Contacts of the helix formed by residues 167 - 178 (chain A) in PDB entry 1N0W
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 ARG 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS* 2.9 20.3 + - - +
164A GLY 3.0 28.7 + - - -
165A THR* 3.4 18.8 - - - +
166A PHE* 1.3 92.0 + - - +
168A PRO* 1.3 69.7 - - - +
169A GLU* 3.1 30.7 - - + +
170A ARG* 2.9 23.5 + - + +
171A LEU* 3.6 2.6 + - - +
506A EDO 3.8 18.2 - - - +
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Residues in contact with PRO 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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166A PHE* 3.7 25.5 - - + +
167A ARG* 1.3 84.9 - - - +
169A GLU* 1.3 69.4 + - - +
171A LEU* 3.0 27.3 + - + +
172A LEU* 3.1 16.2 + - + +
186A LEU* 3.8 11.9 - - + +
1527B ALA* 3.7 25.6 - - + +
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Residues in contact with GLU 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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167A ARG* 3.7 28.2 - - + +
168A PRO* 1.3 92.9 - - - +
170A ARG* 1.3 72.7 + - + +
172A LEU* 3.3 15.8 + - + +
173A ALA* 3.2 20.3 + - - +
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Residues in contact with ARG 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 GLN* 3.8 12.8 - - - +
138A HIS* 3.9 23.1 - - + -
167A ARG* 2.9 15.2 + - + +
169A GLU* 1.3 83.8 + - - +
171A LEU* 1.3 66.2 + - - +
173A ALA* 3.2 7.2 + - - +
174A VAL* 3.1 25.7 + - + +
330A ASN 4.5 2.7 + - - -
331A ALA* 2.8 47.6 + - - +
333A GLY* 4.3 11.7 - - - +
506A EDO 3.1 38.8 + - - +
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Residues in contact with LEU 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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138A HIS* 3.4 43.5 - - + +
141A ALA* 4.1 9.9 - - + -
142A VAL* 3.7 18.6 - - + +
166A PHE* 3.8 29.2 - - + -
167A ARG 4.0 6.5 - - - +
168A PRO* 3.0 10.5 + - + +
170A ARG* 1.3 78.9 - - - +
172A LEU* 1.3 57.9 + - - +
174A VAL* 3.2 3.0 + - - +
175A ALA* 2.8 30.6 + - - +
185A VAL* 4.4 4.0 - - + -
186A LEU* 3.9 11.7 - - + -
189A VAL* 4.1 15.7 - - + -
1527B ALA* 3.9 18.4 - - + -
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Residues in contact with LEU 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 PRO 3.1 13.4 + - - +
169A GLU* 3.5 16.4 - - + +
170A ARG 3.2 0.4 - - - -
171A LEU* 1.3 77.9 - - - +
173A ALA* 1.3 60.4 + - - +
175A ALA* 3.3 4.7 + - + +
176A GLU* 3.0 23.7 + - - +
182A GLY* 3.6 29.4 - - - +
185A VAL* 5.8 0.2 - - + -
186A LEU* 3.6 31.9 - - + -
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Residues in contact with ALA 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 GLU 3.2 9.1 + - - +
170A ARG* 3.2 11.0 + - - +
172A LEU* 1.3 77.5 - - - +
174A VAL* 1.3 65.0 + - - +
176A GLU* 3.3 10.9 + - - +
177A ARG 3.1 17.0 + - - -
331A ALA* 3.3 27.6 - - + +
332A ASP* 3.6 16.1 - - + +
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Residues in contact with VAL 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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138A HIS 4.7 0.9 - - - +
139A THR* 4.2 24.2 - - + +
142A VAL* 3.5 28.7 - - + -
143A THR* 4.8 0.2 - - + -
170A ARG* 3.1 21.6 + - + +
171A LEU* 3.2 6.0 + - - +
173A ALA* 1.3 75.1 - - - +
175A ALA* 1.3 61.9 + - - +
177A ARG* 3.2 3.7 + - - +
178A TYR* 3.1 40.8 + - + -
332A ASP 3.5 28.3 - - - +
333A GLY* 3.9 9.0 - - - +
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Residues in contact with ALA 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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142A VAL* 3.9 10.0 - - - +
171A LEU 2.8 17.7 + - - +
172A LEU* 3.5 6.3 - - - +
173A ALA 3.2 0.2 - - - -
174A VAL* 1.3 77.9 - - - +
176A GLU* 1.3 61.2 + - - +
178A TYR* 3.1 3.0 + - - -
179A GLY 3.0 3.8 + - - -
180A LEU* 2.9 37.1 + - - +
182A GLY* 4.1 12.8 - - - -
185A VAL* 3.7 27.8 - - + -
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Residues in contact with GLU 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 LEU 3.0 16.7 + - - +
173A ALA* 3.7 9.5 - - - +
174A VAL 3.3 0.2 - - - -
175A ALA* 1.3 76.0 - - - +
177A ARG* 1.3 65.0 + - - +
179A GLY* 3.1 13.2 + - - +
180A LEU 4.7 4.0 - - - -
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Residues in contact with ARG 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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105A GLY 3.0 17.8 + - - -
139A THR* 4.5 4.4 - - - +
150A ARG* 5.5 0.2 + - - -
173A ALA 3.1 13.7 + - - +
174A VAL 3.3 7.2 - - - +
176A GLU* 1.3 78.7 - - - +
178A TYR* 1.3 95.9 + - + +
179A GLY 3.3 0.7 + - - -
330A ASN* 6.0 0.7 - - - -
332A ASP* 3.0 48.5 + - + +
333A GLY* 3.6 9.3 + - - -
334A VAL 2.8 31.4 + - - +
335A GLY* 3.9 6.6 - - - -
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Residues in contact with TYR 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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103A THR* 4.5 6.8 + - + +
105A GLY* 3.4 28.4 + - - -
139A THR* 5.1 0.7 - - + -
142A VAL* 5.1 1.3 - - + -
143A THR* 3.7 22.5 - - + +
146A LEU* 3.8 34.3 - - + -
150A ARG* 2.9 46.9 + - - +
174A VAL* 3.1 35.2 + - + +
175A ALA* 3.1 3.5 + - - +
177A ARG* 1.3 111.6 + - + +
179A GLY* 1.3 61.7 + - - +
180A LEU* 3.2 9.0 + - + +
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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