Contacts of the helix formed by residues 172 - 185 (chain A) in PDB entry 2HU2
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 GLY 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A GLY 3.4 7.3 + - - -
171A LEU* 1.3 74.2 - - - +
173A ARG* 1.3 62.4 + - - -
174A VAL 3.6 1.1 - - - -
175A GLY 4.4 2.2 - - - +
176A GLN* 2.8 38.4 + - - +
196A LEU* 6.0 0.4 - - - -
225A HIS 4.7 0.4 + - - -
600A NAD 3.3 33.9 + - - -
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Residues in contact with ARG 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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89A SER* 5.6 1.4 + - - -
110A PRO* 3.6 52.6 + - - +
111A ALA* 4.8 6.6 - - - +
114A VAL* 3.7 31.0 - - + +
172A GLY* 1.3 72.1 - - - +
174A VAL* 1.3 62.6 + - - +
176A GLN* 3.6 4.5 - - - +
177A ALA* 3.3 15.9 + - - +
600A NAD 2.8 48.6 + - - +
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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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114A VAL* 4.0 25.8 - - + +
117A THR* 3.9 28.9 - - + +
118A ALA* 4.2 8.7 - - - +
173A ARG* 1.3 69.0 - - - +
175A GLY* 1.3 59.1 + - - +
177A ALA* 3.0 6.5 + - - +
178A VAL* 2.8 32.6 + - + +
225A HIS* 3.4 28.5 - - + +
600A NAD 2.8 46.1 + - + +
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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
----------------------------------------------------------
168A ILE* 3.7 8.0 - - - +
170A GLY 3.9 20.2 + - - -
171A LEU* 3.8 7.8 - - - +
172A GLY 4.1 3.2 + - - -
173A ARG 3.5 0.2 - - - -
174A VAL* 1.3 77.9 - - - +
176A GLN* 1.3 56.6 + - - +
178A VAL* 3.4 3.1 + - - +
179A ALA* 2.9 28.8 + - - +
225A HIS* 3.9 23.5 - - - +
600A NAD 4.4 0.6 + - - -
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Residues in contact with GLN 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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171A LEU* 3.0 28.0 + - + +
172A GLY* 2.8 34.9 + - - +
173A ARG* 3.6 5.8 - - - +
174A VAL 3.1 0.4 - - - -
175A GLY* 1.3 77.7 - - - +
177A ALA* 1.3 59.7 + - - +
179A ALA* 3.4 4.2 + - - +
180A LEU* 3.2 31.1 + - + +
196A LEU* 5.3 2.2 - - - +
200A ILE* 4.8 6.8 - - - +
204A LEU* 3.6 39.5 - - + +
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Residues in contact with ALA 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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114A VAL* 4.5 11.9 - - + -
115A GLU* 5.1 4.7 - - + -
118A ALA* 3.7 13.9 - - + -
173A ARG 3.3 9.7 + - - +
174A VAL 3.0 8.6 + - - +
176A GLN* 1.3 76.0 - - - +
178A VAL* 1.3 64.0 + - - +
180A LEU* 3.6 9.1 + - - +
181A ARG* 3.2 49.7 + - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 3.9 23.3 - - + +
121A THR* 4.0 5.8 - - + -
122A LEU* 3.7 18.5 - - + +
125A ILE* 4.4 8.5 - - + -
166A LEU* 4.3 20.4 - - + -
168A ILE* 4.4 5.4 - - + -
174A VAL* 2.8 18.6 + - + +
175A GLY* 3.6 5.2 - - - +
177A ALA* 1.3 74.9 - - - +
179A ALA* 1.3 59.3 + - - +
181A ARG* 3.3 2.6 + - - +
182A ALA* 2.8 28.6 + - - +
223A THR* 4.5 1.3 - - + -
225A HIS* 3.7 34.8 - - + +
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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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168A ILE* 3.8 18.6 - - + +
171A LEU* 4.3 2.5 - - + -
175A GLY 2.9 18.3 + - - +
176A GLN* 3.5 7.9 - - - +
177A ALA 3.3 0.2 - - - -
178A VAL* 1.3 76.5 - - - +
180A LEU* 1.3 62.2 + - + +
182A ALA* 3.3 5.0 + - - +
183A LYS* 3.2 26.9 + - - +
189A VAL* 4.2 6.9 - - + +
204A LEU* 6.1 0.2 - - + -
206A LEU* 4.0 31.9 - - + -
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Residues in contact with LEU 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 GLN* 3.2 18.0 + - + +
177A ALA* 3.9 10.5 - - - +
178A VAL 3.3 0.4 - - - -
179A ALA* 1.3 78.6 - - + +
181A ARG* 1.3 66.7 + - + +
183A LYS* 3.5 38.5 + - + +
184A ALA* 4.0 4.2 + - - +
204A LEU* 5.2 18.2 - - + +
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Residues in contact with ARG 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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115A GLU* 3.3 38.0 + - - +
118A ALA* 4.3 13.4 - - - +
119A ASP* 2.8 31.0 + - - -
122A LEU* 3.8 29.2 - - + -
177A ALA* 3.2 39.7 + - - +
178A VAL 3.7 3.4 - - - +
180A LEU* 1.3 82.4 - - + +
182A ALA* 1.3 63.5 + - - +
184A ALA* 3.3 13.3 + - - +
185A PHE* 3.2 24.4 - - + -
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Residues in contact with ALA 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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122A LEU* 4.6 5.8 - - + +
166A LEU* 3.7 28.0 - - + -
178A VAL* 2.8 18.6 + - + +
179A ALA 3.3 6.0 + - - +
181A ARG* 1.3 76.1 - - - +
183A LYS* 1.3 64.3 + - - +
185A PHE* 3.2 13.3 + - - -
187A PHE* 3.4 33.8 + - + +
189A VAL* 3.7 11.2 - - + -
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Residues in contact with LYS 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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162A ARG* 5.1 2.3 + - - -
179A ALA* 3.2 12.2 + - - +
180A LEU* 3.5 32.8 - - + +
181A ARG 3.2 0.6 - - - -
182A ALA* 1.3 76.7 - - - +
184A ALA* 1.3 62.4 + - - +
186A GLY* 3.2 14.2 + - - -
187A PHE 4.5 8.0 - - - +
189A VAL* 4.5 8.0 - - + +
204A LEU* 3.0 29.2 + - - +
205A GLY* 3.7 15.5 - - - -
206A LEU* 3.4 17.4 - - + +
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Residues in contact with ALA 184 (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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162A ARG* 5.1 5.4 + - - -
180A LEU 4.0 2.8 + - - +
181A ARG* 3.3 13.9 + - - +
182A ALA 3.2 0.8 - - - -
183A LYS* 1.3 78.6 - - - +
185A PHE* 1.3 65.8 + - + +
186A GLY 3.4 0.6 + - - -
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Residues in contact with PHE 185 (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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122A LEU* 3.8 24.7 - - + -
126A LEU* 3.9 40.8 - - + -
161A ILE* 3.5 32.8 - - + +
162A ARG* 3.8 16.3 + - - +
181A ARG* 3.2 30.5 - - + -
182A ALA* 3.2 7.1 + - - +
183A LYS 3.2 1.2 - - - -
184A ALA* 1.3 83.2 - - + +
186A GLY* 1.3 59.0 + - - +
187A PHE* 3.5 6.3 - + + -
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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