Contacts of the strand formed by residues 294 - 301 (chain A) in PDB entry 1KPI
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 ASP 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ILE* 3.2 9.9 - - - +
185A THR* 2.7 44.9 + - - +
186A ILE 6.3 0.2 - - - -
187A PRO* 6.4 1.3 - - + -
223A ILE* 5.6 1.4 - - - +
242A ARG* 3.6 36.3 + - - +
243A ILE 4.1 1.0 + - - -
244A GLY* 2.9 22.5 + - - -
245A ALA 4.6 0.3 + - - -
288A PHE* 3.7 4.8 - - - -
291A LYS* 5.5 7.8 + - + +
293A THR* 1.3 75.9 - - - +
295A VAL* 1.3 84.3 + - - +
296A CYS* 5.2 1.0 - - - +
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Residues in contact with VAL 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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43A CYS* 4.1 4.3 - - + -
182A HIS* 3.9 27.6 - - + +
183A THR 3.5 9.9 - - - +
184A ILE* 4.3 4.7 - - + -
242A ARG* 3.2 4.5 - - - -
243A ILE* 2.7 44.8 + - + -
244A GLY* 3.4 17.9 - - - +
247A TYR* 3.3 36.8 - - + -
288A PHE* 3.8 4.0 - - + -
294A ASP* 1.3 91.4 + - - +
296A CYS* 1.3 67.0 + - - +
902A CO3 4.5 0.7 - - - +
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Residues in contact with CYS 296 (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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181A LEU 3.3 4.5 - - - +
182A HIS* 3.5 0.5 - - - -
183A THR 3.0 30.8 + - - +
185A THR* 4.3 11.2 - - + +
223A ILE* 5.0 6.7 - - + -
240A TYR* 4.2 10.8 - - - -
241A HIS 3.5 23.6 - - - -
242A ARG* 4.5 10.8 - - + -
294A ASP* 5.2 0.9 - - - +
295A VAL* 1.3 77.6 - - - +
297A GLN* 1.3 68.0 + - - +
298A PHE* 3.7 42.5 + - + -
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Residues in contact with GLN 297 (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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60A LYS* 4.3 13.1 + - - +
63A LEU* 3.5 20.2 - - - +
64A ALA* 4.0 20.5 - - - +
67A LYS* 2.9 30.0 + - - +
180A LEU* 4.0 13.3 - - + +
181A LEU 3.2 4.7 - - - -
182A HIS* 2.7 40.6 + - + +
239A ARG 3.3 4.5 - - - +
241A HIS* 3.0 32.2 + - + +
243A ILE* 4.3 12.2 - - + +
296A CYS* 1.3 76.0 - - - +
298A PHE* 1.3 63.6 + - - +
299A THR* 3.5 4.7 + - - -
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Residues in contact with PHE 298 (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 MET 3.3 5.2 - - - +
180A LEU* 3.4 2.9 - - - +
181A LEU* 2.7 60.4 + - + +
183A THR* 4.0 14.6 - - + -
185A THR* 4.5 3.6 - - + -
223A ILE* 3.8 21.5 - - + -
226A VAL* 3.7 44.4 - - + -
227A ASP* 5.1 0.7 - - - -
237A VAL* 4.3 7.4 - - + -
239A ARG 3.6 4.7 - - - -
240A TYR* 3.6 39.7 - + - -
296A CYS* 3.7 26.5 - - + -
297A GLN* 1.3 70.9 - - - +
299A THR* 1.3 60.6 + - - +
300A LEU* 3.4 14.0 + - + +
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Residues in contact with THR 299 (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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67A LYS* 3.4 39.4 + - + +
68A LEU* 6.2 1.6 - - + -
178A ARG* 4.3 17.7 - - + +
179A MET 3.9 3.8 - - - +
180A LEU* 3.6 5.4 - - + +
237A VAL* 3.6 1.8 - - - +
238A GLU* 2.7 57.8 + - + +
239A ARG* 3.0 29.6 + - - +
297A GLN 4.2 2.4 + - - -
298A PHE* 1.3 69.2 - - - +
300A LEU* 1.3 55.6 + - - +
301A VAL* 4.4 4.9 - - + -
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Residues in contact with LEU 300 (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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166A PHE* 3.6 34.1 - - + -
178A ARG* 3.4 6.4 - - - +
179A MET* 2.9 63.7 + - + +
181A LEU* 4.5 9.2 - - + -
226A VAL* 5.1 1.3 - - + -
230A SER* 4.2 13.5 - - - +
235A TRP* 3.6 21.1 - - + -
236A LYS 3.5 4.0 - - - +
237A VAL* 3.5 33.4 - - + +
298A PHE* 4.1 17.0 - - + +
299A THR* 1.3 71.6 - - - +
301A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 301 (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 GLY 3.9 7.2 - - - +
178A ARG* 3.5 41.7 - - + +
235A TRP* 3.7 9.1 - - - -
236A LYS* 2.9 49.1 + - + +
238A GLU* 3.9 26.5 - - + -
299A THR* 4.4 5.6 - - + -
300A LEU* 1.3 79.3 - - - +
302A LYS* 1.3 67.0 + - - +
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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