Contacts of the helix formed by residues 172 - 188 (chain A) in PDB entry 2V8W
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 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASP* 2.7 28.1 + - - +
168A THR* 4.8 1.4 - - - +
169A GLU* 3.1 32.0 + - - +
170A CYS 3.4 0.4 - - - -
171A GLU* 1.3 74.1 - - - +
173A ARG* 1.3 60.0 + - - +
174A GLU 3.2 2.8 + - - -
175A ALA* 3.3 16.5 + - + +
176A VAL* 2.8 31.3 + - - +
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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
----------------------------------------------------------
171A GLU 2.8 12.2 + - - +
172A ASN* 1.3 71.9 - - - +
174A GLU* 1.3 58.6 + - - +
176A VAL* 4.2 0.7 - - - +
177A THR* 2.8 34.0 + - - -
214A ARG 5.0 1.4 + - - -
215A PHE* 3.2 49.6 - - + -
141E SER* 4.6 9.5 + - - +
143E ASP* 2.9 39.9 + - - +
53F ILE* 4.5 25.8 - - + +
55F ASP* 5.6 6.7 + - - -
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.1 31.3 + - + +
172A ASN 3.3 0.6 - - - -
173A ARG* 1.3 76.2 - - - +
175A ALA* 1.3 57.5 + - - +
177A THR* 3.5 8.7 - - + +
178A HIS* 2.8 36.0 + - + +
144E ASP* 5.4 1.3 - - - +
51F ARG* 2.8 66.4 + - + +
53F ILE* 4.6 11.1 - - + +
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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
----------------------------------------------------------
145A TYR* 3.5 34.7 - - + -
148A ASP* 3.5 30.7 - - + +
167A THR* 6.5 0.2 - - - -
172A ASN* 3.3 15.7 + - + +
174A GLU* 1.3 76.4 - - - +
176A VAL* 1.3 65.9 + - + +
178A HIS* 3.9 1.0 - - - +
179A ILE* 3.1 31.3 + - - +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 2.7 29.5 + - + +
148A ASP* 5.8 0.4 - - - +
167A THR* 3.8 17.0 - - - +
169A GLU 3.5 21.1 - - - +
170A CYS* 4.3 5.2 - - - +
172A ASN* 2.8 25.1 + - + +
173A ARG 4.2 0.2 - - - +
175A ALA* 1.3 73.4 - - + +
177A THR* 1.3 58.4 + - - +
179A ILE* 3.4 6.1 + - - +
180A GLY 3.0 12.3 + - - -
197A TYR* 3.4 37.7 - - + -
215A PHE* 3.5 27.8 - - + -
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 4.4 7.8 - - - -
173A ARG* 2.8 22.1 + - - +
174A GLU* 3.5 12.3 - - + +
176A VAL* 1.3 77.8 - - - +
178A HIS* 1.3 68.4 + - - +
180A GLY* 4.1 0.2 - - - -
181A ARG* 3.2 24.3 + - - +
215A PHE* 4.6 15.6 - - - +
216A VAL 5.6 1.4 + - - -
217A VAL* 5.7 1.0 - - - +
143E ASP* 3.2 48.4 + - + +
144E ASP* 4.5 7.7 - - - +
51F ARG* 6.2 0.7 - - - -
53F ILE* 5.9 0.7 - - + -
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.5 23.0 + - + -
143A ASP* 2.7 32.7 + - + +
145A TYR* 3.6 27.4 - + + -
174A GLU* 2.8 22.3 + - + +
177A THR* 1.3 74.3 - - - +
179A ILE* 1.3 58.5 + - - +
181A ARG* 3.5 19.4 + - - +
182A VAL* 3.1 42.8 + - + +
144E ASP* 2.9 33.0 + - - +
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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
----------------------------------------------------------
113A TRP* 4.1 15.3 - - + +
142A PHE* 3.7 42.1 - - + -
145A TYR* 3.3 29.6 - - + +
148A ASP* 4.1 11.4 - - + -
149A VAL* 3.8 11.7 - - + -
165A ILE* 4.2 17.3 - - + -
167A THR* 3.9 16.4 - - + -
175A ALA 3.1 23.1 + - - +
176A VAL 3.7 3.8 - - - +
177A THR 3.3 0.2 - - - -
178A HIS* 1.3 73.7 - - - +
180A GLY* 1.3 59.0 + - - +
182A VAL 3.4 0.2 + - - -
183A TYR* 2.9 34.1 + - + +
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 3.4 37.3 - - - +
176A VAL 3.0 11.1 + - - -
177A THR 3.6 0.6 + - - -
178A HIS 3.4 0.2 - - - -
179A ILE* 1.3 74.1 - - - +
181A ARG* 1.3 54.9 + - - +
183A TYR* 3.7 3.1 - - - +
184A LYS* 2.9 33.3 + - - +
195A ILE* 4.4 2.1 - - - +
217A VAL* 3.6 11.5 - - - +
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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
