Contacts of the strand formed by residues 233 - 239 (chain A) in PDB entry 4KPF
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 LYS 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LYS* 3.5 7.4 - - - +
228A ALA* 3.0 19.4 + - - -
231A THR* 3.2 16.8 + - - +
232A GLY* 1.3 79.5 - - - +
234A GLY* 1.3 59.3 + - - +
327A PHE 3.6 12.1 - - - +
328A ASN* 3.4 29.1 + - - +
339A GLN* 3.5 31.9 - - - +
630C ARG* 5.8 4.3 - - - +
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Residues in contact with GLY 234 (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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224A GLU* 3.2 16.6 - - - -
227A LYS* 4.9 3.4 - - - -
228A ALA* 4.0 9.9 - - - -
233A LYS* 1.3 77.0 - - - +
235A ARG* 1.3 58.2 + - - -
236A VAL 4.1 0.2 - - - -
326A ASN* 3.6 3.6 - - - -
327A PHE* 2.8 41.0 + - - +
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Residues in contact with ARG 235 (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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224A GLU* 2.7 35.4 + - - +
234A GLY* 1.3 70.8 - - - -
236A VAL* 1.3 62.2 + - - +
237A VAL* 6.3 0.4 - - + -
324A ASN* 4.1 29.2 - - + +
325A TYR 3.5 3.6 - - - -
326A ASN* 3.3 23.6 - - - +
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Residues in contact with VAL 236 (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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211A PRO* 5.7 1.1 - - + -
213A PHE* 5.5 1.3 - - + -
219A ILE* 3.7 25.1 - - + -
220A GLN 3.3 20.2 - - - +
221A GLY* 3.9 9.0 - - - +
224A GLU* 4.7 0.9 - - + -
225A ILE* 3.7 31.4 - - + +
234A GLY 4.1 0.4 + - - -
235A ARG* 1.3 76.1 - - - +
237A VAL* 1.3 65.3 + - - +
238A VAL* 4.3 2.9 - - + -
324A ASN* 3.3 8.0 - - - +
325A TYR* 2.8 49.5 + - + +
327A PHE* 4.4 16.4 - - + -
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Residues in contact with VAL 237 (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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218A ILE 3.5 0.3 - - - +
219A ILE* 3.3 5.4 - - - +
220A GLN* 2.7 65.2 + - + +
235A ARG* 6.3 0.7 - - + -
236A VAL* 1.3 75.3 - - - +
238A VAL* 1.3 67.7 + - - +
239A ARG* 4.5 1.3 - - + +
322A GLN* 3.3 38.1 - - + +
323A ILE 3.7 2.5 - - - +
324A ASN* 3.7 19.1 - - - +
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Residues in contact with VAL 238 (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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213A PHE* 3.4 40.4 - - + -
217A ALA* 4.3 12.8 - - + -
218A ILE 3.2 8.3 - - - +
219A ILE* 4.6 3.1 - - + -
236A VAL* 4.2 4.7 + - + -
237A VAL* 1.3 78.2 - - - +
239A ARG* 1.3 62.3 + - - +
260A PRO* 3.8 29.2 - - + +
261A TYR* 4.6 1.3 - - + +
322A GLN* 3.4 3.1 - - - +
323A ILE* 3.0 44.8 + - + +
325A TYR* 4.1 16.8 - - + -
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Residues in contact with ARG 239 (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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217A ALA* 3.4 4.3 - - - +
218A ILE* 2.7 54.8 + - + +
220A GLN* 3.9 29.6 + - - +
237A VAL* 4.7 3.8 - - + -
238A VAL* 1.3 76.5 - - - +
240A SER* 1.3 76.5 + - - +
242A THR* 5.8 0.4 - - - -
260A PRO* 5.0 1.1 - - - -
313A ASN* 5.5 2.8 + - - -
316A PHE* 3.5 39.7 - - + +
321A LEU 4.1 2.9 - - - -
322A GLN* 3.1 33.1 + - + +
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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