Contacts of the strand formed by residues 255 - 261 (chain A) in PDB entry 1P4K
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 VAL 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A THR 3.4 5.4 - - - +
205A HIS 4.2 12.6 - - - +
208A GLU* 4.3 12.3 - - + -
209A VAL* 3.9 27.1 - - + -
236A VAL* 4.7 2.9 - - + +
239A ILE* 5.1 7.4 - - + -
253A ILE* 4.6 1.6 - - + -
254A GLN* 1.3 88.6 - - - +
256A GLY* 1.3 68.3 + - - +
257A PHE* 3.7 34.1 - - + -
270A CYS* 3.1 3.6 - - - +
271A ILE* 3.0 45.5 + - + +
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Residues in contact with GLY 256 (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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201A THR 4.1 0.2 - - - +
202A ALA* 3.2 7.1 - - - +
203A THR* 2.9 38.9 + - - +
254A GLN* 5.2 0.4 - - - +
255A VAL* 1.3 76.6 - - - +
257A PHE* 1.3 63.0 + - - -
269A TYR 3.4 9.6 - - - -
270A CYS* 3.8 7.6 - - - -
275A PHE* 4.4 16.1 - - - -
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Residues in contact with PHE 257 (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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200A ALA* 5.7 0.2 - - + -
201A THR 3.4 3.6 - - - +
202A ALA* 3.4 28.3 - - + -
209A VAL* 4.4 4.3 - - + -
212A THR* 5.1 0.4 - - - -
214A GLY* 3.5 40.2 - - - -
215A THR* 3.8 7.6 - - + -
218A VAL* 3.9 13.9 - - + -
232A CYS* 3.8 19.3 - - + -
235A ALA* 4.0 22.9 - - + -
236A VAL* 3.8 25.1 - - + -
239A ILE* 4.5 11.7 - - + -
255A VAL* 3.7 20.2 - - + -
256A GLY* 1.3 75.7 - - - -
258A ILE* 1.3 65.2 + - - +
268A ALA* 3.2 6.4 - - - +
269A TYR 3.0 27.9 + - - +
275A PHE* 4.8 0.7 - - - -
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Residues in contact with ILE 258 (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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8A LEU* 3.9 18.4 - - + +
9A SER* 3.9 27.1 - - - +
10A THR* 3.8 15.0 - - + -
156A ILE* 3.8 5.1 - - + +
200A ALA* 3.3 5.2 - - - +
201A THR* 3.1 51.1 + - + +
232A CYS* 4.0 0.4 - - - -
257A PHE* 1.3 80.8 - - - +
259A ALA* 1.3 62.4 + - - +
267A GLY 3.4 8.1 - - - +
268A ALA* 3.8 9.9 - - + -
275A PHE* 4.0 13.2 - - + -
277A PHE* 3.7 26.0 - - + -
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Residues in contact with ALA 259 (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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8A LEU* 3.9 2.3 - - - +
156A ILE* 3.7 4.0 - - - +
199A ALA 3.3 11.4 - - - +
218A VAL* 3.9 18.2 - - + -
222A MET* 4.1 7.0 - - + -
228A PRO* 4.1 12.6 - - + +
232A CYS* 3.6 19.3 - - - -
258A ILE* 1.3 76.9 - - - +
260A LEU* 1.3 63.3 + - - +
266A TYR* 3.1 8.5 - - - +
267A GLY 2.8 29.5 + - - +
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Residues in contact with LEU 260 (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 ILE* 3.7 27.4 - - + +
8A LEU* 3.9 11.0 - - + -
156A ILE* 3.9 21.1 - - + +
157A ALA* 3.7 37.7 - - - +
158A LEU* 3.8 5.6 - - + +
164A LEU* 4.2 10.9 - - + +
198A GLY* 3.0 2.3 - - - -
199A ALA* 2.8 31.1 + - + +
222A MET* 3.7 6.0 - - - +
228A PRO* 4.4 0.2 - - - -
259A ALA* 1.3 75.5 - - - +
261A ASN* 1.3 66.6 + - - +
264A GLY 3.9 7.9 - - - +
265A GLU 3.4 15.9 - - - +
266A TYR* 3.8 15.7 - - + -
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Residues in contact with ASN 261 (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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158A LEU* 4.0 5.5 - - - +
164A LEU* 4.3 3.8 - - - +
197A ILE 3.4 14.8 - - - +
198A GLY* 3.8 3.1 - - - -
222A MET* 4.1 9.0 - - + -
226A ARG 5.7 0.8 + - - -
227A THR* 5.3 1.2 - - - +
228A PRO* 3.5 19.6 - - + +
260A LEU* 1.3 79.3 - - - +
262A LYS* 1.3 59.4 + - - +
263A LYS* 2.8 21.7 + - - +
264A GLY* 2.9 18.7 + - - -
265A GLU* 2.9 58.2 + - - +
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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