Contacts of the helix formed by residues 167 - 183 (chain A) in PDB entry 1H13
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 ASN 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 3.6 29.0 + - - +
165A GLU 4.3 0.8 + - - -
166A PHE* 1.3 68.7 - - - +
168A TYR* 1.3 65.2 + - - +
169A TYR* 3.5 6.6 + - - +
170A ASN* 2.9 33.5 + - + +
171A ASP* 2.9 27.5 + - - +
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Residues in contact with TYR 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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93A GLN* 3.0 21.8 + - - -
96A PHE* 3.7 20.6 - + - -
97A ASP* 2.5 32.7 + - - -
153A LEU* 3.5 28.8 - - + +
156A ALA* 3.6 20.2 - - + -
157A SER 3.6 3.1 - - - +
160A TRP* 3.6 22.1 - + + -
161A GLY 3.2 28.0 - - - -
162A ASN* 2.9 6.8 + - - +
164A GLY* 6.2 0.9 - - - -
165A GLU* 6.0 0.3 + - - +
166A PHE* 3.2 32.0 + + + -
167A ASN* 1.3 74.2 - - - +
169A TYR* 1.3 56.9 + - - +
171A ASP* 3.3 7.6 + - - +
172A ALA* 2.8 29.6 + - - +
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Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.8 20.6 - - + -
157A SER* 3.4 25.1 - - - +
162A ASN* 2.9 15.8 + - - +
167A ASN* 3.7 4.0 - - - +
168A TYR* 1.3 76.9 - - - +
170A ASN* 1.3 66.5 + - - +
172A ALA* 3.1 4.8 + - - +
173A ILE* 2.9 51.3 + - + +
215A ASN 2.6 30.8 + - - -
216A VAL* 3.8 5.5 - - - -
217A THR* 4.0 10.5 + - + +
402A ASN* 4.1 8.5 - - + -
404A PHE* 3.6 26.3 - + - -
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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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167A ASN* 2.9 32.3 + - + +
169A TYR* 1.3 82.2 - - + +
171A ASP* 1.3 65.7 + - - +
173A ILE* 3.3 5.5 + - - +
174A THR* 3.0 29.3 + - - +
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Residues in contact with ASP 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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100A TRP* 2.9 40.6 + - + +
104A LYS* 2.8 31.9 + - - -
153A LEU* 4.1 8.2 - - + +
166A PHE* 3.8 11.6 - - - +
167A ASN* 2.9 18.2 + - - +
168A TYR* 3.6 8.2 - - - +
170A ASN* 1.3 80.2 - - - +
172A ALA* 1.3 56.8 + - - +
174A THR* 3.4 7.6 + - - -
175A MET* 2.9 29.6 + - - +
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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
----------------------------------------------------------
150A ALA* 4.0 4.5 - - - +
153A LEU* 3.7 20.1 - - + +
154A LEU* 3.6 36.3 - - + +
168A TYR 2.8 14.0 + - - +
169A TYR 3.4 7.6 - - - +
171A ASP* 1.3 74.5 - - - +
173A ILE* 1.3 61.7 + - - +
175A MET* 3.1 5.5 + - - +
176A LEU* 2.8 32.2 + - - +
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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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154A LEU* 4.6 3.4 - - + -
169A TYR* 2.9 62.0 + - + +
170A ASN* 4.0 5.6 - - - +
172A ALA* 1.3 73.1 - - - +
174A THR* 1.3 66.2 + - - +
176A LEU* 3.3 11.6 + - + +
177A ASN* 2.9 24.4 + - + +
215A ASN 4.2 1.3 - - - +
216A VAL* 4.0 24.9 - - + -
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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
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108A LYS* 5.7 8.5 - - - +
111A ASP* 6.0 1.3 - - - +
170A ASN* 3.0 19.2 + - - +
171A ASP* 3.5 8.3 - - - +
173A ILE* 1.3 78.4 - - - +
175A MET* 1.3 58.2 + - + +
177A ASN* 3.2 7.5 + - + +
178A THR* 2.9 36.9 + - - +
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Residues in contact with MET 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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100A TRP* 3.6 26.9 - - + -
122A TYR* 3.5 31.0 - - + +
146A GLU* 3.4 50.9 - - - +
