Contacts of the strand formed by residues 175 - 182 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.3 26.2 - - + +
5A LEU* 3.8 30.3 - - + -
163A PHE* 4.1 28.0 - + + -
166A PHE* 4.1 10.8 - + - -
167A GLN* 3.5 45.5 - - + +
170A VAL* 3.9 11.2 - - + -
171A LYS 4.1 3.8 - - - +
172A ARG* 2.9 16.7 + - - +
173A GLU 3.3 1.6 + - - -
174A ASN* 1.3 80.0 - - - +
176A CYS* 1.3 75.4 + - - +
177A ASN* 4.3 13.2 - - + -
209A LEU* 5.9 2.2 - - + -
212A ASP* 5.3 0.9 - - - -
269A ARG* 3.1 17.5 + - - -
270A LEU* 4.3 2.4 - - - +
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Residues in contact with CYS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR 2.8 7.8 + - - +
4A ILE* 4.0 20.0 - - + -
5A LEU 2.8 27.5 + - - +
175A PHE* 1.3 82.1 - - - +
177A ASN* 1.3 62.2 + - - +
178A ILE* 3.6 27.8 + - - -
212A ASP* 3.4 19.7 - - - -
213A LEU* 5.3 1.1 - - - -
265A TYR* 5.3 0.4 - - - -
266A PHE* 3.6 20.0 - - - -
269A ARG* 4.8 6.5 - - + -
270A LEU* 4.1 11.4 - - + -
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.0 4.5 - - - +
7A THR* 3.8 11.2 + - - +
167A GLN* 5.4 2.8 + - - +
175A PHE* 4.3 14.8 - - + -
176A CYS* 1.3 72.6 - - - +
178A ILE* 1.3 74.1 + - - +
179A HIS* 3.9 1.7 + - - +
204A LEU* 4.3 5.1 - - - +
209A LEU* 3.4 36.2 - - - +
210A SER 3.4 24.9 - - - +
211A PRO* 3.5 13.9 - - - +
212A ASP* 2.7 40.4 + - - +
213A LEU 3.3 6.2 + - - -
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.5 27.4 - - + -
5A LEU 2.8 13.2 + - - +
6A VAL* 4.2 12.8 - - + -
7A THR* 2.8 31.1 + - - -
19A ILE* 5.2 6.5 - - + -
23A VAL* 6.6 0.2 - - + -
176A CYS* 3.6 22.4 - - - -
177A ASN* 1.3 77.5 - - - +
179A HIS* 1.3 62.2 + - - +
180A VAL* 4.5 7.6 - - + -
213A LEU* 3.7 22.0 - - + +
215A VAL* 3.9 26.9 - - + -
266A PHE* 4.0 16.6 - - + -
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR* 3.0 20.1 + - - +
8A GLY* 3.6 25.5 - - - -
151A VAL* 3.7 13.9 - - + -
177A ASN* 3.9 0.4 + - - +
178A ILE* 1.3 75.4 - - - +
180A VAL* 1.3 63.6 + - - +
181A SER* 4.3 6.3 - - - -
200A SER* 2.9 33.9 + - - -
201A VAL* 3.8 25.4 - - + +
204A LEU* 3.6 13.8 - - + +
211A PRO* 3.5 23.8 - - + -
213A LEU 3.1 8.1 + - - +
214A VAL* 3.2 8.6 - - + +
215A VAL 2.7 30.9 + - - +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.2 10.8 - - + -
7A THR 2.8 19.6 + - - +
8A GLY* 3.0 21.0 - - - -
9A GLY 3.0 8.3 + - - +
14A ILE* 3.6 35.1 - - + +
15A GLY 5.0 2.5 - - - +
16A LYS* 4.0 22.9 - - + +
19A ILE* 4.8 7.6 - - + -
178A ILE* 4.5 2.9 - - + -
179A HIS* 1.3 78.3 + - - +
181A SER* 1.3 66.9 + - - +
215A VAL* 3.4 32.3 - - + +
217A ARG* 5.1 1.6 - - + +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 4.7 5.4 - - - +
10A VAL* 3.9 8.7 - - - +
14A ILE* 3.4 9.9 - - - +
179A HIS* 4.3 11.9 - - - -
180A VAL* 1.3 77.0 - - - +
182A LEU* 1.3 66.6 + - - -
197A THR* 2.7 44.1 + - - -
200A SER* 4.5 2.1 - - - -
214A VAL* 4.6 3.1 - - - -
215A VAL 2.8 12.6 + - - +
216A CYS* 4.5 1.8 - - - -
217A ARG* 2.9 28.6 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.8 32.6 - - + +
11A ILE* 4.5 10.8 - - + -
14A ILE* 3.6 22.2 - - + -
181A SER* 1.3 83.7 + - - +
183A VAL* 1.4 73.8 + - - +
184A PRO* 3.2 33.5 - - + +
193A LYS 4.2 0.9 - - - +
196A PRO* 4.4 1.9 - - - +
197A THR* 2.9 19.4 + - - -
217A ARG* 3.6 19.5 - - + +
184B PRO* 5.9 8.1 - - + -
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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