Contacts of the helix formed by residues 174 - 185 (chain B) in PDB entry 4O8M
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 SER 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ASP* 3.7 11.8 + - - -
93B GLY* 3.6 11.8 - - - -
94B ALA* 4.1 7.6 - - - +
172B GLN* 3.0 24.5 + - - +
173B HIS* 1.3 76.5 - - - +
175B ARG* 1.3 62.9 + - - +
176B LEU* 3.2 8.5 + - - +
177B PHE* 3.2 23.9 + - - +
178B LEU* 2.9 26.7 + - - +
190B PRO* 5.8 0.2 - - - +
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Residues in contact with ARG 175 (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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93B GLY 4.0 4.2 + - - -
96B MET* 4.2 15.0 - - + -
97B ASP* 4.4 15.1 + - - +
174B SER* 1.3 72.7 + - - +
176B LEU* 1.3 65.1 + - - +
178B LEU* 4.4 7.6 - - - -
179B GLN* 3.1 54.1 + - + +
309B GLY 3.5 9.6 + - - -
310B PHE* 4.0 11.1 - - + +
311B PRO* 3.4 22.0 - - - +
312B GLU* 2.6 41.3 + - - +
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Residues in contact with LEU 176 (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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91B ASP* 6.1 0.2 - - - +
93B GLY* 3.9 17.3 - - - +
96B MET* 3.8 7.3 - - - -
103B GLY 3.4 25.6 - - - +
106B ASN* 3.5 30.3 - - + +
107B ALA* 3.9 15.9 - - + -
108B PRO* 4.4 1.1 - - + -
174B SER* 3.2 7.7 + - - +
175B ARG* 1.3 80.2 - - - +
177B PHE* 1.3 75.6 + - + +
179B GLN* 3.8 1.9 - - - +
180B THR* 2.8 37.3 + - - +
310B PHE* 3.8 28.4 - - + -
313B TRP* 4.2 8.7 - - + -
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Residues in contact with PHE 177 (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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91B ASP* 4.4 6.1 - - - -
106B ASN* 4.2 2.9 - - + -
108B PRO* 6.3 0.4 - - + -
150B ARG* 3.6 30.7 - - - -
171B VAL* 4.0 19.3 - - + -
172B GLN* 3.6 36.1 - - + -
174B SER* 3.2 14.4 + - - +
176B LEU* 1.3 101.4 - - + +
178B LEU* 1.3 68.2 + - - +
180B THR* 3.8 10.0 - - + -
181B ILE* 3.0 29.1 + - + +
209B GLU* 4.3 15.3 - - - +
232B HIS* 5.3 2.0 - + - -
233B THR* 3.7 22.7 - - + -
235B HIS* 3.7 19.1 - + - -
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Residues in contact with LEU 178 (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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171B VAL* 4.0 14.8 - - + +
174B SER 2.9 18.8 + - - +
175B ARG* 3.9 7.4 - - - +
177B PHE* 1.3 76.9 - - - +
179B GLN* 1.3 82.2 + - - +
181B ILE 3.4 0.2 + - - -
182B ASN* 3.0 28.7 + - + +
188B PRO* 3.5 27.7 - - + +
190B PRO* 4.2 22.4 - - + -
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Residues in contact with GLN 179 (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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175B ARG* 3.1 45.8 + - + +
178B LEU* 1.3 104.0 - - - +
180B THR* 1.3 61.2 + - - +
182B ASN* 3.7 13.9 + - - +
183B ALA* 3.0 29.1 + - - +
305B VAL* 3.9 15.6 - - + +
309B GLY* 4.5 7.5 - - - +
310B PHE* 3.5 29.6 - - + -
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Residues in contact with THR 180 (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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108B PRO* 3.5 44.4 - - + +
176B LEU* 2.8 25.9 + - - +
177B PHE* 3.8 12.6 - - + -
178B LEU 3.3 0.2 - - - -
179B GLN* 1.3 78.1 - - - +
181B ILE* 1.3 58.8 + - + +
183B ALA* 3.1 6.6 + - - +
184B MET* 3.0 45.5 + - - +
232B HIS* 5.0 10.8 - - + -
233B THR* 5.9 0.2 - - - +
302B VAL* 4.3 5.1 - - + +
305B VAL* 5.0 3.2 - - - +
310B PHE* 4.9 2.1 - - - -
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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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152B LEU* 4.3 9.4 - - + -
164B LEU* 5.0 2.9 - - + +
169B VAL* 3.8 37.2 - - + -
171B VAL* 3.4 24.7 - - + -
177B PHE* 3.0 13.6 + - + +
178B LEU 3.9 2.5 - - - +
180B THR* 1.3 74.6 - - + +
182B ASN* 1.3 67.7 + - - +
184B MET* 3.4 22.7 + - + +
185B GLY 3.2 5.2 + - - -
186B GLY* 3.0 29.7 + - - -
188B PRO* 3.9 23.8 - - + -
209B GLU* 4.3 16.4 - - + -
232B HIS* 5.3 3.1 - - - +
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Residues in contact with ASN 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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178B LEU* 3.0 22.2 + - + +
179B GLN* 3.7 17.4 + - - +
181B ILE* 1.3 78.9 - - - +
183B ALA* 1.3 62.1 - - - +
185B GLY* 3.3 12.6 + - - -
186B GLY 3.7 16.5 - - - +
188B PRO* 4.1 13.1 - - + +
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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 GLN 3.0 17.7 + - - +
180B THR 3.1 4.9 + - - +
182B ASN* 1.3 81.8 - - - +
184B MET* 1.3 59.9 + - - +
185B GLY* 3.3 2.1 + - - -
301B SER* 3.4 29.6 - - - +
302B VAL* 4.1 3.6 - - + -
305B VAL* 3.7 30.3 - - + +
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Residues in contact with MET 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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109B TYR* 4.7 2.5 - - - +
152B LEU* 4.4 11.2 - - + -
161B PRO* 3.2 32.7 - - - +
164B LEU* 3.7 13.1 - - + +
180B THR* 3.0 34.6 + - - +
181B ILE* 3.8 19.3 - - + +
182B ASN 3.3 0.4 - - - -
183B ALA* 1.3 75.5 - - - +
185B GLY* 1.3 57.4 + - - +
186B GLY 3.8 0.2 - - - -
230B THR* 3.9 23.1 - - + +
232B HIS* 4.2 19.7 - - + +
298B PHE* 3.3 34.5 - - + +
301B SER* 3.4 17.5 - - - +
302B VAL* 4.1 9.9 - - + -
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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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161B PRO* 4.3 4.9 - - - +
164B LEU* 3.2 25.7 - - - +
165B LYS* 3.7 6.9 + - - -
166B GLY 4.5 1.0 + - - -
181B ILE 3.2 2.0 + - - -
182B ASN 3.3 6.9 + - - -
183B ALA 3.1 4.3 - - - -
184B MET* 1.3 79.4 - - - +
186B GLY* 1.3 62.6 + - - +
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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