Contacts of the helix formed by residues 158 - 164 (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 ASP 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A SER* 3.2 9.7 + - - +
157A LYS* 1.3 80.1 + - - +
159A ASP* 1.3 59.5 + - - +
161A ALA* 3.5 5.5 - - - +
162A TYR* 2.9 32.6 + - - +
194A LYS 3.6 18.1 - - - +
195A LYS* 3.2 42.0 + - + +
197A ARG* 4.6 7.8 + - - -
207A MET* 4.1 17.2 - - - +
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Residues in contact with ASP 159 (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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155A LEU* 3.6 12.0 - - + -
156A SER* 3.0 35.9 + - - +
158A ASP* 1.3 76.2 - - - +
160A ILE* 1.3 57.6 + - - +
163A TYR* 2.9 54.7 + - - +
164A VAL* 4.8 0.6 - - - +
184A ILE* 4.3 17.3 - - + +
188A ARG* 2.8 32.4 + - - -
193A THR* 5.4 3.1 + - - -
194A LYS 5.0 6.1 + - - +
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Residues in contact with ILE 160 (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 ILE* 4.5 13.0 - - + -
144A VAL* 5.6 2.0 - - + -
145A LEU* 4.2 14.4 - - + -
155A LEU* 4.4 17.9 - - + -
156A SER 3.1 9.4 + - - +
157A LYS* 3.8 6.3 - - - +
159A ASP* 1.3 75.8 - - - +
161A ALA* 1.3 59.3 + - - +
164A VAL* 3.2 21.8 + - + +
165A LEU* 2.8 45.0 + - + +
214A LEU* 4.2 19.7 - - + -
230A VAL* 3.6 44.0 - - + -
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Residues in contact with ALA 161 (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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157A LYS 2.9 17.7 + - - +
158A ASP* 3.5 7.9 - - - +
159A ASP 3.2 0.2 - - - -
160A ILE* 1.3 77.8 - - - +
162A TYR* 1.3 59.3 + - - +
165A LEU 4.4 0.7 - - - +
166A ASN* 2.8 34.5 + - - +
196A VAL* 3.6 10.3 - - + +
207A MET* 3.5 31.2 - - + -
210A ILE* 3.8 19.5 - - + +
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Residues in contact with TYR 162 (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* 3.7 30.8 - - + +
6A GLU* 3.7 28.1 + - - +
8A GLN* 3.0 49.1 + - + -
158A ASP 2.9 15.7 + - - +
161A ALA* 1.3 78.6 - - - +
163A TYR* 1.3 79.8 - + + +
164A VAL 3.7 0.2 + - - -
167A SER* 3.8 6.2 + - - -
194A LYS* 3.6 58.8 + - + -
195A LYS 3.7 20.0 - - - -
196A VAL* 3.6 9.6 - - + -
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Residues in contact with TYR 163 (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* 2.6 35.0 + + - +
5A PRO* 4.1 9.2 - - + -
159A ASP* 2.9 42.1 + - - +
162A TYR* 1.3 100.3 - + + +
164A VAL* 1.3 61.1 + - + +
167A SER* 3.4 4.1 - - - -
170A VAL* 3.3 15.2 - - - +
180A VAL* 3.9 15.1 - - + +
183A LYS* 4.0 16.2 - - + -
184A ILE* 3.7 32.2 - - + -
187A ASP* 2.6 40.7 + - - +
192A ILE 4.6 3.1 + - - -
193A THR* 5.4 0.3 - - - -
194A LYS* 3.6 20.4 + - + +
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Residues in contact with VAL 164 (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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137A GLN* 5.7 0.4 - - + +
140A TYR* 4.0 26.7 - - + -
141A ILE* 4.3 14.8 - - + -
144A VAL* 4.3 21.1 - - + -
155A LEU* 6.1 0.4 - - + -
159A ASP 4.8 0.2 - - - +
160A ILE* 3.2 21.8 + - + +
162A TYR 3.4 0.2 - - - -
163A TYR* 1.3 85.5 - - + +
165A LEU* 1.4 81.2 + - + +
166A ASN 3.3 1.6 - - - -
167A SER* 3.2 13.3 + - - +
170A VAL* 3.7 20.5 - - + +
171A LEU* 4.1 4.0 - - - +
180A VAL* 4.1 18.4 - - + -
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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