Contacts of the helix formed by residues 180 - 190 (chain B) in PDB entry 7A62
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 VAL 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B SER 3.6 19.5 - - - +
177B ALA* 3.5 8.1 - - - +
178B ILE 3.0 1.2 - - - -
179B LYS* 1.3 84.6 - - + +
181B ILE* 1.3 57.5 + - - +
182B PRO* 3.3 1.3 - - - -
183B THR* 2.8 32.2 + - + +
184B VAL* 3.3 3.7 + - + +
199B ALA* 3.5 40.2 - - + +
202B GLU* 3.9 21.8 - - + -
203B ILE* 3.7 11.7 - - + -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY* 4.9 2.7 - - - +
177B ALA 4.0 7.4 - - - +
178B ILE* 3.1 23.3 + - + +
180B VAL* 1.3 76.0 - - - +
182B PRO* 1.3 67.6 - - + +
184B VAL* 3.0 19.9 + - - +
185B PHE* 3.4 36.4 + - + -
203B ILE* 4.6 1.6 - - + -
272B CYS* 3.7 28.9 - - - -
273B PHE* 4.2 4.7 - - + -
276B LEU* 4.0 28.5 - - + -
306B PHE* 4.4 8.7 - - + -
310B LEU* 4.1 17.5 - - + -
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Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY* 3.4 32.5 - - - +
12B SER* 5.8 1.1 - - - +
178B ILE 3.8 0.7 - - - +
179B LYS 3.6 12.3 - - - +
180B VAL 3.5 3.4 - - - -
181B ILE* 1.3 95.8 - - + +
183B THR* 1.3 61.5 + - - +
184B VAL 3.3 0.2 + - - -
185B PHE* 3.4 6.1 + - + +
186B LYS* 3.0 27.0 + - - +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LYS 4.6 2.9 + - - -
180B VAL* 2.8 29.1 + - + +
182B PRO* 1.3 74.2 - - - +
184B VAL* 1.3 56.4 + - - +
186B LYS* 4.0 5.7 - - - +
187B ALA* 2.9 28.8 + - - +
195B THR* 4.0 23.1 - - + +
199B ALA* 4.0 12.6 - - + -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL 3.9 8.5 - - - +
181B ILE* 3.0 11.1 + - - +
183B THR* 1.3 77.2 - - - +
185B PHE* 1.3 64.8 + - + +
187B ALA* 3.2 4.6 + - - +
188B MET* 3.1 27.3 + - - +
196B LEU* 3.8 20.4 - - + +
199B ALA* 3.9 21.3 - - + -
200B LEU* 4.5 10.1 - - + -
203B ILE* 4.0 22.0 - - + -
276B LEU* 4.8 7.9 - - + -
316B VAL* 3.7 33.0 - - + -
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ILE* 3.4 42.7 + - + -
182B PRO* 4.2 5.6 - - + +
184B VAL* 1.3 80.9 - - + +
186B LYS* 1.3 63.1 - - - +
188B MET* 3.2 16.3 + - + +
189B GLN* 3.1 24.4 + - - +
276B LEU* 3.7 21.5 - - + -
310B LEU* 3.7 26.0 - - + -
313B ASN* 3.4 43.3 - - + +
314B PRO* 3.6 19.5 - - + -
316B VAL* 4.1 10.8 - - + -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO 3.0 18.4 + - - +
183B THR* 4.0 5.4 - - - +
185B PHE* 1.3 77.7 - - - +
187B ALA* 1.3 57.7 + - - +
189B GLN* 3.1 9.0 + - + +
190B MET* 2.8 51.4 + - + +
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B THR 2.9 20.9 + - - +
184B VAL 3.5 4.9 - - - +
186B LYS* 1.3 76.7 - - - +
188B MET* 1.3 56.9 + - - +
190B MET* 3.2 2.3 + - - +
191B GLN 2.8 25.5 + - - -
192B GLU* 3.0 20.2 + - - +
195B THR* 3.9 13.0 - - + -
196B LEU* 3.8 35.2 - - + +
319B PHE* 5.1 0.2 - - - -
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Residues in contact with MET 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B VAL* 3.1 18.4 + - - +
185B PHE* 3.5 17.3 - - - +
186B LYS 3.2 0.2 - - - -
187B ALA* 1.3 75.1 - - - +
189B GLN* 1.3 62.4 + - + +
191B GLN* 3.1 15.6 + - - +
196B LEU* 4.3 10.1 - - + -
314B PRO* 4.1 27.4 - - + +
315B SER 3.7 21.3 - - - +
316B VAL* 3.7 26.9 - - - -
319B PHE* 3.6 58.0 - - + -
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B PHE 3.1 9.2 + - - +
186B LYS* 3.1 10.8 + - - +
188B MET* 1.3 80.8 - - + +
190B MET* 1.3 67.9 + - - +
191B GLN* 3.3 5.4 + - - +
314B PRO* 5.5 13.5 - - + +
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Residues in contact with MET 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LYS* 2.8 45.3 + - + +
187B ALA* 3.9 1.1 - - - +
189B GLN* 1.3 85.0 - - + +
191B GLN* 1.3 72.1 + - - +
192B GLU* 3.2 26.6 + - + +
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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