Contacts of the helix formed by residues 182 - 187 (chain E) in PDB entry 2NVX
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 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1340A GLY* 3.0 26.5 - - - -
1341A ILE* 3.2 35.5 + - - +
178E ILE* 3.4 17.3 - - + +
179E GLN* 3.2 33.3 + - + +
180E ARG 3.2 2.6 - - - -
181E ALA* 1.3 77.8 - - - +
183E PRO* 1.4 62.6 - - - +
184E VAL* 3.4 6.9 + - - +
185E ALA* 2.9 10.2 + - + -
186E LEU* 2.8 32.8 + - - +
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Residues in contact with PRO 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336A MET 4.3 3.1 - - - +
1337A GLU* 3.3 22.2 - - - +
1338A VAL 3.1 28.5 - - - +
1340A GLY* 3.3 18.6 - - - +
135E PHE* 5.8 0.5 - - - -
144E ILE* 3.4 18.3 - - + +
181E ALA 3.4 6.0 - - - +
182E ASP* 1.4 92.8 - - - +
184E VAL* 1.3 61.0 + - - +
186E LEU* 3.7 9.2 + - + +
187E TYR* 3.4 15.2 + - - +
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Residues in contact with VAL 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339A LEU 3.7 10.3 - - - +
1340A GLY* 3.7 24.2 - - - -
1341A ILE 5.0 0.2 - - - +
1342A GLU* 5.8 0.7 - - + +
144E ILE* 4.3 6.5 - - + -
145E THR* 4.2 16.8 - - + -
150E VAL* 3.9 7.2 - - + -
153E HIS* 3.4 56.1 - - + +
178E ILE* 5.1 2.2 - - + -
182E ASP* 3.3 4.1 + - - +
183E PRO* 1.3 71.8 - - - +
185E ALA* 1.3 61.6 + - - +
187E TYR* 3.0 25.8 + - + +
188E LEU* 3.4 13.1 + - + +
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Residues in contact with ALA 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E HIS* 6.4 0.2 - - - -
178E ILE* 3.8 14.5 - - + +
179E GLN 3.6 24.9 - - - +
180E ARG 4.7 5.3 - - - +
182E ASP* 2.9 13.5 + - + +
184E VAL* 1.3 79.2 - - - +
186E LEU* 1.3 56.9 + - - +
188E LEU* 5.3 0.2 - - - -
189E GLY 2.9 22.2 + - - -
190E LEU* 3.3 38.6 + - + +
214E CYS* 5.4 0.2 - - - -
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Residues in contact with LEU 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG* 3.5 3.1 + - - -
133E GLU* 3.4 21.7 - - + +
134E THR 6.0 2.0 - - - +
135E PHE* 3.0 37.1 - - + -
180E ARG 3.6 16.4 - - - +
181E ALA* 3.4 33.0 - - + +
182E ASP 2.8 15.4 + - - +
183E PRO* 3.9 8.3 - - + +
185E ALA* 1.3 75.5 - - - +
187E TYR* 1.3 58.5 + - - +
188E LEU 3.1 6.4 + - - -
189E GLY* 3.5 1.8 + - - +
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Residues in contact with TYR 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E THR* 4.3 5.2 - - + -
21E GLU* 3.4 18.4 + - - +
22E MET* 3.5 52.0 - - + +
25E ASP* 3.5 23.1 + - + -
26E ARG* 3.8 7.7 + - - +
135E PHE* 4.3 5.3 - + + -
140E LEU* 5.8 2.0 - - + -
143E ASN* 3.2 38.4 + - - -
144E ILE* 5.0 8.7 - - + -
145E THR* 3.6 24.5 + - + -
146E HIS* 5.8 0.3 - - - -
183E PRO 3.4 11.2 + - - +
184E VAL* 3.0 13.3 + - - +
186E LEU* 1.3 77.6 - - - +
188E LEU* 1.3 76.2 + - + +
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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