Contacts of the helix formed by residues 177 - 182 (chain B) in PDB entry 3O9Z
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 GLY 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B LYS 5.1 2.5 - - - -
170B VAL* 6.0 1.3 - - - -
172B GLU* 3.8 19.7 - - - +
175B SER* 3.0 14.2 + - - -
176B GLY* 1.3 77.2 - - - +
178B LEU* 1.3 60.9 + - - -
179B ALA 3.3 3.6 - - - -
180B THR 3.0 2.8 + - - -
181B ASN* 2.8 29.4 + - - +
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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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164B TYR* 4.1 9.4 - - + +
169B LYS 5.3 1.0 + - - -
177B GLY* 1.3 71.2 - - - -
179B ALA* 1.3 59.0 + - - +
181B ASN* 4.5 2.9 - - - +
182B ILE* 2.9 53.5 + - + +
183B GLY 3.1 5.2 + - - -
206B THR 5.5 0.4 - - - +
207B PRO 4.0 11.2 - - - +
208B THR 3.8 30.3 - - - +
209B VAL 3.9 7.9 - - - +
210B ASN* 4.0 22.8 - - - +
225B LEU* 3.6 14.9 - - + +
227B ILE* 3.8 26.2 - - + +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY 5.9 0.4 - - - +
177B GLY 3.3 1.0 - - - -
178B LEU* 1.3 79.2 - - - +
180B THR* 1.3 57.7 + - - +
183B GLY* 3.1 23.8 - - - -
184B ILE* 3.2 0.9 + - - -
187B PHE* 3.5 24.3 - - + -
210B ASN* 3.5 23.3 - - + +
223B TRP* 5.2 1.1 - - + -
225B LEU* 3.8 12.3 - - + -
289B ALA* 4.3 4.2 - - - +
292B LEU* 4.2 22.0 - - + -
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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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102B PRO* 3.7 27.3 - - + +
104B VAL 5.5 0.7 - - - +
105B LEU* 3.9 1.6 - - + -
175B SER 3.5 13.0 - - - +
176B GLY 3.2 18.8 + - - -
177B GLY 3.0 2.7 + - - -
179B ALA* 1.3 79.1 - - - +
181B ASN* 1.3 69.3 + - - +
184B ILE* 3.1 29.7 + - + +
289B ALA* 3.4 20.9 + - + +
293B ARG* 2.9 33.1 + - - +
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Residues in contact with ASN 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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80B ASN* 2.8 29.3 + - - +
101B LYS* 2.8 30.9 + - - +
102B PRO* 5.0 0.7 - - - -
164B TYR* 3.0 29.6 + - - +
168B TRP* 3.7 7.7 - - - -
169B LYS* 3.8 18.7 - - - +
175B SER* 3.8 19.1 - - - +
177B GLY 2.8 20.9 + - - +
178B LEU* 4.5 0.7 - - - +
180B THR* 1.3 75.0 - - - +
182B ILE* 1.3 64.2 + - - +
311B NAD 3.6 11.8 + - - -
312B AKG 3.9 7.2 + - - +
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Residues in contact with ILE 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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156B TYR* 3.9 11.2 - - + -
158B THR* 3.6 23.8 - - + -
160B ARG* 3.8 14.1 - - - +
164B TYR* 3.5 29.2 - - + +
178B LEU* 2.9 21.4 + - + +
181B ASN* 1.3 81.5 - - - +
183B GLY* 1.3 67.9 + - - +
184B ILE 3.2 3.5 + - - -
185B HIS* 3.4 21.5 + - - +
225B LEU* 3.7 21.5 - - + -
227B ILE* 4.0 6.1 - - + -
312B AKG 3.7 31.0 - - + +
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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