Contacts of the helix formed by residues 162 - 175 (chain F) in PDB entry 2VLR
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 162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158F ALA 2.9 14.1 + - - -
159F TYR 3.3 1.0 + - - -
161F GLU* 1.3 77.7 - - - +
163F THR* 1.3 64.7 + - - +
164F CYS 3.3 1.3 - - - -
165F VAL* 3.2 6.6 + - - +
166F GLU* 3.1 33.2 + - - +
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Residues in contact with THR 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F ALA 3.9 2.8 + - - -
159F TYR* 3.2 35.6 + - + +
162F GLY* 1.3 69.4 - - - -
164F CYS* 1.3 62.5 + - - +
166F GLU* 3.3 14.8 + - - +
167F TRP* 3.2 50.0 + - + +
2H ILE 6.0 0.4 - - - +
95I SER* 6.2 0.2 - - - -
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Residues in contact with CYS 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 3.8 22.8 - - - +
100F GLY* 3.9 8.3 - - - -
101F CYS* 2.1 55.3 - - - -
159F TYR* 2.9 39.0 + - + +
160F LEU* 3.5 11.9 - - - +
163F THR* 1.3 74.9 - - - +
165F VAL* 1.3 61.8 + - - +
167F TRP* 3.4 4.9 + - - +
168F LEU* 3.3 18.0 + - - +
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Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F CYS* 4.1 9.6 - - + -
103F VAL* 4.0 25.8 - - + -
107F TRP 4.3 3.6 - - - +
108F ARG* 5.4 0.2 - - - -
109F PHE* 3.8 33.2 - - + +
160F LEU 3.7 17.5 - - - +
161F GLU 4.0 7.2 - - - +
162F GLY 3.2 7.8 + - - +
164F CYS* 1.3 78.2 - - - +
166F GLU* 1.3 58.3 + - - +
168F LEU* 3.6 5.4 + - - +
169F ARG* 3.2 54.7 + - - +
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Residues in contact with GLU 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F GLY* 3.1 18.3 + - - +
163F THR* 3.6 16.6 + - - +
165F VAL* 1.3 75.8 - - - +
167F TRP* 1.3 63.6 + - - +
169F ARG* 3.6 28.6 + - - +
170F ARG* 3.3 22.0 + - - +
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Residues in contact with TRP 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 4.0 4.7 - - + -
55F GLU* 5.1 0.4 - - - -
59F TYR* 3.9 30.5 - + - -
63F GLU* 5.0 4.5 - - - -
66F LYS* 5.3 4.2 - - - +
159F TYR* 5.2 0.2 - + - -
163F THR* 3.2 46.1 + - + +
164F CYS* 3.4 8.5 + - - +
166F GLU* 1.3 75.3 - - + +
168F LEU* 1.3 56.9 + - - +
170F ARG* 3.4 32.2 + - - +
171F TYR* 3.1 56.4 + + + -
1H GLY* 3.4 43.9 + - - +
2H ILE 5.4 1.0 + - - -
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Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F HIS* 4.3 0.9 - - + +
4F SER* 3.5 33.0 - - - +
5F MET* 4.0 13.2 - - + +
28F VAL* 4.1 18.4 - - + -
101F CYS* 4.1 26.0 - - - +
103F VAL* 3.8 34.3 - - + -
164F CYS 3.3 9.8 + - - +
165F VAL 3.7 7.6 - - - +
166F GLU 3.4 0.2 - - - -
167F TRP* 1.3 75.6 - - - +
169F ARG* 1.3 60.1 + - + +
171F TYR* 3.5 7.0 + - - +
172F LEU* 3.0 49.2 + - + +
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Residues in contact with ARG 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL* 5.8 2.5 - - + -
107F TRP* 3.6 47.9 + - + +
108F ARG* 6.1 0.8 - - - +
165F VAL* 3.2 35.1 + - + +
166F GLU* 4.0 28.1 + - - +
167F TRP 3.5 0.2 - - - -
168F LEU* 1.3 75.5 - - + +
170F ARG* 1.3 60.3 + - - +
172F LEU* 3.6 10.0 + - + +
173F GLU* 3.2 31.3 + - - +
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Residues in contact with ARG 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F GLU* 2.7 44.4 + - - +
166F GLU 3.3 11.5 + - - +
167F TRP* 3.4 34.7 - - - +
169F ARG* 1.3 76.3 - - - +
171F TYR* 1.3 63.7 + - + +
173F GLU* 3.3 7.2 + - - +
174F ASN* 3.1 49.0 + - - +
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Residues in contact with TYR 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 3.6 30.3 - - - -
28F VAL* 4.1 18.4 - - + -
33F PHE* 3.8 14.4 - + - -
51F TRP* 3.7 28.8 - + + -
52F ILE* 3.5 18.2 - - + -
55F GLU* 4.0 15.7 - - - -
59F TYR* 3.0 19.6 + - - -
167F TRP* 3.1 37.6 + + + +
168F LEU* 3.9 4.3 - - - +
170F ARG* 1.3 83.0 - - + +
172F LEU* 1.3 57.5 + - - +
174F ASN* 4.5 4.7 - - - -
175F GLY 2.9 26.0 + - - -
179F LEU* 3.4 11.2 - - - +
1H GLY 2.8 23.6 + - - -
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F HIS* 3.9 44.2 - - + +
28F VAL* 4.2 20.0 - - + -
29F ASP* 4.6 0.4 - - - +
103F VAL* 5.0 2.7 - - + -
107F TRP* 3.8 39.0 - - + -
168F LEU* 3.0 38.9 + - + +
169F ARG* 3.8 6.7 - - + +
170F ARG 3.3 0.2 - - - -
171F TYR* 1.3 74.1 - - - +
173F GLU* 1.3 63.2 + - - +
175F GLY 4.1 0.5 - - - -
176F LYS* 3.5 9.9 + - - -
179F LEU* 4.3 16.6 - - + +
180F GLN* 2.8 27.7 + - + +
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Residues in contact with GLU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F TRP* 2.9 35.6 - - - -
169F ARG 3.2 13.0 + - - +
170F ARG* 3.4 9.4 - - - +
172F LEU* 1.3 74.4 - - - +
174F ASN* 1.3 69.5 + - - +
176F LYS* 3.0 23.9 + - - +
180F GLN* 4.0 4.2 + - - +
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Residues in contact with ASN 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F TRP* 4.0 15.3 + - + +
54F GLN* 3.8 39.7 + - - +
55F GLU* 4.0 19.6 + - - +
170F ARG* 3.1 35.1 + - - +
171F TYR* 4.0 6.7 - - - +
173F GLU* 1.3 80.4 - - - +
175F GLY* 1.3 58.1 + - - +
176F LYS* 3.6 1.9 + - - +
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Residues in contact with GLY 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F TRP* 3.8 26.6 - - - +
171F TYR 2.9 16.3 + - - -
172F LEU 4.1 3.6 - - - -
174F ASN* 1.3 73.8 - - - +
176F LYS* 1.3 55.0 + - - +
177F GLU 3.4 2.0 - - - -
178F THR* 2.9 7.6 + - - -
179F LEU* 2.8 38.2 + - - -
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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