Contacts of the strand formed by residues 277 - 287 (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 PRO 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A MET* 3.7 26.2 - - + -
182A SER 3.7 13.0 - - - +
183A GLU 3.9 2.0 - - - +
184A LEU* 4.1 7.2 - - + -
272A VAL* 3.3 26.0 - - + +
275A PHE 3.5 2.7 - - - -
276A LYS* 1.3 93.1 - - - +
278A GLY* 1.3 59.2 + - - +
279A LYS 3.7 11.0 - - - +
280A PHE* 3.8 24.0 - - + -
305A PHE* 3.2 20.2 - - + -
327A LYS* 4.7 5.7 - - - +
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Residues in contact with GLY 278 (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 3.1 1.2 + - - -
183A GLU* 2.7 32.4 + - - +
277A PRO* 1.3 74.1 - - - +
279A LYS* 1.3 62.4 + - - +
305A PHE* 4.0 1.5 - - - -
326A ALA* 3.7 0.5 - - - +
327A LYS* 2.8 51.3 + - - +
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Residues in contact with LYS 279 (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* 5.2 0.8 - - - +
118A MET* 6.5 0.2 - - - -
155A ASP* 3.0 40.6 + - - +
181A MET* 3.7 0.5 - - - -
182A SER* 2.9 49.1 + - - +
183A GLU* 3.4 35.3 + - - +
277A PRO* 3.3 2.6 - - - +
278A GLY* 1.3 81.6 - - - +
280A PHE* 1.3 68.9 + - - +
308A LEU* 6.3 0.2 - - + -
325A PHE 3.5 14.8 - - - +
326A ALA* 4.2 9.6 - - + +
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Residues in contact with PHE 280 (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* 6.3 0.7 - - - +
179A ILE* 4.2 6.7 - - + -
180A LEU 3.2 15.7 - - - +
181A MET* 3.7 16.6 - - + -
182A SER* 6.0 0.2 - - - -
268A ILE* 4.3 5.6 - - + -
272A VAL* 3.6 26.5 - - + -
277A PRO* 3.8 14.4 - - + -
279A LYS* 1.3 81.8 - - - +
281A VAL* 1.3 65.6 + - - +
282A THR* 3.9 24.7 - - + -
302A ILE* 4.1 13.9 - - + -
305A PHE* 3.9 22.2 - + - -
324A SER* 3.6 1.0 - - - -
325A PHE* 2.8 71.5 + + + +
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Residues in contact with VAL 281 (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* 4.4 16.8 - - + -
155A ASP* 4.3 18.6 - - + +
157A TRP* 5.5 2.0 - - + -
179A ILE* 3.6 0.7 - - - -
180A LEU* 3.0 61.8 + - + +
280A PHE* 1.3 80.1 - - - +
282A THR* 1.3 68.5 + - - +
283A THR* 5.3 2.2 - - + -
322A PHE* 3.7 27.6 - - + -
323A THR 3.0 9.4 - - - +
324A SER* 3.7 18.6 - - - +
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Residues in contact with THR 282 (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* 4.5 8.7 - - - -
178A GLU 3.2 12.6 - - - +
179A ILE* 4.2 14.6 - - + -
180A LEU* 6.0 0.2 - - - -
268A ILE* 4.2 8.7 - - + -
280A PHE* 3.9 24.2 - - + -
281A VAL* 1.3 79.0 - - - +
283A THR* 1.3 66.2 + - - +
284A LEU* 6.1 0.4 - - - +
300A GLN* 3.5 20.0 + - - +
321A VAL 4.3 1.1 + - - -
322A PHE* 3.3 7.4 - - - -
323A THR* 2.8 50.3 + - - +
325A PHE* 5.1 0.4 - - + -
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Residues in contact with THR 283 (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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157A TRP* 3.6 43.6 - - + +
176A THR 3.6 1.9 + - - +
177A LEU* 3.4 6.8 - - - +
178A GLU* 3.0 54.9 + - + +
180A LEU* 5.3 2.2 - - + -
281A VAL* 5.3 3.6 - - + -
282A THR* 1.3 80.3 - - - +
284A LEU* 1.3 61.4 + - - +
285A PHE* 5.1 4.2 - - - -
320A PHE* 3.7 15.9 - - + -
321A VAL 3.4 5.2 - - - -
322A PHE* 4.2 6.7 - - + -
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Residues in contact with LEU 284 (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* 5.1 0.2 - - + -
176A THR 3.3 18.8 - - - +
177A LEU* 4.1 13.7 - - + -
264A TYR* 3.8 42.2 - - + -
282A THR* 6.1 0.2 - - - +
283A THR* 1.3 76.0 - - - +
285A PHE* 1.3 71.0 + - - +
286A VAL* 3.9 15.7 - - + -
292A CYS* 4.5 5.8 - - - -
300A GLN* 5.4 9.6 - - - +
319A ASN 3.7 0.9 - - - +
320A PHE* 3.2 11.7 - - - -
321A VAL* 3.0 47.9 + - + +
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A PHE* 3.9 23.3 - + - -
157A TRP* 3.7 27.8 - + - -
159A LEU* 4.1 14.1 - - + -
175A GLN* 3.1 4.3 - - - +
176A THR* 2.9 35.6 + - + +
178A GLU* 5.8 0.7 - - - -
283A THR* 5.1 4.5 - - - -
284A LEU* 1.3 75.5 - - - +
286A VAL* 1.3 69.3 + - - +
315A PHE* 3.9 16.4 - + - -
318A TYR* 3.9 20.0 - - + -
319A ASN 3.6 2.5 - - - -
320A PHE* 3.7 28.3 - + + -
350A PUT 3.8 47.8 - - + -
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Residues in contact with VAL 286 (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 ASP 3.8 4.7 - - - -
175A GLN* 4.1 5.2 - - + -
284A LEU* 3.9 24.5 - - + -
285A PHE* 1.3 84.6 - - - +
287A ASN* 1.3 59.0 + - - +
290A SER* 3.4 20.4 - - - +
292A CYS* 3.1 43.7 - - + +
293A ARG* 3.5 9.6 - - - +
317A ASP 4.2 0.2 - - - +
318A TYR* 3.8 4.5 - - - -
319A ASN* 2.9 41.6 + - + +
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Residues in contact with ASN 287 (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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171A SER* 3.8 15.5 + - - +
172A GLN 2.9 25.7 + - - -
174A ASP* 3.0 38.6 + - - +
286A VAL* 1.3 74.7 - - - +
288A GLN* 1.3 67.5 + - - +
289A SER* 3.4 6.5 + - - -
290A SER* 3.1 15.1 + - - -
293A ARG* 3.2 18.8 + - - -
317A ASP* 3.7 16.2 - - + +
318A TYR* 3.7 23.3 + - + -
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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