----------------------------------------------------------
177A THR 3.2 18.3 + - - +
178A HIS* 3.5 19.1 + - - +
180A GLY* 1.3 75.9 - - - +
182A VAL* 1.3 69.8 + - - +
184A LYS* 3.8 2.4 - - - +
185A GLU* 3.0 56.6 + - - +
217A VAL* 3.9 14.2 - - + +
144E ASP* 2.6 44.1 + - + +
145E TYR* 3.2 47.6 + - + +
51F ARG* 5.7 1.6 - - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER* 3.6 25.1 - - - +
142A PHE* 3.6 16.8 - - + -
143A ASP* 4.9 1.3 - - - +
178A HIS* 3.1 44.1 + - + +
181A ARG* 1.3 87.4 - - - +
183A TYR* 1.3 60.5 + - - +
185A GLU* 3.2 17.0 + - - +
186A ARG* 2.9 37.7 + - + +
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 4.3 17.9 - + + -
115A ILE* 3.7 27.0 - - + +
133A THR* 2.7 37.6 + - - +
136A CYS* 4.6 11.7 - - - -
142A PHE* 3.9 9.8 - - + -
163A ILE* 3.4 19.9 - - - +
164A ALA 4.7 0.2 - - - -
165A ILE* 3.7 42.0 - - + +
179A ILE 2.9 19.2 + - - +
180A GLY 3.7 2.5 - - - +
182A VAL* 1.3 78.1 - - - +
184A LYS* 1.3 57.2 + - - +
186A ARG* 3.1 4.9 + - + +
187A LEU* 2.9 49.9 + - + +
195A ILE* 4.7 4.7 - - + -
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Residues in contact with LYS 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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180A GLY 2.9 18.7 + - - +
181A ARG 3.8 5.2 - - - +
182A VAL 3.3 0.2 - - - -
183A TYR* 1.3 77.3 - - - +
185A GLU* 1.3 61.7 + - - +
187A LEU* 3.3 7.2 + - - -
188A GLY* 3.1 16.8 + - - -
189A LEU* 3.4 40.3 + - + +
190A PRO 3.6 11.9 + - - -
191A PRO* 3.9 4.4 + - - +
193A ILE* 2.7 30.3 + - - -
194A VAL* 4.9 0.2 - - - +
195A ILE* 4.3 14.1 - - + +
217A VAL* 3.0 34.3 + - + +
174E GLU* 2.4 41.8 + - + +
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Residues in contact with GLU 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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181A ARG* 3.0 58.6 + - - +
182A VAL* 3.2 16.9 + - - +
184A LYS* 1.3 76.8 - - - +
186A ARG* 1.3 60.7 + - + +
188A GLY* 3.0 20.1 + - - +
189A LEU 5.9 0.2 - - - -
145E TYR* 4.2 9.7 + - - +
174E GLU* 6.1 1.8 - - + -
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Residues in contact with ARG 186 (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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132A GLU* 2.5 55.5 + - + +
135A LEU* 4.3 5.9 + - - +
136A CYS* 3.6 38.2 - - - +
141A SER* 2.8 32.7 + - - -
182A VAL* 2.9 25.0 + - + +
183A TYR* 3.4 9.4 - - + +
185A GLU* 1.3 76.9 - - + +
187A LEU* 1.3 61.2 + - - +
188A GLY 3.4 0.3 + - - -
54B TYR 4.4 5.9 + - - -
55B ASP* 5.2 0.8 - - - +
56B ARG* 3.8 34.6 - - - +
59B LEU* 6.0 0.4 - - - +
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Residues in contact with LEU 187 (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 27.1 - - + -
128A ARG* 4.3 8.0 + - - -
129A PHE* 3.4 65.9 - - + +
132A GLU* 4.2 10.5 - - + -
133A THR* 4.1 1.1 - - - +
183A TYR* 2.9 54.8 + - + +
184A LYS* 3.8 4.9 - - - +
186A ARG* 1.3 76.5 - - - +
188A GLY* 1.3 61.6 + - - +
189A LEU* 3.9 20.4 - - + -
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Residues in contact with GLY 188 (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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184A LYS 3.1 1.9 + - - -
185A GLU* 3.0 18.8 + - - -
186A ARG 3.1 1.4 + - - -
187A LEU* 1.3 79.1 - - - +
189A LEU* 1.3 65.1 + - - +
190A PRO* 3.5 5.5 - - - +
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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
------------------------------------------------------------
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