Contacts of the helix formed by residues 167 - 181 (chain A) in PDB entry 2NPJ
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 VAL 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A PHE* 3.9 30.3 - - + +
110A ILE* 4.6 2.9 - - + -
111A THR* 3.4 29.1 - - - +
114A LEU* 4.0 14.6 - - + -
140A TYR* 4.6 2.7 - - + -
148A TRP* 4.5 3.8 - - + -
163A GLY* 2.9 19.0 + - - +
165A THR 3.9 0.4 - - - -
166A VAL* 1.3 80.2 - - + +
168A HIS* 1.3 80.9 + - + +
169A ILE 3.7 0.4 - - - -
171A ALA* 2.9 34.8 + - - +
215A PHE* 4.0 14.6 - - + -
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Residues in contact with HIS 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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23A MET* 6.3 0.2 - - + -
114A LEU* 5.0 0.4 - - + -
163A GLY 3.2 7.1 + - - -
164A GLY* 3.6 9.9 - - - +
167A VAL* 1.3 90.1 - - + +
169A ILE* 1.3 61.5 + - - +
171A ALA* 4.0 1.0 - - - +
172A ALA* 3.0 30.7 + - - +
212A TRP* 3.4 29.2 - + - -
215A PHE* 4.1 7.6 - + - -
270A VAL* 3.7 21.1 - - + -
273A THR* 3.0 45.7 + - + +
318A PHE* 3.4 42.1 - + + +
322A GLY* 4.5 0.9 - - - -
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Residues in contact with ILE 169 (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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164A GLY 2.9 24.4 + - - +
165A THR* 4.0 10.8 - - + +
168A HIS* 1.3 69.6 - - - +
170A ASN* 1.3 67.2 - - - +
172A ALA* 4.4 4.7 - - - -
173A ILE* 3.1 28.9 + - + +
318A PHE 4.7 0.4 - - - -
319A GLY* 4.3 4.3 - - - +
322A GLY* 3.8 32.5 - - - +
323A ILE* 3.8 20.2 - - + +
326A CYS* 4.0 11.2 - - - -
359A ILE* 4.1 14.4 - - + +
362A THR* 3.9 12.8 - - + -
363A ILE* 3.6 32.1 - - + -
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Residues in contact with ASN 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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135A TRP* 3.1 22.5 - - + -
139A SER* 3.0 20.8 + - - -
140A TYR* 3.7 22.2 - - - +
143A ILE* 3.3 20.2 - - - +
165A THR 3.0 12.8 + - - +
166A VAL 3.0 31.2 + - - +
169A ILE* 1.3 77.9 - - - +
171A ALA* 1.3 61.3 + - - +
174A ALA 3.3 6.1 + - - -
362A THR* 3.9 6.3 - - + +
366A SER* 2.7 37.6 + - - -
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Residues in contact with ALA 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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111A THR* 3.7 26.7 - - + +
114A LEU* 4.0 19.1 - - + -
115A ILE* 3.7 20.0 - - + +
135A TRP* 4.2 1.5 - - - -
167A VAL 2.9 19.8 + - - +
168A HIS 4.1 1.3 - - - +
170A ASN* 1.3 73.7 - - - +
172A ALA* 1.3 61.0 + - - +
174A ALA* 3.2 1.7 + - - +
175A GLY* 2.8 28.4 + - - -
315A PHE* 4.2 4.7 - - + -
318A PHE* 6.1 0.4 - - + -
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Residues in contact with ALA 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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168A HIS 3.0 18.8 + - - +
169A ILE 3.8 2.9 - - - +
171A ALA* 1.3 75.5 - - - +
173A ILE* 1.3 59.2 + - + +
175A GLY 3.4 0.5 + - - -
176A LEU* 2.9 39.0 + - + +
315A PHE* 3.5 21.2 - - - +
318A PHE* 4.0 4.6 - - + +
319A GLY* 3.4 35.4 - - - +
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Residues in contact with ILE 173 (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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169A ILE* 3.1 20.3 + - + +
172A ALA* 1.3 78.1 - - + +
174A ALA* 1.3 58.8 + - - +
176A LEU* 3.2 15.8 + - + +
177A VAL* 2.9 33.2 + - + +
319A GLY* 6.1 2.2 - - - -
323A ILE* 6.1 2.0 - - + -
363A ILE* 3.6 61.9 - - + +
366A SER* 4.1 8.1 - - - +
367A GLY* 3.6 20.0 - - - +
