Contacts of the helix formed by residues 182 - 188 (chain A) in PDB entry 6XYU
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A CYS* 4.4 9.7 - - + +
67A VAL 3.8 16.1 - - - +
68A GLN* 4.0 14.1 - - - +
148A TYR* 4.2 3.8 - - - +
152A PHE* 3.5 14.8 - - - +
153A MET 3.6 21.8 - - - +
154A THR 3.7 18.6 - - - +
155A GLY 5.0 0.2 - - - +
180A TYR* 3.6 35.4 - - + +
181A ARG* 1.3 72.6 - - - +
183A GLY* 1.3 70.3 + - - +
185A PHE* 3.5 16.7 - - - +
186A GLY 3.4 6.6 + - - -
187A PHE* 4.3 1.3 - - - -
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Residues in contact with GLY 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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152A PHE 2.5 18.3 + - - -
153A MET* 3.7 9.8 - - - +
182A VAL* 1.3 74.2 - - - +
184A ALA* 1.3 58.6 + - - -
185A PHE* 4.9 0.4 - - - -
186A GLY 2.9 3.5 + - - -
187A PHE* 2.8 29.0 + - - +
320A GLN* 3.2 15.0 - - - -
332A SER* 3.2 16.8 - - - -
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Residues in contact with ALA 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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44A PHE* 3.5 6.0 - - + -
183A GLY* 1.3 71.7 - - - -
185A PHE* 1.3 61.2 + - - +
187A PHE 4.6 0.4 - - - -
188A LEU* 2.9 39.3 + - + +
286A LEU* 3.5 32.8 - - + -
316A ILE* 3.8 13.5 - - + -
320A GLN* 2.5 24.1 + - + +
332A SER* 3.6 5.0 + - - +
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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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43A ARG* 4.6 6.1 - - + -
44A PHE* 4.1 15.7 + + - +
67A VAL* 3.5 37.0 - - + +
91A GLU* 3.4 32.5 - - + -
181A ARG* 3.6 28.1 + - + -
182A VAL 3.5 14.8 - - - +
183A GLY* 3.1 1.1 - - - -
184A ALA* 1.3 80.6 - - - +
186A GLY* 1.3 56.9 + - - +
188A LEU 5.1 0.3 + - - -
206A VAL* 3.4 15.4 - - - +
313A ALA* 3.4 37.7 - - + -
316A ILE* 3.6 28.9 - - + -
317A SER* 4.2 8.5 - - - -
320A GLN* 4.8 5.6 - - - -
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Residues in contact with GLY 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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181A ARG* 3.5 30.7 - - - +
182A VAL 3.4 3.6 + - - -
183A GLY 2.9 6.4 + - - -
185A PHE* 1.3 79.4 - - - +
187A PHE* 1.3 66.3 + - - +
188A LEU 3.9 0.4 - - - -
205A ASN 3.5 0.2 - - - -
206A VAL* 2.8 35.7 + - - -
207A GLY 3.0 4.7 + - - -
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Residues in contact with PHE 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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152A PHE* 3.6 38.8 - + + -
180A TYR* 5.0 3.1 - + - -
181A ARG 3.7 18.2 - - - -
182A VAL* 4.3 0.9 - - - -
183A GLY 2.8 17.1 + - - +
184A ALA* 4.6 0.9 - - - -
186A GLY* 1.3 85.1 - - - +
188A LEU* 1.3 69.1 + - - +
189A HIS* 3.1 11.6 + - - +
204A GLY* 4.3 2.2 - - - -
205A ASN* 3.8 26.0 + - - +
207A GLY* 4.4 6.3 - - - -
208A LEU* 4.0 25.1 - - + -
279A ALA* 5.3 1.9 - - - +
331A PRO 5.7 0.7 - - - +
332A SER* 3.6 27.1 - - - -
333A ALA 3.6 17.5 - - - +
334A PRO 4.0 11.4 - - - -
335A THR* 4.8 4.9 + - - +
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Residues in contact with LEU 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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44A PHE* 3.5 51.7 - - + +
184A ALA* 2.9 24.1 + - + +
185A PHE 5.1 0.2 + - - -
186A GLY 3.9 0.4 - - - -
187A PHE* 1.3 75.8 - - - +
189A HIS* 1.3 59.5 + - - +
190A LEU* 3.7 28.5 - - + -
202A ALA* 3.6 9.8 - - + +
204A GLY* 3.3 17.2 + - - -
206A VAL* 5.8 0.3 - - - +
283A GLY* 3.5 33.2 - - - +
286A LEU* 4.0 17.3 - - + -
287A ILE* 5.0 1.6 - - + -
305A MET* 4.6 2.0 - - + -
308A MET* 4.8 5.2 - - + -
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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