Contacts of the strand formed by residues 227 - 237 (chain A) in PDB entry 1KP5
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 HIS 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.3 5.4 - - - -
56A PHE 3.0 16.8 - - - +
57A ILE* 4.0 12.6 - - + -
67A TRP* 3.4 12.4 + - - -
219A LYS* 3.0 42.3 + - + +
220A ASP* 2.6 58.3 + - + +
223A GLU* 3.4 20.6 - - + +
225A ARG 2.9 18.6 + - - +
226A ASP* 1.3 77.2 + - - +
228A MET* 1.3 65.2 + - - +
229A VAL* 4.2 11.4 - - + -
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Residues in contact with MET 228 (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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55A LYS* 3.4 1.6 - - - -
56A PHE* 2.8 49.3 + - + -
67A TRP* 3.7 49.6 - - + +
71A VAL* 3.9 22.0 - - + -
74A PHE* 3.7 33.4 - - + -
153A TYR* 3.3 17.3 - - + +
217A LEU* 4.0 16.4 - - + -
218A SER 4.1 1.1 - - - -
227A HIS* 1.3 80.2 - - - +
229A VAL* 1.3 72.2 + - - +
230A LEU* 4.7 4.0 - - + +
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Residues in contact with VAL 229 (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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53A THR* 6.5 0.4 - - - -
54A LEU 3.5 8.1 - - - +
55A LYS* 4.2 18.8 - - + -
216A ALA 3.8 0.5 - - - +
217A LEU* 3.4 5.9 - - - -
218A SER* 3.0 57.2 + - - +
219A LYS 4.3 9.6 - - - +
220A ASP* 4.3 7.2 - - + +
227A HIS* 4.2 12.3 - - + -
228A MET* 1.3 79.2 - - - +
230A LEU* 1.3 67.7 - - - +
231A LEU* 4.4 1.3 - - + -
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Residues in contact with LEU 230 (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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52A LEU* 3.9 7.9 - - + +
53A THR* 3.3 6.2 - - - -
54A LEU* 2.7 43.2 + - + +
56A PHE* 4.0 28.3 - - + -
71A VAL* 4.5 15.3 - - + +
74A PHE* 5.6 0.2 - - + -
76A GYS 3.8 22.7 - - - +
215A SER* 4.1 5.6 - - - -
216A ALA 3.7 1.1 - - - +
217A LEU* 3.4 26.2 - - + -
228A MET* 4.0 5.4 + - + -
229A VAL* 1.3 78.8 - - - +
231A LEU* 1.3 68.7 + - - +
232A GLU* 3.7 30.5 - - + +
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Residues in contact with LEU 231 (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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51A LYS* 4.4 15.5 - - + -
52A LEU 3.7 2.2 - - - +
53A THR* 3.3 30.3 - - + -
214A GLN 5.4 0.7 - - - +
215A SER* 3.3 1.1 - - - -
216A ALA* 2.9 49.8 + - + +
229A VAL* 6.1 1.8 - - + -
230A LEU* 1.3 74.1 - - - +
232A GLU* 1.3 73.6 + - - +
233A PHE* 3.5 32.8 - - + -
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Residues in contact with GLU 232 (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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50A GLY 3.5 0.6 - - - +
51A LYS* 3.4 6.6 - - - +
52A LEU* 3.0 52.4 + - + +
71A VAL* 3.7 15.8 - - - +
76A GYS 2.9 34.8 + - - -
213A THR* 4.3 11.8 - - - +
214A GLN 3.2 4.9 - - - +
215A SER* 2.6 32.4 + - - +
230A LEU* 3.7 15.8 - - + +
231A LEU* 1.3 84.2 - - - +
233A PHE* 1.3 66.9 + - - +
234A VAL* 4.3 7.7 - - + +
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Residues in contact with PHE 233 (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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49A TYR* 4.0 15.0 - - + +
50A GLY 3.1 4.7 - - - -
51A LYS* 3.6 45.5 - - + -
212A SER 3.5 2.9 - - - +
214A GLN* 3.0 56.2 + - + +
231A LEU* 3.5 28.9 - - + -
232A GLU* 1.3 72.2 - - - +
234A VAL* 1.3 64.1 + - - +
235A THR* 5.4 1.3 - - + -
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Residues in contact with VAL 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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49A TYR 5.2 0.4 + - - -
50A GLY* 2.7 22.3 + - - +
52A LEU* 5.2 7.9 - - + -
79A GLN* 5.7 4.0 - - + -
81A PHE 5.1 0.9 - - - +
82A SER* 3.0 35.2 - - - +
83A ARG 2.7 26.7 + - - -
211A LEU* 4.2 18.6 - - + -
212A SER 3.4 7.4 - - - +
213A THR* 3.8 23.6 - - + +
232A GLU* 4.3 13.2 - - + +
233A PHE* 1.3 80.1 - - - +
235A THR* 1.3 60.6 + - - +
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Residues in contact with THR 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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49A TYR 6.0 0.7 - - - -
83A ARG* 3.4 36.5 + - - +
85A PRO* 4.7 0.7 - - - +
211A LEU* 4.6 2.9 - - - -
212A SER* 2.9 46.7 + - - +
214A GLN* 4.5 10.5 - - - +
233A PHE* 5.4 1.1 - - + -
234A VAL* 1.3 78.2 - - - +
236A ALA* 1.3 72.2 + - - +
237A ALA* 4.6 1.3 - - + +
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Residues in contact with ALA 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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83A ARG 2.8 17.5 + - - +
84A TYR* 3.6 32.3 - - + -
85A PRO* 3.6 16.1 - - + +
88A MET* 3.5 21.5 - - + -
209A HIS* 4.3 0.4 - - + -
210A TYR 3.5 7.4 - - - +
211A LEU* 3.8 10.4 - - + +
235A THR* 1.3 79.4 + - - +
237A ALA* 1.3 65.0 + - - +
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Residues in contact with ALA 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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88A MET* 3.5 10.2 - - - +
209A HIS* 3.2 9.0 - - - +
210A TYR* 2.8 59.7 + - + +
212A SER* 5.4 2.7 - - - -
235A THR* 4.6 3.4 - - + +
236A ALA* 1.3 78.3 - - - +
238A GLY* 1.3 61.8 + - - +
239A LEU 3.5 2.2 - - - -
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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