Contacts of the strand formed by residues 175 - 182 (chain C) in PDB entry 5U03
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 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C TYR* 3.3 25.6 - - + +
5C LEU* 3.8 31.2 - - + -
163C PHE* 4.1 27.1 - + + -
166C PHE* 4.1 11.7 - + - -
167C GLN* 3.5 46.7 - - + +
170C VAL* 3.9 12.6 - - + -
171C LYS 4.1 3.6 - - - +
172C ARG* 2.9 16.8 + - - +
173C GLU 3.3 1.8 + - - -
174C ASN* 1.3 80.8 - - - +
176C CYS* 1.3 77.7 + - - +
177C ASN* 4.3 13.2 - - + -
209C LEU* 5.9 2.0 - - + -
212C ASP* 5.3 0.9 - - - -
269C ARG* 3.1 17.1 + - - -
270C LEU* 4.3 2.6 - - - +
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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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3C TYR 2.8 8.2 + - - +
4C ILE* 3.6 20.5 - - + -
5C LEU 2.8 27.0 + - - -
175C PHE* 1.3 81.7 - - - +
177C ASN* 1.3 63.4 + - - +
178C ILE* 3.6 26.9 - - - -
212C ASP* 3.4 19.5 - - - -
213C LEU* 5.3 1.1 - - - -
265C TYR* 5.3 0.2 - - - -
266C PHE* 3.6 20.4 - - - -
269C ARG* 4.8 6.3 - - + -
270C LEU* 4.1 11.9 - - + +
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Residues in contact with ASN 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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5C LEU* 4.0 4.3 - - - +
7C THR* 3.8 12.3 + - - +
167C GLN* 5.4 3.2 + - - +
175C PHE* 4.3 14.8 - - + -
176C CYS* 1.3 73.0 - - - +
178C ILE* 1.3 74.4 + - - +
179C HIS* 3.9 1.4 + - - +
204C LEU* 4.3 4.4 - - - +
209C LEU* 3.4 36.4 - - - +
210C SER 3.4 24.9 - - - +
211C PRO* 3.5 14.1 - - - +
212C ASP* 2.7 38.9 + - - +
213C LEU 3.3 7.1 + - - -
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Residues in contact with ILE 178 (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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4C ILE* 3.5 26.9 - - + -
5C LEU 2.8 12.9 + - - +
6C VAL* 4.2 13.5 - - + -
7C THR* 2.8 31.0 + - - -
19C ILE* 5.2 6.3 - - + -
23C VAL* 6.6 0.4 - - + -
176C CYS* 3.6 22.4 - - - -
177C ASN* 1.3 78.0 - - - +
179C HIS* 1.3 62.9 + - - +
180C VAL* 4.5 7.2 - - + -
213C LEU* 3.7 22.4 - - + +
215C VAL* 3.9 26.0 - - + -
266C PHE* 4.0 16.6 - - + -
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Residues in contact with HIS 179 (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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7C THR* 3.0 20.2 + - - +
8C GLY* 3.6 25.9 - - - -
9C GLY 3.6 0.6 + - - -
151C VAL* 3.7 14.1 - - + -
177C ASN* 3.9 0.4 + - - +
178C ILE* 1.3 75.2 - - - +
180C VAL* 1.3 63.0 + - - +
181C SER* 4.3 5.9 - - - -
200C SER* 2.9 33.8 + - - -
201C VAL* 3.8 25.2 - - + +
204C LEU* 3.6 13.5 - - + +
211C PRO* 3.5 23.8 - - + -
213C LEU 3.1 7.7 + - - -
214C VAL* 3.2 9.1 - - + +
215C VAL 2.7 30.9 + - - +
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Residues in contact with VAL 180 (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 VAL* 4.2 11.0 - - + -
7C THR 2.8 18.9 + - - +
8C GLY* 3.0 21.3 - - - -
9C GLY 3.0 7.3 + - - +
14C ILE* 3.6 35.1 - - + +
15C GLY 5.0 2.0 - - - +
16C LYS* 4.0 23.3 - - + +
19C ILE* 4.8 7.2 - - + -
178C ILE* 4.5 3.4 - - + -
179C HIS* 1.3 78.6 + - - +
181C SER* 1.3 66.3 + - - +
215C VAL* 3.4 32.5 - - + +
217C ARG* 5.1 2.0 - - + +
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Residues in contact with SER 181 (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 GLY 4.7 5.2 - - - -
10C VAL* 3.9 9.2 - - - +
14C ILE* 3.4 9.9 - - - +
179C HIS* 4.3 12.3 - - - -
180C VAL* 1.3 75.9 - - - +
182C LEU* 1.3 68.2 + - - +
197C THR* 2.7 44.7 + - - -
200C SER* 4.5 2.3 - - - -
214C VAL* 4.6 2.9 - - - -
215C VAL 2.8 12.6 + - - -
216C CYS* 4.5 2.2 - - - -
217C ARG* 2.9 28.2 + - - +
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Residues in contact with LEU 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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10C VAL* 3.8 32.1 - - + +
11C ILE* 4.5 10.5 - - + -
14C ILE* 3.6 22.7 - - + -
181C SER* 1.3 84.5 + - - +
183C VAL* 1.4 73.9 + - - +
184C PRO* 3.2 32.7 - - + +
193C LYS 4.2 1.2 - - - +
196C PRO* 4.4 1.9 - - - +
197C THR* 2.9 19.6 + - - -
217C ARG* 3.6 18.6 - - + +
218C CYS 6.2 0.2 - - - -
184D PRO* 5.9 8.3 - - + -
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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