Contacts of the helix formed by residues 177 - 190 (chain A) in PDB entry 2VLA
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 PRO 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A TYR* 3.5 25.5 - - + +
143A GLN* 3.6 34.3 - - + +
144A VAL* 3.9 24.0 - - + +
147A THR* 4.1 9.9 - - - +
176A LYS* 1.3 83.7 - - + +
178A ILE* 1.3 62.1 + - - +
180A VAL* 3.0 14.5 + - + +
181A ILE* 3.1 15.4 + - - +
247A TRP* 3.5 27.8 - - + -
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Residues in contact with ILE 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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147A THR* 3.7 26.3 + - + +
151A ASN* 3.7 20.9 - - - +
176A LYS* 3.1 19.9 + - + -
177A PRO* 1.3 78.3 - - - +
179A GLU* 1.3 65.1 + - + +
181A ILE* 3.3 3.3 + - + -
182A GLU* 2.9 57.1 + - + +
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Residues in contact with GLU 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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1A MET* 2.8 41.8 + - - -
2A ASN 4.2 0.3 + - - -
3A TYR* 3.6 20.5 + - + +
174A LYS 4.3 0.9 - - - +
175A ILE* 3.7 13.9 - - + +
176A LYS* 2.8 44.9 + - + +
178A ILE* 1.3 82.8 - - + +
180A VAL* 1.3 60.1 + - - +
182A GLU* 4.0 11.8 - - - +
183A LYS* 3.1 24.9 + - - +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.8 16.8 - - + -
140A TYR* 3.7 27.1 - - + +
144A VAL* 4.6 9.6 - - + -
163A TYR* 3.9 27.4 - - + +
164A VAL* 4.1 13.0 - - + -
170A VAL* 4.1 8.3 - - + -
175A ILE* 3.9 14.1 - - + -
176A LYS 4.0 1.6 - - - +
177A PRO* 3.0 9.3 + - + +
179A GLU* 1.3 75.8 - - - +
181A ILE* 1.3 65.3 + - + +
183A LYS* 3.2 4.0 + - - +
184A ILE* 3.0 33.4 + - + +
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Residues in contact with ILE 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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144A VAL* 3.8 30.5 - - + +
147A THR* 3.7 21.3 - - + +
148A ALA* 3.8 18.4 - - + +
151A ASN* 4.1 25.1 - - + +
153A ILE* 4.2 8.7 - - + -
155A LEU* 4.2 13.7 - - + -
177A PRO 3.1 13.0 + - - +
178A ILE* 3.8 9.0 - - + +
179A GLU 3.3 0.2 - - - -
180A VAL* 1.3 76.7 - - - +
182A GLU* 1.3 63.8 + - + +
184A ILE* 3.2 7.5 + - + +
185A ILE* 3.0 40.7 + - + +
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Residues in contact with GLU 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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178A ILE* 2.9 45.2 + - + +
179A GLU* 4.0 12.3 - - - +
181A ILE* 1.3 76.3 - - + +
183A LYS* 1.3 58.0 + - - +
185A ILE* 3.3 10.6 + - + +
186A GLU* 3.0 29.0 + - - +
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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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3A TYR* 3.6 31.2 - - + +
5A PRO* 4.0 21.1 - - + -
163A TYR* 4.0 10.3 - - + -
179A GLU 3.1 18.4 + - - +
180A VAL 3.2 4.2 + - - +
182A GLU* 1.3 74.5 - - - +
184A ILE* 1.3 60.4 + - - +
186A GLU* 3.3 22.8 + - - +
187A ASP* 2.8 58.5 + - - +
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Residues in contact with ILE 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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153A ILE* 4.3 8.5 - - + -
155A LEU* 3.8 24.9 - - + -
159A ASP* 4.3 12.3 - - + +
163A TYR* 3.7 40.2 - - + +
164A VAL* 6.1 0.4 - - + -
180A VAL* 3.0 35.3 + - + +
181A ILE* 3.7 7.6 - - + +
183A LYS* 1.3 74.9 - - - +
185A ILE* 1.3 58.7 + - - +
187A ASP* 3.3 5.8 + - - +
188A ARG* 2.9 64.4 + - + +
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Residues in contact with ILE 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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151A ASN* 4.6 13.7 - - + +
153A ILE* 3.9 31.6 - - + -
181A ILE* 3.0 36.5 + - + +
182A GLU* 3.6 9.6 - - + +
184A ILE* 1.3 76.9 - - - +
186A GLU* 1.3 62.6 + - - +
188A ARG* 3.8 7.9 - - - +
189A SER* 3.0 24.3 + - - -
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Residues in contact with GLU 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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182A GLU 3.0 16.5 + - - +
183A LYS* 3.7 27.6 + - - +
185A ILE* 1.3 78.1 - - - +
187A ASP* 1.3 63.6 + - - +
189A SER* 2.6 26.7 + - - +
190A ASN* 3.2 26.1 + - - +
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Residues in contact with ASP 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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5A PRO* 5.3 0.2 - - - +
162A TYR* 5.6 0.2 - - - -
163A TYR* 2.6 37.5 + - - +
183A LYS* 2.8 48.2 + - - +
184A ILE 3.7 3.1 - - - +
186A GLU* 1.3 80.1 - - - +
188A ARG* 1.3 61.0 + - + +
190A ASN* 3.0 8.8 + - - -
192A ILE* 2.8 61.4 + - + +
194A LYS* 4.7 4.7 - - - +
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Residues in contact with ARG 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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153A ILE* 3.9 24.0 - - - +
154A GLN 2.8 27.7 + - - +
155A LEU* 3.9 6.1 - - - +
156A SER 4.6 0.8 - - - +
159A ASP* 2.8 31.3 + - - -
184A ILE* 2.9 36.4 + - + +
185A ILE* 3.8 7.0 - - - +
187A ASP* 1.3 76.7 - - + +
189A SER* 1.3 58.0 + - - +
190A ASN 3.1 0.2 - - - -
191A ASP* 3.0 24.2 + - - +
192A ILE 4.1 10.3 - - - +
229A LEU* 6.0 0.2 - - - +
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Residues in contact with SER 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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185A ILE* 3.0 15.9 + - - -
186A GLU* 2.6 24.9 + - - +
188A ARG* 1.3 76.2 - - - +
190A ASN* 1.3 65.8 + - - +
191A ASP* 3.3 6.3 + - - +
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Residues in contact with ASN 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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186A GLU* 3.2 33.3 + - - +
187A ASP* 3.0 8.4 + - - +
189A SER* 1.3 84.2 + - - +
191A ASP* 1.3 74.0 + - - +
192A ILE* 3.2 24.4 + - + +
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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