Contacts of the helix formed by residues 182 - 190 (chain B) in PDB entry 2QFI
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 PHE 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PHE* 4.3 8.0 - - - +
99B LEU 3.4 18.6 - - - +
100B THR* 3.2 38.4 - - + +
103B GLN* 6.5 0.4 - - - -
177B ARG 3.2 8.2 + - - +
178B ALA* 3.3 28.9 - - - +
179B ASP* 3.5 19.4 - - - -
181B LEU* 1.3 76.5 - - - +
183B ALA* 1.3 81.8 + - + +
184B LEU 3.1 2.0 + - - -
185B GLY* 3.6 9.2 + - - -
186B ILE* 3.7 26.1 + - + +
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Residues in contact with ALA 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 ASP* 5.1 5.6 - - - +
180B ALA 5.4 2.4 - - - +
181B LEU 4.7 0.8 - - - +
182B PHE* 1.3 95.2 - - + +
184B LEU* 1.3 67.5 + - - +
186B ILE* 2.8 29.1 + - + -
187B GLY* 3.2 12.3 + - - -
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Residues in contact with LEU 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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156B SER 5.3 0.9 - - - +
159B MET* 3.1 57.9 - - + +
161B ASN* 3.6 20.6 - - + +
180B ALA* 5.2 1.3 - - - +
181B LEU* 3.4 40.6 - - + +
182B PHE 4.1 0.6 - - - +
183B ALA* 1.3 75.7 - - - +
185B GLY* 1.3 63.6 + - - +
188B ILE* 2.9 30.3 - - + +
189B TYR* 4.6 3.6 - - + -
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Residues in contact with GLY 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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95B LEU* 4.5 11.0 - - - -
98B PHE 4.9 7.4 + - - -
181B LEU 4.5 1.0 + - - -
182B PHE 3.6 5.9 + - - -
183B ALA 3.2 0.4 - - - -
184B LEU* 1.3 77.5 - - - +
186B ILE* 1.3 68.3 + - - +
188B ILE 2.9 2.8 + - - -
189B TYR* 2.7 47.2 + - - +
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Residues in contact with ILE 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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95B LEU* 4.9 6.7 - - + +
98B PHE 5.4 0.8 + - - -
99B LEU* 3.4 35.6 - - + +
182B PHE* 3.7 32.4 + - + +
183B ALA* 2.8 25.5 + - + +
185B GLY* 1.3 72.3 - - - +
187B GLY* 1.3 74.0 + - - +
190B ILE* 3.2 42.4 + - + +
191B LEU 3.6 1.2 + - - -
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Residues in contact with GLY 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 ALA 3.2 6.3 + - - -
184B LEU 4.5 0.9 - - - -
186B ILE* 1.3 86.1 - - - +
188B ILE* 1.3 71.0 + - - +
189B TYR 3.8 0.4 - - - -
191B LEU* 4.3 21.4 - - - +
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Residues in contact with ILE 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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152B LEU* 5.3 12.2 - - + +
155B GLN 5.8 0.2 - - - +
156B SER* 3.3 23.9 + - - +
159B MET* 5.1 15.3 - - + -
184B LEU* 2.9 23.7 + - + +
185B GLY 2.9 2.4 + - - -
187B GLY* 1.3 86.4 - - - +
189B TYR* 1.3 73.4 + - + +
191B LEU 4.2 5.4 - - - +
192B TYR* 3.1 22.6 - - + +
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B SER* 3.4 19.7 - - - -
92B GLY* 3.2 34.4 - - - -
94B ALA* 4.8 5.8 - - + -
95B LEU* 3.3 34.5 - - + -
152B LEU 4.9 0.4 - - - -
153B HIS* 3.6 8.5 + + - -
156B SER* 2.8 51.7 + - - -
157B ASP* 4.5 0.9 - - - -
184B LEU* 4.5 3.8 - - + -
185B GLY* 2.7 24.7 + - - +
187B GLY 3.8 0.4 - - - -
188B ILE* 1.3 99.9 - - + +
190B ILE* 1.3 68.2 + - - +
192B TYR* 2.9 20.0 + + - +
193B SER 3.2 11.8 + - - -
194B ALA 3.3 1.6 + - - -
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Residues in contact with ILE 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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92B GLY 5.2 0.2 - - - +
95B LEU* 3.5 21.7 - - + +
96B PHE* 4.1 22.0 - - + -
99B LEU* 5.7 2.2 - - + -
186B ILE* 3.2 25.0 + - + +
189B TYR* 1.3 77.0 - - - +
191B LEU* 1.3 76.6 + - + +
192B TYR 2.8 6.8 + - - -
194B ALA* 3.0 38.2 - - + +
195B LEU* 4.3 0.2 - - - +
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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