Contacts of the helix formed by residues 174 - 187 (chain A) in PDB entry 2VRB
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 THR 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A THR* 4.1 14.8 - - + +
145A ASP* 3.3 13.9 - - - +
173A VAL* 1.3 77.9 - - - +
175A ARG* 1.3 65.8 + - - +
176A ASN* 3.1 9.4 + - - +
177A GLU* 3.1 37.2 + - - +
178A LEU* 3.0 21.4 + - - +
275A THR* 4.5 8.5 + - + +
280A THR* 3.7 28.7 - - + +
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Residues in contact with ARG 175 (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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11A GLN* 3.4 47.9 + - - +
12A LEU* 3.5 15.4 - - + +
15A LEU* 3.9 13.0 - - + -
143A TYR* 3.6 45.9 - - + +
145A ASP* 2.9 46.7 + - - +
146A PHE* 5.7 1.4 - - - +
173A VAL 3.8 1.4 + - - -
174A THR* 1.3 69.9 - - - +
176A ASN* 1.3 57.1 + - - +
178A LEU* 3.2 3.7 + - - -
179A ALA* 2.8 30.8 + - - +
1286A NAP 2.8 29.3 + - - -
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Residues in contact with ASN 176 (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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15A LEU* 3.7 27.8 - - + +
19A HIS* 2.7 33.3 + - - -
145A ASP* 5.3 0.4 + - - -
174A THR* 3.0 9.3 + - - +
175A ARG* 1.3 77.3 - - - +
177A GLU* 1.3 68.7 + - - +
179A ALA* 3.4 1.7 + - - +
180A LEU* 3.0 24.4 + - - +
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Residues in contact with GLU 177 (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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173A VAL* 3.9 8.3 - - + +
174A THR* 3.1 34.4 + - - +
176A ASN* 1.3 81.6 - - - +
178A LEU* 1.3 63.2 + - - +
180A LEU* 3.4 8.3 + - + +
181A ALA* 3.0 23.2 + - - +
267A LEU* 4.1 8.7 - - + +
271A ILE* 3.6 24.7 - - + +
273A SER 4.1 2.4 - - - +
274A LEU* 3.0 22.2 - - - +
275A THR* 2.6 46.2 + - - +
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Residues in contact with LEU 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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12A LEU* 4.2 6.9 - - + +
140A ASN* 3.4 42.1 + - + +
141A ALA 3.9 4.5 - - - +
143A TYR* 3.5 36.8 - - + -
173A VAL* 3.4 35.4 - - + +
174A THR 3.0 11.1 + - - +
175A ARG 3.6 6.3 - - - +
177A GLU* 1.3 79.2 - - - +
179A ALA* 1.3 56.4 + - - +
181A ALA* 3.4 5.3 + - - +
182A ALA* 3.1 26.2 + - - +
198A LEU* 3.7 25.6 - - + +
267A LEU* 4.8 3.8 - - + -
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Residues in contact with ALA 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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12A LEU* 3.8 7.3 - - + +
15A LEU* 3.5 31.4 - - + -
16A VAL* 3.6 26.9 - - + +
19A HIS* 3.9 4.5 - - + -
175A ARG 2.8 17.8 + - - +
176A ASN 3.6 5.4 - - - +
178A LEU* 1.3 73.2 - - - +
180A LEU* 1.3 59.3 + - - +
182A ALA* 3.4 2.6 + - - +
183A ALA* 3.0 28.4 + - - +
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Residues in contact with LEU 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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19A HIS* 3.7 33.5 - - + +
23A LYS* 3.5 27.6 - - - +
176A ASN* 3.0 16.5 + - - +
177A GLU* 3.6 10.3 - - + +
179A ALA* 1.3 76.3 - - - +
181A ALA* 1.3 50.6 + - - +
183A ALA* 3.3 1.4 + - - +
184A THR* 2.5 42.0 + - - +
271A ILE* 3.8 34.3 - - + +
