -
146A MET* 3.7 23.8 - - + -
170A MET* 2.6 51.5 + - + +
171A ARG 2.9 15.6 - - - +
173A MET* 1.3 83.2 - - + +
175A ARG* 1.3 63.0 + - - +
176A MET* 3.9 2.1 - - - +
242A GLY* 5.1 2.0 - - - -
243A LYS 5.8 0.2 - - - +
328A PRO 5.5 0.2 - - - -
329A GLU* 5.2 0.7 - - - +
330A ASN* 2.8 24.1 + - - +
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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