Contacts of the helix formed by residues 179 - 188 (chain C) in PDB entry 4U9W
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 ASN 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C MET* 3.7 21.6 - - - +
84C MET* 3.5 21.5 - - - +
175C VAL* 4.2 2.2 - - + +
176C PHE* 3.0 24.9 + - + +
177C LYS 4.1 0.4 - - - -
178C HIS* 1.3 76.2 - - - +
180C HIS* 1.3 63.7 + - - +
181C GLY* 4.1 1.9 + - - -
182C ALA* 3.2 25.7 + - + +
183C TYR* 3.0 21.0 + - - +
301C COA 3.2 30.1 + - - +
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Residues in contact with HIS 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS* 3.5 56.3 + - + +
180B HIS* 5.0 6.9 + - - -
183B TYR* 3.5 44.0 - + - -
212B GLU* 2.7 31.6 + - - +
177C LYS 4.2 7.0 - - - +
178C HIS* 3.4 6.2 + - - +
179C ASN* 1.3 74.4 - - - +
181C GLY* 1.3 63.5 + - - +
183C TYR* 3.3 8.8 + + - +
184C GLN* 3.1 43.9 + - + +
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASN* 3.2 3.3 + - - -
180C HIS* 1.3 81.6 - - - +
182C ALA* 1.3 55.2 + - - +
184C GLN* 3.3 4.7 + - - +
185C PHE* 3.0 22.0 + - - +
301C COA 3.4 47.4 - - - -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C VAL* 4.1 7.9 - - + -
179C ASN* 3.2 36.3 + - - +
181C GLY* 1.3 72.8 - - - +
183C TYR* 1.3 65.8 + - - +
185C PHE* 3.1 9.1 + - - +
186C PHE* 2.9 32.1 + - + -
301C COA 3.8 33.1 + - + +
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Residues in contact with TYR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B HIS* 3.6 23.8 - + + -
183B TYR* 4.3 20.2 - + - -
184B GLN* 2.7 20.8 + - - -
188B GLU* 2.5 30.4 + - - -
175C VAL* 4.0 26.6 - - + +
176C PHE 4.8 3.4 - - - +
177C LYS* 5.4 0.9 - - - +
179C ASN 3.0 12.6 + - - +
180C HIS* 3.4 15.5 - - - +
181C GLY 3.3 0.2 - - - -
182C ALA* 1.3 78.0 - - - +
184C GLN* 1.3 57.6 + - + +
186C PHE* 3.8 1.7 - - - +
187C ARG* 2.7 75.1 + - + +
188C GLU* 4.7 1.8 - - - -
194C ILE* 3.9 0.5 - - - +
212C GLU* 3.5 20.2 - - + -
214C LEU* 4.5 7.6 - - + -
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Residues in contact with GLN 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 2.8 28.1 + - + +
194B ILE* 3.6 16.0 - - - +
200B SER* 5.4 2.4 + - - -
212B GLU* 2.7 26.4 + - - +
180C HIS* 3.1 32.5 + - + +
181C GLY* 3.6 5.5 - - - +
183C TYR* 1.3 77.5 - - + +
185C PHE* 1.3 58.8 + - - +
188C GLU* 2.9 44.0 + - + +
189C ALA* 3.0 8.8 + - - +
301C COA 3.1 33.5 + - - +
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 4.9 0.2 - - + -
152C GLY* 3.4 26.9 - - - -
153C LYS* 3.4 4.9 - - + -
156C ILE* 4.2 5.2 - - + -
181C GLY 3.0 14.1 + - - +
182C ALA* 3.2 10.1 - - - +
184C GLN* 1.3 76.9 - - - +
186C PHE* 1.3 83.4 + + - +
189C ALA* 3.3 5.2 - - + +
190C LEU* 3.0 52.5 + - + +
301C COA 3.2 99.9 + + + +
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Residues in contact with PHE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C CYS* 5.6 0.4 - - - -
140C VAL* 3.7 24.7 - - + -
156C ILE* 4.1 15.7 - - + -
173C LEU* 3.5 48.2 - - + -
175C VAL* 4.6 5.8 - - + -
182C ALA* 2.9 33.1 + - + +
183C TYR 4.0 0.2 - - - +
185C PHE* 1.3 93.7 - + - +
187C ARG* 1.3 55.2 + - - +
190C LEU* 3.3 8.3 - - + -
191C GLN 3.0 11.6 + - - -
192C PHE* 2.8 44.2 + + + +
214C LEU* 3.7 17.9 - - + -
301C COA 3.6 25.4 - - - -
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Residues in contact with ARG 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B GLU* 2.8 35.4 + - - +
183C TYR* 2.7 64.2 + - + +
186C PHE* 1.3 75.0 - - - +
188C GLU* 1.3 65.3 + - + +
191C GLN* 3.2 20.8 - - - +
192C PHE 2.8 35.8 + - - +
193C GLU* 3.7 10.9 - - - +
194C ILE* 3.9 24.0 - - - +
214C LEU* 3.8 12.3 - - + -
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Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 2.5 39.9 + - - -
187B ARG* 2.6 39.8 + - - +
188B GLU* 5.0 4.7 - - + +
194B ILE* 4.0 8.8 - - - +
183C TYR* 4.7 3.7 - - + -
184C GLN* 2.9 25.2 + - + +
187C ARG* 1.3 88.8 - - + +
189C ALA* 1.3 65.8 + - - +
190C LEU 3.6 0.2 + - - -
191C GLN* 3.8 12.0 + - - +
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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