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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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138A LEU* 4.8 1.3 - - - -
177A GLU 3.0 14.3 + - - +
178A LEU* 3.5 11.0 - - - +
179A ALA 3.3 0.2 - - - -
180A LEU* 1.3 72.8 - - - +
182A ALA* 1.3 65.0 + - - +
184A THR* 3.4 2.6 + - - -
185A VAL* 3.0 30.1 + - - +
198A LEU* 4.2 12.8 - - + -
267A LEU* 3.7 22.2 - - + -
270A LEU* 3.9 16.1 - - + +
271A ILE* 3.7 9.5 - - + +
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Residues in contact with ALA 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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12A LEU* 6.2 1.3 - - + -
16A VAL* 4.1 7.2 - - + -
71A LEU* 4.0 22.2 - - + -
105A THR* 5.6 3.4 - - + -
138A LEU* 3.7 29.5 - - + +
178A LEU 3.1 13.9 + - - +
179A ALA 3.7 7.4 - - - +
180A LEU 3.4 0.2 - - - -
181A ALA* 1.3 76.0 - - - +
183A ALA* 1.3 63.8 + - - +
185A VAL* 3.2 4.0 + - - +
186A LEU* 3.0 29.7 + - - +
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Residues in contact with ALA 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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16A VAL* 4.2 5.3 - - + +
19A HIS* 3.6 27.8 - - + -
20A LEU* 3.9 26.2 - - + +
23A LYS* 4.5 6.7 - - + +
179A ALA 3.0 17.4 + - - +
180A LEU 3.6 2.9 - - - +
182A ALA* 1.3 75.5 - - - +
184A THR* 1.3 61.7 + - - +
186A LEU* 3.4 3.1 + - - +
187A THR* 2.8 32.2 + - - +
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Residues in contact with THR 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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23A LYS* 3.6 17.6 + - - +
180A LEU* 2.5 36.6 + - - +
181A ALA* 3.6 8.0 - - - -
182A ALA 3.3 0.2 - - - -
183A ALA* 1.3 73.6 - - - +
185A VAL* 1.3 62.2 + - - +
187A THR* 3.2 13.7 + - - -
188A GLU* 3.0 48.5 + - - +
270A LEU* 4.0 26.4 + - + +
271A ILE* 4.3 3.8 - - - +
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Residues in contact with VAL 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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69A LYS* 5.3 3.3 + - - -
103A ALA* 5.1 8.1 - - + -
136A THR* 3.7 29.8 - - + +
138A LEU* 4.1 15.5 - - + -
181A ALA 3.0 20.2 + - - +
182A ALA 3.6 4.0 - - - +
184A THR* 1.3 77.5 - - - +
186A LEU* 1.3 63.0 + - + +
188A GLU 3.3 16.3 - - - +
191A HIS* 3.8 28.2 - - + +
196A TYR* 4.4 5.2 - - + -
270A LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 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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3A ILE* 3.9 34.4 - - + +
5A VAL* 5.0 0.4 - - + -
16A VAL* 4.5 6.1 - - + -
20A LEU* 4.3 12.8 - - + -
69A LYS* 3.3 45.5 - - + +
70A LEU 4.6 4.3 - - - +
71A LEU* 3.8 37.0 - - + +
103A ALA* 4.2 23.8 - - + +
182A ALA 3.0 22.7 + - - +
183A ALA 3.9 4.7 - - - +
184A THR 3.3 0.2 - - - -
185A VAL* 1.3 77.2 - - + +
187A THR* 1.3 59.9 + - - +
188A GLU 3.6 0.7 - - - -
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Residues in contact with THR 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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3A ILE* 4.2 5.4 - - + -
20A LEU* 3.6 21.8 - - + -
23A LYS* 3.5 26.8 - - + +
24A VAL* 4.1 23.1 - - + -
183A ALA 2.8 23.3 + - - +
184A THR* 3.2 6.3 + - - -
186A LEU* 1.3 82.7 - - - +
188A GLU* 1.3 59.6 + - - +
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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