Contacts of the helix formed by residues 179 - 191 (chain A) in PDB entry 2VMO
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A TYR* 2.9 29.7 + - + +
177A ILE* 4.0 2.6 + - + +
178A ILE* 1.3 68.8 - - - +
180A PHE* 1.3 62.9 + - - +
181A ALA* 3.2 13.7 + - - +
182A LYS* 3.1 46.2 + - - +
183A PHE* 3.2 25.4 + - - -
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Residues in contact with PHE 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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169A ALA* 4.6 5.8 - - + -
178A ILE* 3.3 33.7 + - + -
179A ASP* 1.3 70.6 + - - +
181A ALA* 1.3 59.5 + - - +
183A PHE* 3.4 5.4 + - - +
184A ARG* 3.0 30.0 + - - +
194A LEU* 4.1 2.1 - - + +
196A VAL* 3.4 43.7 - - + -
201A ILE* 4.2 10.3 - - + -
210A HIS* 3.4 23.8 - + - -
211A PRO* 3.3 31.1 - - + +
212A ASN 4.1 2.7 - - - -
213A PRO* 3.6 25.1 - - + -
216A TYR* 3.8 25.9 - + + +
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Residues in contact with ALA 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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179A ASP* 3.2 9.3 + - - +
180A PHE* 1.3 79.0 - - - +
182A LYS* 1.3 58.1 + - + +
184A ARG* 3.3 3.6 + - - +
185A GLU* 2.9 29.9 + - - +
216A TYR* 3.7 35.9 - - + +
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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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152A TYR* 3.7 42.2 - - + +
179A ASP* 3.1 37.0 + - - +
180A PHE 3.3 0.2 - - - -
181A ALA* 1.3 74.4 - - + +
183A PHE* 1.3 65.3 - - - +
185A GLU* 3.3 13.2 + - - +
186A ILE* 3.0 29.9 + - - +
701A MPD 4.2 23.4 + - + +
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Residues in contact with PHE 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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141A TYR* 3.4 46.2 - + - -
150A ILE* 4.2 8.3 - - + -
152A TYR* 3.5 20.2 - + - -
155A VAL* 3.7 27.1 - - + -
167A ILE* 3.9 20.0 - - + +
169A ALA* 3.7 20.6 - - + -
178A ILE* 3.7 22.0 - - + -
179A ASP 3.2 22.3 + - - -
180A PHE* 3.6 9.0 - - - +
181A ALA 3.3 0.2 - - - -
182A LYS* 1.3 78.7 - - - +
184A ARG* 1.3 57.0 + - - +
186A ILE* 3.3 6.7 + - - +
187A ALA* 2.9 28.4 + - - +
194A LEU* 3.9 17.3 - - + +
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Residues in contact with ARG 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 PHE 3.0 16.4 + - - +
181A ALA 3.7 4.3 - - - +
183A PHE* 1.3 73.2 - - - +
185A GLU* 1.3 55.7 + - - +
187A ALA* 3.3 6.0 + - - -
188A ASP* 2.8 67.9 + - - +
194A LEU* 3.7 7.7 - - + +
215A PRO 4.6 4.6 + - - -
216A TYR* 2.9 51.3 + - + +
217A ALA 4.4 2.6 - - - +
218A HIS* 3.5 40.0 + - - -
239A GLN* 4.7 7.1 - - - +
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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 ALA 2.9 12.8 + - - +
182A LYS* 3.3 16.8 + - - +
184A ARG* 1.3 76.3 - - - +
186A ILE* 1.3 57.4 + - - +
188A ASP* 3.4 9.1 + - - +
189A GLU* 3.0 27.0 + - - +
701A MPD 3.9 38.3 + - + +
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Residues in contact with ILE 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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152A TYR* 3.5 31.2 - - + +
155A VAL* 3.7 23.1 - - + +
156A ARG* 3.7 22.7 - - + +
159A ALA* 3.7 28.0 - - + -
167A ILE* 4.0 7.6 - - + -
182A LYS 3.0 23.8 + - - +
183A PHE* 3.7 4.3 - - - +
185A GLU* 1.3 73.7 - - - +
187A ALA* 1.3 64.8 + - - +
189A GLU* 3.1 19.1 + - - +
190A VAL* 3.2 13.9 + - + +
701A MPD 3.6 22.2 - - + -
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Residues in contact with ALA 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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167A ILE* 3.8 19.9 - - + +
183A PHE 2.9 17.1 + - - +
184A ARG* 3.5 13.0 - - - +
186A ILE* 1.3 75.7 - - - +
188A ASP* 1.3 57.3 + - - +
190A VAL* 3.3 2.5 + - - -
191A GLY* 2.9 10.2 + - - -
192A ALA* 2.9 45.1 + - - +
193A TYR 4.4 0.7 - - - +
194A LEU* 4.2 17.0 - - + -
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Residues in contact with ASP 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 ARG* 2.8 58.5 + - - +
185A GLU* 3.5 8.2 - - - +
186A ILE 3.2 0.2 - - - -
187A ALA* 1.3 73.3 - - - +
189A GLU* 1.3 63.3 + - - +
190A VAL 3.4 0.3 + - - -
191A GLY* 3.5 9.4 + - - -
192A ALA 5.2 0.7 - - - +
218A HIS* 5.0 2.8 - - - -
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Residues in contact with GLU 189 (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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156A ARG* 2.8 50.9 + - - +
160A ARG* 3.5 17.1 + - + +
163A ARG* 5.4 0.5 + - - -
185A GLU 3.0 14.2 + - - +
186A ILE* 3.1 13.8 + - - +
188A ASP* 1.3 77.4 - - - +
190A VAL* 1.3 63.0 + - + +
701A MPD 5.5 2.2 - - - +
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Residues in contact with VAL 190 (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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159A ALA* 3.7 43.1 - - + +
160A ARG* 3.8 22.0 - - + -
163A ARG* 2.9 40.7 + - - +
164A PRO* 4.7 9.3 - - + +
167A ILE* 4.2 1.3 - - + -
186A ILE* 3.2 15.9 + - + +
187A ALA* 3.7 8.3 - - - +
189A GLU* 1.3 80.7 - - + +
191A GLY* 1.3 60.5 + - - +
192A ALA* 3.8 18.1 - - + -
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Residues in contact with GLY 191 (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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163A ARG* 5.2 0.2 - - - -
164A PRO 5.0 1.7 - - - +
165A LYS* 4.7 3.1 - - - +
187A ALA 2.9 5.6 + - - -
188A ASP* 3.5 10.1 + - - -
189A GLU 3.5 0.4 + - - -
190A VAL* 1.3 80.0 - - - +
192A ALA* 1.3 60.6 + - - +
193A TYR* 5.8 1.0 - - - -
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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