Contacts of the helix formed by residues 180 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A SER 3.7 17.5 - - - +
177A ALA* 3.0 9.3 + - - +
178A ILE 3.0 0.2 + - - -
179A LYS* 1.3 83.6 - - + +
181A ILE* 1.3 65.2 + - - +
182A PRO 3.3 1.1 - - - -
183A THR* 2.8 24.9 + - - -
184A VAL* 3.2 3.7 + - + +
199A ALA* 3.6 40.8 - - + +
202A GLU* 3.8 22.7 - - + -
203A ILE* 3.7 12.8 - - + -
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Residues in contact with ILE 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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177A ALA 4.0 7.4 - - - +
178A ILE* 2.9 25.2 + - - +
180A VAL* 1.3 76.0 - - - +
182A PRO* 1.3 67.1 - - + +
184A VAL* 3.0 19.2 + - - +
185A PHE* 3.3 35.8 + - + -
203A ILE* 4.6 2.9 - - + -
272A CYS* 3.7 29.6 - - - -
273A PHE* 4.3 7.9 - - + -
276A LEU* 4.0 24.7 - - + -
306A PHE* 4.4 15.0 - - + -
310A LEU* 4.1 13.9 - - + -
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Residues in contact with PRO 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 SER* 5.1 17.5 - - - +
178A ILE 3.8 5.2 - - - +
179A LYS* 3.7 13.2 - - - +
180A VAL 3.6 3.1 - - - -
181A ILE* 1.3 94.8 - - + +
183A THR* 1.3 61.6 + - - +
184A VAL 3.2 0.2 + - - -
185A PHE* 3.3 7.2 + - + +
186A LYS* 3.1 25.8 + - - +
306A PHE* 6.5 1.1 - - + -
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Residues in contact with THR 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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179A LYS 4.6 3.3 + - - -
180A VAL* 2.8 28.1 + - + -
182A PRO* 1.3 74.0 - - - +
184A VAL* 1.3 60.9 + - - +
186A LYS* 4.0 12.4 - - - +
187A ALA* 3.0 23.0 + - - +
195A THR* 4.0 24.1 - - + +
199A ALA* 4.3 10.1 - - + -
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Residues in contact with VAL 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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180A VAL 3.2 9.1 + - - +
181A ILE* 3.0 10.9 + - - +
183A THR* 1.3 76.7 - - - +
185A PHE* 1.3 66.1 + - + +
187A ALA* 3.1 8.7 + - - +
188A MET* 3.0 22.0 + - - +
196A LEU* 3.8 19.3 - - + +
199A ALA* 3.8 22.4 - - + -
200A LEU* 4.5 10.1 - - + -
203A ILE* 4.0 21.8 - - + -
276A LEU* 4.8 9.0 - - + -
316A VAL* 3.8 29.2 - - + -
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Residues in contact with PHE 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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181A ILE* 3.3 41.1 + - + -
182A PRO* 3.3 6.7 + - + +
184A VAL* 1.3 80.0 - - + +
186A LYS* 1.3 63.5 + - - +
188A MET* 3.2 26.3 + - + +
189A GLN* 3.0 22.3 + - - +
276A LEU* 3.9 20.2 - - + -
310A LEU* 3.8 18.8 - - + -
313A ASN* 3.5 46.7 - - + +
314A PRO* 3.5 16.8 - - + -
316A VAL* 4.2 9.9 - - + -
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Residues in contact with LYS 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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182A PRO 3.1 16.8 + - - +
183A THR* 4.2 12.3 - - - +
185A PHE* 1.3 76.3 - - - +
187A ALA* 1.3 53.0 + - - +
189A GLN* 3.0 16.3 + - - +
190A MET* 2.7 55.5 + - + +
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Residues in contact with ALA 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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183A THR 3.0 20.5 + - - +
184A VAL 3.1 6.0 + - - +
186A LYS* 1.3 76.7 - - - +
188A MET* 1.3 62.7 + - - +
190A MET* 3.3 1.3 + - - -
191A GLN* 2.9 18.7 + - - -
192A GLU* 3.0 22.6 + - - +
195A THR* 4.0 10.3 - - + -
196A LEU* 3.7 36.1 - - + +
319A PHE* 5.2 0.2 - - - -
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Residues in contact with MET 188 (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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184A VAL* 3.0 14.2 + - - +
185A PHE* 3.2 34.5 + - + +
187A ALA* 1.3 75.7 - - - +
189A GLN* 1.3 62.4 + - - +
191A GLN* 3.1 18.2 + - - +
196A LEU* 4.2 10.1 - - + -
314A PRO* 3.8 29.4 - - + +
315A SER 4.4 0.7 - - - +
316A VAL* 3.7 37.7 - - - -
319A PHE* 3.9 50.0 - - + -
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Residues in contact with GLN 189 (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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185A PHE 3.0 14.0 + - - +
186A LYS* 3.0 15.6 + - - +
188A MET* 1.3 76.6 - - - +
190A MET* 1.3 85.5 + - - +
191A GLN* 3.3 4.3 + - - +
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Residues in contact with MET 190 (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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186A LYS* 2.7 41.5 + - + +
187A ALA* 4.8 0.2 - - - -
189A GLN* 1.3 98.0 - - - +
191A GLN* 1.3 70.8 + - - +
192A GLU* 3.2 27.0 + - + +
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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