Contacts of the helix formed by residues 182 - 188 (chain Q) in PDB entry 2JA7
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1340M GLY* 3.3 10.7 - - - -
1341M ILE* 3.0 38.1 + - - +
153Q HIS* 5.8 0.2 + - - -
178Q ILE* 3.4 24.3 - - + +
179Q GLN* 2.6 39.2 + - + +
181Q ALA* 1.3 71.8 - - - +
183Q PRO* 1.3 83.9 - - - +
184Q VAL* 3.3 13.0 + - - +
185Q ALA* 2.8 24.7 + - + +
186Q LEU* 3.1 9.4 + - - +
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Residues in contact with PRO 183 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336M MET 4.3 5.2 - - - +
1337M GLU* 3.5 19.7 - - - +
1338M VAL 3.1 32.1 - - - +
1339M LEU 4.0 0.2 - - - -
1340M GLY* 3.8 12.8 - - - +
144Q ILE* 3.3 22.1 - - + +
181Q ALA 3.3 6.2 - - - +
182Q ASP* 1.3 93.5 - - - +
184Q VAL* 1.3 55.7 + - - +
186Q LEU* 3.4 10.5 + - + +
187Q TYR* 3.1 20.3 + - - +
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Residues in contact with VAL 184 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339M LEU 3.7 22.4 - - - +
1340M GLY* 4.3 3.4 - - - -
144Q ILE* 4.2 7.9 - - + -
145Q THR* 4.7 13.9 - - + -
150Q VAL* 4.0 17.9 - - + -
153Q HIS* 3.8 44.4 - - + +
178Q ILE* 5.0 1.3 - - + -
182Q ASP* 3.3 9.7 + - - +
183Q PRO* 1.3 70.6 - - - +
185Q ALA* 1.3 64.5 + - - +
186Q LEU 3.0 2.8 + - - -
187Q TYR* 3.7 6.0 - - + +
188Q LEU* 3.2 30.9 + - + +
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Residues in contact with ALA 185 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Q ILE* 4.0 7.4 - - + +
179Q GLN 3.2 23.6 - - - +
180Q ARG* 4.5 6.1 - - - +
182Q ASP* 2.8 18.8 + - + +
184Q VAL* 1.3 79.7 - - - +
186Q LEU* 1.3 59.2 + - - +
189Q GLY* 2.8 4.4 + - - -
190Q LEU* 2.7 59.6 + - + +
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Residues in contact with LEU 186 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q ARG* 3.4 11.4 + - - -
133Q GLU* 3.9 5.6 - - - +
135Q PHE* 3.9 20.9 - - + -
180Q ARG 3.4 23.8 - - - +
181Q ALA* 3.8 21.1 - - + +
182Q ASP 3.1 10.7 + - - +
183Q PRO* 3.6 10.1 - - + +
184Q VAL 3.0 0.2 - - - -
185Q ALA* 1.3 79.1 - - - +
187Q TYR* 1.3 60.5 + - - +
188Q LEU 2.9 2.0 - - - -
189Q GLY* 2.5 25.2 + - - +
190Q LEU 5.8 0.2 - - - +
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Residues in contact with TYR 187 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q THR* 4.5 7.0 - - + -
21Q GLU 3.7 0.9 - - - -
22Q MET* 2.9 72.0 + - + +
25Q ASP* 2.9 37.7 + - + -
26Q ARG* 3.5 5.9 + - - +
135Q PHE* 4.8 2.9 - + - -
140Q LEU* 6.1 1.8 - - + -
143Q ASN* 2.7 45.5 + - - -
144Q ILE* 5.0 5.6 - - + -
145Q THR* 3.3 25.4 + - + -
183Q PRO 3.1 12.7 + - - +
184Q VAL* 3.7 13.2 - - + +
186Q LEU* 1.3 77.3 - - - +
188Q LEU* 1.3 72.4 + - + +
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Residues in contact with LEU 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q ASP* 4.8 20.4 - - + +
26Q ARG* 3.7 25.3 + - - +
153Q HIS* 4.0 35.2 - - + +
154Q ILE* 4.7 3.8 - - - +
155Q ARG* 4.4 26.3 + - + +
184Q VAL* 3.2 20.0 + - + +
186Q LEU 2.9 0.8 - - - -
187Q TYR* 1.3 100.2 - - + +
189Q GLY* 1.3 67.1 + - - +
190Q LEU* 4.0 20.6 - - + -
196Q VAL* 4.8 3.1 - - + -
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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