Contacts of the helix formed by residues 169 - 177 (chain C) in PDB entry 4U2M
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 HIS 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ALA* 3.7 24.2 - - + +
145C LEU* 3.6 25.0 - - + +
148C LEU* 3.9 7.2 - - + +
149C ARG* 3.7 20.2 - - + -
153C ILE 3.0 21.0 + - - -
154C LEU 3.4 26.2 - - - -
155C THR* 3.7 7.4 + - + -
156C ASP* 3.3 6.5 - - - +
168C ALA* 1.3 71.4 - - - +
170C LYS* 1.3 65.1 + - - +
171C THR* 3.1 6.1 + - - +
172C VAL* 3.1 22.7 + - + +
173C LEU* 3.2 14.3 + - - +
214C TYR* 2.7 33.1 + - - +
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Residues in contact with LYS 170 (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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23C LEU* 3.7 25.3 - - + +
156C ASP* 2.9 48.3 + - - +
157C VAL* 3.9 11.4 - - + +
168C ALA 4.0 0.8 + - - -
169C HIS* 1.3 70.9 - - - +
171C THR* 1.3 58.7 + - - +
173C LEU* 3.2 5.2 + - - +
174C MET* 2.8 31.0 + - - +
184C PHE* 3.7 39.3 - - + -
190C CYS 2.9 26.7 + - - -
191C ASN* 4.3 3.4 - - - +
192C LEU 3.1 25.2 + - - -
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Residues in contact with THR 171 (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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14C LEU* 2.9 29.2 - - + -
17C GLN* 2.9 41.9 + - - +
23C LEU* 3.4 18.9 + - - +
38C HIS* 2.9 37.3 - - + +
40C ALA* 6.1 3.8 - - - -
41C VAL* 4.9 1.6 - - + -
156C ASP* 5.1 0.8 + - - -
169C HIS* 3.1 5.8 + - - +
170C LYS* 1.3 78.3 - - - +
172C VAL* 1.3 57.5 + - + +
175C ALA* 3.1 13.2 + - - +
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Residues in contact with VAL 172 (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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10C VAL* 5.3 3.8 - - + -
14C LEU* 5.0 5.6 - - + -
142C LEU* 5.2 4.5 - - + -
145C LEU* 3.9 31.0 - - + -
169C HIS* 3.1 16.4 + - + +
171C THR* 1.3 75.1 - - - +
173C LEU* 1.3 67.4 + - - +
175C ALA* 3.1 16.8 + - - +
176C CYS* 3.2 26.0 + - - -
213C MET* 4.4 9.0 - - + +
214C TYR* 3.7 46.4 - - + +
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Residues in contact with LEU 173 (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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157C VAL* 4.1 7.0 - - + -
159C ILE* 3.8 33.9 - - + -
168C ALA* 4.0 13.9 - - + -
169C HIS 3.2 10.1 + - - +
170C LYS 3.2 6.2 + - - +
172C VAL* 1.3 77.3 - - - +
174C MET* 1.3 61.6 + - - +
176C CYS* 3.2 1.6 + - - +
177C SER* 3.0 29.6 + - - -
180C PHE* 3.7 27.5 - - + +
184C PHE* 3.9 13.7 - - + -
206C PHE* 5.3 0.9 - - + -
210C LEU* 3.6 21.8 - - + -
213C MET* 3.6 25.6 - - - -
214C TYR* 4.9 2.7 - - + -
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Residues in contact with MET 174 (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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13C GLN* 4.7 5.0 + - - -
17C GLN* 3.7 30.5 - - + +
22C LEU* 4.3 12.8 - - + -
23C LEU* 3.7 17.9 - - + -
170C LYS 2.8 16.3 + - - +
171C THR 3.8 4.3 - - - +
173C LEU* 1.3 76.7 - - - +
175C ALA* 1.3 62.2 + - - +
176C CYS 3.3 0.5 + - - -
177C SER 3.8 9.9 + - - +
180C PHE* 4.1 1.7 - - - +
181C TYR* 3.8 41.1 - - + +
184C PHE* 3.7 30.1 - - + +
185C THR* 3.9 24.9 - - + -
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Residues in contact with ALA 175 (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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9C HIS* 4.1 9.7 + - - -
10C VAL* 4.4 20.6 - - + +
13C GLN* 3.4 45.9 + - + +
14C LEU* 4.5 2.7 - - + -
17C GLN* 3.7 6.2 - - - +
171C THR 3.1 15.9 + - - +
172C VAL* 3.1 13.4 + - - +
174C MET* 1.3 77.7 - - - +
176C CYS* 1.3 59.2 + - - +
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Residues in contact with CYS 176 (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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6C HIS* 3.8 24.7 - - + -
9C HIS* 5.7 1.1 - - - -
10C VAL* 3.9 14.1 - - - -
172C VAL* 3.2 20.1 + - - +
173C LEU 3.2 0.2 + - - -
175C ALA* 1.3 81.3 - - - +
177C SER* 1.3 58.6 + - - +
212C PHE* 5.8 1.3 - - + -
213C MET* 3.6 45.5 - - + -
236C GLN 5.1 0.5 - - - +
237C MET* 3.7 20.3 - - - +
200D GLU* 5.0 9.8 - - - +
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Residues in contact with SER 177 (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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173C LEU 3.0 11.8 + - - +
174C MET 3.8 5.4 - - - +
175C ALA 3.7 1.0 - - - -
176C CYS* 1.3 80.8 - - - +
178C GLY* 1.3 58.4 + - - +
179C LEU* 3.2 2.8 + - - +
180C PHE* 3.1 32.5 + - - -
181C TYR* 2.9 26.7 + - - +
213C MET* 4.1 11.2 - - - -
235C LEU* 2.8 23.3 + - - +
236C GLN 4.8 0.2 - - - -
237C MET* 4.4 4.3 - - - -
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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