149A PHE* 3.7 14.8 - - + -
150A ALA* 3.8 15.9 - - + +
153A LEU* 4.5 2.0 - - + -
171A ASP 2.9 13.3 + - - +
172A ALA* 3.1 9.4 + - - +
174A THR* 1.3 77.0 - - - +
176A LEU* 1.3 56.2 + - - +
178A THR* 3.1 9.5 + - - -
179A ILE* 2.9 33.3 + - + +
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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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150A ALA* 3.6 15.3 - - + -
154A LEU* 4.4 11.0 - - + -
172A ALA 2.8 20.8 + - - +
173A ILE* 3.6 16.6 - - + +
175A MET* 1.3 72.9 - - - +
177A ASN* 1.3 63.0 + - - +
179A ILE* 3.2 6.9 + - + +
180A LYS* 2.9 24.1 + - - +
212A PHE* 3.4 47.3 - - + -
216A VAL* 3.7 30.3 - - + -
225A TRP* 3.7 23.8 - - + +
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Residues in contact with ASN 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 14.9 + - + +
174A THR* 3.2 10.3 + - - +
176A LEU* 1.3 77.3 - - - +
178A THR* 1.3 58.3 + - - +
180A LYS* 3.3 7.2 + - - +
181A ASN* 2.9 47.5 + - - +
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Residues in contact with THR 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 GLN 4.6 0.9 + - - +
120A GLY* 3.5 35.8 + - - +
121A VAL* 4.0 18.2 - - + -
146A GLU* 4.9 6.1 - - + -
174A THR* 2.9 20.0 + - - +
175A MET* 3.4 13.7 - - - +
177A ASN* 1.3 73.2 - - - +
179A ILE* 1.3 65.9 + - - +
181A ASN* 4.8 1.3 - - - +
182A LYS* 2.8 37.7 + - + +
183A LEU* 4.1 5.8 - - + +
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Residues in contact with ILE 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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146A GLU* 3.6 44.9 - - + +
147A GLU* 3.9 14.6 - - + +
150A ALA* 4.2 11.9 - - + -
175A MET 2.9 20.0 + - - +
176A LEU* 3.5 14.1 - - + +
178A THR* 1.3 74.5 - - - +
180A LYS* 1.3 61.3 + - - +
183A LEU* 2.8 31.8 + - + -
184A MET* 3.3 25.8 + - + +
189A ILE* 4.0 15.9 - - + -
212A PHE* 4.9 3.6 - - + -
225A TRP* 3.8 17.3 - - + -
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Residues in contact with LYS 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 2.9 16.1 + - - +
177A ASN* 3.7 7.6 - - - +
179A ILE* 1.3 81.4 - - - +
181A ASN* 1.3 69.5 + - - +
184A MET* 3.8 15.6 + - - +
220A ALA* 5.5 0.6 + - - +
221A ASP* 3.1 29.1 + - - -
224A TYR* 3.6 62.1 + - + +
225A TRP* 4.5 5.1 - - + +
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Residues in contact with ASN 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 ASN* 2.9 31.7 + - - +
178A THR* 4.3 1.8 - - - +
180A LYS* 1.3 89.6 - - - +
182A LYS* 1.3 80.0 + - + +
184A MET 5.3 0.9 - - - -
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Residues in contact with LYS 182 (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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116A ALA* 2.8 36.4 + - - +
117A LYS* 4.2 10.5 - - - +
119A GLN* 3.6 37.1 + - - +
121A VAL* 3.7 21.8 - - + -
178A THR* 2.8 21.0 + - + +
181A ASN* 1.3 96.2 + - + +
183A LEU* 1.3 64.9 + - + +
184A MET 3.7 2.7 - - - -
190A ARG* 4.0 8.1 + - - -
193A PRO* 4.0 15.8 - - - +
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Residues in contact with LEU 183 (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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121A VAL* 3.9 13.2 - - + -
141A PRO* 3.8 27.1 - - + -
143A PRO* 4.0 19.3 - - + +
146A GLU* 3.6 44.6 - - + +
178A THR* 4.1 4.3 - - + +
179A ILE* 2.8 24.9 + - + +
182A LYS* 1.3 92.4 - - + +
184A MET* 1.3 54.8 + - - +
189A ILE* 3.4 16.0 - - + +
190A ARG* 2.8 36.7 + - - +
193A PRO* 4.2 5.8 - - + -
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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