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Residues in contact with ALA 174 (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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115A ILE* 3.8 12.8 - - + -
131A PHE* 4.2 4.7 - - + -
135A TRP* 3.5 34.3 - - + +
170A ASN 3.3 8.0 + - - +
171A ALA 3.2 7.9 + - - +
173A ILE* 1.3 78.5 - - - +
175A GLY* 1.3 62.0 + - - +
177A VAL 3.4 0.3 + - - -
178A GLY 3.2 10.0 + - - -
366A SER* 3.8 1.7 + - - -
370A ALA* 3.8 16.4 - - + -
374A TYR* 2.8 23.7 + - - -
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Residues in contact with GLY 175 (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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115A ILE* 4.4 4.0 - - - +
119A LEU* 4.0 11.7 - - - +
171A ALA 2.8 12.2 + - - -
174A ALA* 1.3 77.4 - - - +
176A LEU* 1.3 54.9 + - - +
178A GLY* 3.2 2.4 + - - -
179A ALA* 2.8 28.9 + - - +
315A PHE* 3.5 36.9 - - - -
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Residues in contact with LEU 176 (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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172A ALA* 2.9 29.5 + - + +
173A ILE* 3.2 16.4 + - + +
175A GLY* 1.3 72.7 - - - +
177A VAL* 1.3 65.4 + - + +
179A ALA* 3.4 9.8 + - + +
180A TYR* 3.1 23.9 + - - +
302A LEU* 3.8 31.6 - - + -
312A CYS* 4.3 6.7 - - + +
315A PHE* 3.7 30.1 - - + +
316A GLY* 5.2 1.6 - - - +
319A GLY* 5.8 2.0 - - - -
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Residues in contact with VAL 177 (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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173A ILE* 2.9 24.3 + - + +
174A ALA 3.8 4.7 - - - +
176A LEU* 1.3 75.8 - - + +
178A GLY* 1.3 64.0 + - - +
180A TYR* 3.3 8.0 + - + +
181A LEU* 3.0 33.6 + - + +
367A GLY* 3.9 26.2 - - - +
370A ALA* 4.2 2.9 - - + -
371A PHE* 4.0 22.4 - - + +
374A TYR* 3.8 20.0 - - + -
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Residues in contact with GLY 178 (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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119A LEU* 3.9 13.5 - - - +
122A ARG* 6.1 0.2 - - - -
174A ALA 3.2 6.9 + - - -
175A GLY 3.2 7.6 + - - -
177A VAL* 1.3 74.9 - - - +
179A ALA* 1.3 58.6 + - - +
181A LEU* 2.9 29.4 + - - +
374A TYR* 3.5 29.1 - - - -
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Residues in contact with ALA 179 (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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119A LEU* 3.9 3.9 - - - +
122A ARG* 6.0 3.9 - - - +
175A GLY 2.8 18.1 + - - +
176A LEU* 3.7 13.7 - - + +
177A VAL 3.4 0.2 - - - -
178A GLY* 1.3 72.4 - - - +
180A TYR* 1.3 61.8 + - - +
181A LEU 3.8 4.0 - - - +
312A CYS* 3.7 33.4 - - + -
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Residues in contact with TYR 180 (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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176A LEU 3.1 13.4 + - - +
177A VAL* 3.5 10.3 - - + +
179A ALA* 1.3 80.1 - - - +
181A LEU* 1.3 78.6 + - + +
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Residues in contact with LEU 181 (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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177A VAL* 3.0 25.7 + - + +
178A GLY* 2.9 21.5 + - - +
179A ALA 3.8 4.2 - - - +
180A TYR* 1.3 98.7 - - + +
371A PHE* 4.3 27.1 - - + -
374A TYR* 3.6 39.7 - - + -
375A LYS* 4.5 17.7 - - - +
383A LEU* 4.6 16.3 - - + +
384A ARG* 5.9 6.9 - - - +
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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