Contacts of the strand formed by residues 175 - 184 (chain A) in PDB entry 1I72
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 GLN 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A PRO* 4.1 6.5 + - - +
174A ASP* 1.3 94.6 + - - +
176A THR* 1.3 65.4 + - - +
258A ASN* 2.7 55.4 + - - +
259A LEU 3.8 0.7 - - - +
260A SER* 3.8 23.0 + - - +
264A TYR* 3.1 29.4 - - + +
284A LEU* 5.1 0.4 - - + -
285A PHE 3.1 16.6 - - - +
286A VAL* 4.1 6.7 - - + -
290A SER* 2.8 32.1 + - - +
291A LYS 4.5 0.2 + - - -
292A CYS* 5.5 0.2 - - + -
318A TYR* 5.1 1.1 - - - -
350A PUT 4.6 0.4 - - - -
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Residues in contact with THR 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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175A GLN* 1.3 75.7 + - - +
177A LEU* 1.3 63.1 + - - +
178A GLU* 4.9 4.7 - - + -
239A TYR* 3.9 18.5 + - - +
256A GLU* 3.9 17.5 - - + +
257A THR 3.4 10.1 - - - +
258A ASN* 4.6 2.3 - - - +
264A TYR* 6.1 0.4 - - - -
283A THR* 3.6 1.9 + - - +
284A LEU* 3.3 7.8 - - - -
285A PHE* 2.9 36.5 + - + +
350A PUT 2.6 53.2 + - + +
15B GLU* 4.3 2.1 + - - -
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Residues in contact with LEU 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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176A THR* 1.3 73.9 - - - +
178A GLU* 1.3 78.2 + - - +
179A ILE* 4.2 13.2 - - + -
255A PHE* 3.8 3.6 - - + +
256A GLU* 3.2 4.2 - - - +
257A THR* 2.8 39.3 + - + +
264A TYR* 3.5 36.8 - - + -
267A LEU* 3.8 19.5 - - + -
268A ILE* 4.1 27.1 - - + -
282A THR* 4.5 4.5 - - - -
283A THR 3.4 12.3 - - - +
284A LEU* 4.1 19.3 - - + -
300A GLN* 5.8 1.1 - - - +
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Residues in contact with GLU 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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80A LYS* 3.5 17.0 + - - -
113A SER* 4.5 0.3 + - - -
157A TRP* 3.9 19.2 + - - -
176A THR* 4.9 5.4 - - + -
177A LEU* 1.3 78.1 - - - +
179A ILE* 1.3 67.2 + - - +
180A LEU* 3.8 24.0 - - + +
255A PHE 3.0 5.2 - - - +
256A GLU* 3.9 18.2 - - + -
282A THR* 3.2 7.2 - - - -
283A THR* 3.0 49.9 + - - +
285A PHE* 5.8 0.7 - - - -
350A PUT 4.8 2.3 + - - -
13B LEU* 3.5 29.6 - - + +
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Residues in contact with ILE 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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177A LEU* 4.2 9.6 - - + -
178A GLU* 1.3 78.1 - - - +
180A LEU* 1.3 62.0 + - - +
181A MET* 3.7 30.9 - - + +
254A SER* 3.5 2.9 - - - -
255A PHE* 2.7 60.9 + - + -
267A LEU 5.0 0.2 - - - -
268A ILE* 3.9 24.5 - - + +
271A VAL* 3.8 24.0 - - + -
272A VAL* 4.9 4.9 - - + -
280A PHE* 4.2 20.0 - - + -
281A VAL 3.6 4.0 - - - -
282A THR* 4.2 9.6 - - + -
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Residues in contact with LEU 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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114A ARG* 6.1 0.2 - - - -
115A LYS* 3.9 38.4 - - + +
157A TRP* 4.2 16.4 - - + +
178A GLU* 3.8 32.3 - - + +
179A ILE* 1.3 78.4 - - - +
181A MET* 1.3 61.4 + - - +
182A SER* 5.1 0.4 + - - -
252A TYR* 3.5 25.8 - - + +
253A VAL 3.7 2.7 - - - -
254A SER* 3.8 13.5 - - - -
255A PHE 4.6 0.9 - - - +
280A PHE* 3.2 3.9 - - - -
281A VAL* 3.0 49.8 + - + +
283A THR* 5.3 2.2 - - + -
11B GLU* 4.6 1.8 - - - +
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Residues in contact with MET 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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179A ILE* 3.7 26.5 - - + +
180A LEU* 1.3 73.1 - - - +
182A SER* 1.3 62.4 + - - +
184A LEU* 4.1 9.4 - - + -
252A TYR* 3.4 10.1 - - - -
253A VAL* 2.7 67.0 + - + +
255A PHE* 4.2 5.8 - - + -
271A VAL* 3.5 31.0 - - + +
272A VAL* 4.8 2.5 - - - -
275A PHE* 3.7 26.5 - - + -
277A PRO* 3.7 23.8 - - + -
279A LYS 3.7 3.8 - - - -
280A PHE* 3.7 16.8 - - + -
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Residues in contact with SER 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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115A LYS* 4.5 14.7 + - - -
118A MET* 4.1 12.5 - - - +
180A LEU 4.3 0.4 + - - -
181A MET* 1.3 76.5 + - - +
183A GLU* 1.3 74.7 + - - +
184A LEU* 3.3 4.8 + - - -
251A SER 3.7 10.8 - - - -
252A TYR* 4.0 12.1 - - - -
277A PRO* 3.7 3.1 - - - +
278A GLY 3.1 14.2 + - - -
279A LYS* 2.9 40.1 + - - +
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Residues in contact with GLU 183 (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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182A SER* 1.3 76.5 - - - +
184A LEU* 1.3 62.4 + - - +
251A SER* 3.5 13.8 + - - -
276A LYS 4.4 0.2 - - - +
277A PRO 3.7 0.3 - - - -
278A GLY* 2.7 36.6 + - - -
279A LYS* 3.4 37.7 + - + +
327A LYS* 5.7 0.5 + - - -
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Residues in contact with LEU 184 (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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181A MET* 3.9 15.9 - - + +
182A SER* 4.0 6.5 - - - +
183A GLU* 1.3 79.4 - - - +
185A ASP* 1.3 66.5 + - - +
186A PRO* 3.3 9.4 - - - +
189A MET* 3.7 23.8 - - + +
251A SER* 3.0 15.9 + - - +
252A TYR* 3.5 42.4 - - - +
253A VAL* 3.6 25.6 - - + +
275A PHE* 3.5 31.6 - - + +
276A LYS 3.8 3.6 - - - -
277A PRO* 4.1 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