Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 1RL3
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 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.8 17.1 - - - -
169A GLY 3.8 1.2 - - - -
170A ASP* 1.3 104.6 + - - +
172A PHE* 1.3 57.6 + - - +
173A TYR* 2.6 63.9 + - - -
199A GLY 4.3 0.2 - - - +
203A LEU* 3.7 13.1 - - - +
209A ARG* 3.7 14.4 + - - -
224A ILE 2.3 39.4 - - - +
225A ASP* 3.7 2.8 + - - +
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Residues in contact with PHE 172 (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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135A LEU* 5.2 14.8 - - + -
136A PHE* 5.7 1.8 - + - -
151A MET* 6.2 0.2 - - - -
171A ASN* 1.3 70.5 - - - +
173A TYR* 1.3 75.2 + - - +
174A VAL* 3.6 24.7 - - + -
197A SER* 3.0 29.4 - - - -
198A PHE* 3.1 27.8 - - - -
199A GLY 4.3 1.6 - - - -
200A GLU* 3.6 29.4 - - + -
203A LEU* 3.4 8.8 - - + +
223A GLY* 3.1 21.2 - - - -
224A ILE* 3.1 20.8 + - + -
229A TYR* 3.4 44.0 - + + -
233A LEU* 4.2 10.5 - - + -
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Residues in contact with TYR 173 (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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152A PHE* 4.9 4.8 - + - -
154A VAL* 4.1 20.2 - - + +
156A PHE* 4.6 8.3 - + - -
162A VAL* 3.7 23.3 - - + +
163A ILE* 5.2 0.9 - - + -
170A ASP* 3.8 8.1 + - - -
171A ASN* 2.6 50.6 + - - -
172A PHE* 1.3 85.9 - - - +
174A VAL* 1.3 64.0 + - - +
197A SER* 3.0 5.8 - - - -
198A PHE* 2.7 74.1 + + + +
209A ARG* 4.8 5.8 - - - -
221A LEU* 3.7 23.1 - - + -
222A TRP 3.2 12.8 - - - -
223A GLY* 4.4 4.7 - - - -
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Residues in contact with VAL 174 (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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129A ALA* 5.5 5.8 - - + -
133A ASN* 3.9 21.3 - - + +
135A LEU* 6.5 0.2 - - + -
136A PHE* 4.4 20.0 - - + -
151A MET* 5.1 5.4 - - + -
172A PHE* 3.6 25.1 - - + -
173A TYR* 1.3 78.1 - - - +
175A ILE* 1.3 70.9 + - - +
176A ASP 3.5 0.6 + - - -
195A GLY* 4.8 1.3 - - - +
196A GLY 3.7 11.7 - - - +
197A SER* 4.1 3.6 - - - -
221A LEU* 3.4 7.3 - - - +
222A TRP* 2.9 52.7 + - + +
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Residues in contact with ILE 175 (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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174A VAL* 1.3 74.7 - - - +
176A ASP* 1.3 64.2 + - - +
177A GLN 3.8 14.1 - - - +
178A GLY 3.8 12.3 - - - +
180A MET* 3.3 20.9 - - + +
192A VAL* 3.3 35.4 - - + +
193A GLY 3.1 23.8 - - - +
194A GLU* 3.3 20.4 - - - -
195A GLY* 3.2 18.1 + - - +
196A GLY 3.0 16.6 + - - +
198A PHE* 3.8 8.5 - - + -
219A VAL* 5.6 0.2 - - + -
221A LEU* 3.6 19.5 - - + -
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Residues in contact with ASP 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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125A ALA* 4.3 6.3 - - - +
129A ALA* 4.0 10.8 - - - +
132A LYS* 5.4 3.5 + - - -
174A VAL* 3.5 4.6 + - - -
175A ILE* 1.3 73.7 - - - +
177A GLN* 1.3 64.5 + - - +
194A GLU* 3.1 19.7 - - - +
220A LYS* 3.1 38.8 + - + +
222A TRP* 2.4 48.6 + - + +
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Residues in contact with GLN 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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175A ILE* 3.4 4.9 - - - +
176A ASP* 1.3 87.4 + - + +
178A GLY* 1.3 62.5 + - - +
194A GLU* 3.0 20.6 - - - +
218A ASN 5.1 0.4 - - - -
219A VAL* 3.3 22.5 - - - +
220A LYS* 3.3 21.2 + - + +
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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