Contacts of the strand formed by residues 289 - 295 (chain A) in PDB entry 3C9G
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 ILE 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A ILE* 3.6 28.9 - - + -
194A ARG 3.7 1.8 - - - -
195A THR* 3.8 17.5 - - + -
209A ALA* 5.6 0.4 - - + -
210A ILE* 3.6 31.0 - - + +
213A ILE* 6.3 2.7 - - + -
214A PHE* 5.8 2.0 - - + -
266A TYR* 3.5 3.3 - - - -
267A LEU* 2.8 53.7 + - + +
268A ASN 4.8 0.4 - - - +
269A LYS* 3.8 31.0 - - + -
272A ALA* 5.3 6.1 - - + -
288A PRO* 1.3 70.3 - - - +
290A LYS* 1.3 60.7 + - - +
291A VAL* 3.6 18.1 + - + +
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Residues in contact with LYS 290 (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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192A GLU* 3.5 5.2 + - - +
193A ILE* 3.4 3.8 - - - -
194A ARG* 2.6 78.0 + - + +
264A THR* 3.9 15.0 - - + -
265A ILE 3.7 3.4 - - - -
266A TYR* 3.8 30.3 - - + +
288A PRO* 3.7 3.1 + - + +
289A ILE* 1.3 72.3 - - - +
291A VAL* 1.3 62.2 + - - +
292A THR* 2.7 37.3 + - - +
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Residues in contact with VAL 291 (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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191A ILE* 4.1 16.2 - - + -
192A GLU 3.3 2.7 - - - -
193A ILE* 3.9 10.8 - - + -
214A PHE* 4.2 13.5 - - + -
263A VAL 3.5 3.3 - - - +
264A THR* 3.5 0.4 - - - -
265A ILE* 3.0 42.2 + - + +
267A LEU* 4.5 11.2 - - + -
289A ILE* 3.6 26.2 - - + +
290A LYS* 1.3 78.8 - - - +
292A THR* 1.3 62.2 + - - +
293A PHE* 3.6 36.4 + - + -
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Residues in contact with THR 292 (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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190A GLU 3.5 2.4 - - - +
191A ILE* 3.7 0.2 - - - -
192A GLU* 2.8 61.6 + - - +
262A GLU* 4.2 21.3 - - + +
263A VAL 3.2 6.3 - - - +
264A THR* 3.2 22.2 + - - +
290A LYS* 2.7 28.7 + - - +
291A VAL* 1.3 73.9 - - - +
293A PHE* 1.3 69.7 + - - +
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Residues in contact with PHE 293 (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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189A VAL* 4.1 8.1 - - + -
190A GLU 3.2 2.0 - - - +
191A ILE* 3.5 34.8 - - + -
214A PHE* 4.2 7.6 - + - -
234A LEU* 3.7 14.4 - - + -
237A PHE* 4.0 24.7 - + - -
254A ILE* 5.2 4.0 - - + -
261A LYS 3.7 0.2 - - - +
262A GLU* 3.4 6.4 - - - -
263A VAL* 2.8 47.6 + - + +
265A ILE* 3.9 20.0 - - + -
291A VAL* 3.6 27.6 - - + -
292A THR* 1.3 73.3 - - - +
294A ARG* 1.3 61.2 + - - +
295A LEU* 3.6 4.5 + - + +
303A PHE* 3.7 35.2 - + + -
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Residues in contact with ARG 294 (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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188A ASN 3.7 0.5 - - - +
189A VAL* 3.5 3.0 - - - -
190A GLU* 2.5 64.6 + - + +
192A GLU* 4.5 12.3 - - - +
261A LYS* 4.0 7.4 - - + +
262A GLU* 4.9 11.2 - - + +
293A PHE* 1.3 73.0 - - - +
295A LEU* 1.3 61.0 + - - +
296A ASN* 3.2 16.3 + - - +
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Residues in contact with LEU 295 (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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188A ASN 4.3 1.1 - - - -
189A VAL* 3.7 23.3 - - + -
261A LYS* 3.0 44.6 + - + +
263A VAL* 4.4 12.6 - - + -
293A PHE 4.7 4.5 - - - +
294A ARG* 1.3 68.5 - - - +
296A ASN* 1.3 63.6 + - - +
297A ASN 3.9 0.9 - - - -
298A ILE* 3.6 24.4 - - + +
300A PHE* 3.9 22.2 - - + -
303A PHE* 3.6 59.9 - - + -
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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