Contacts of the strand formed by residues 178 - 185 (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 ARG 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LYS* 2.7 35.8 + - - +
68A LEU* 3.9 21.7 - - + +
69A ASN* 3.3 25.8 + - - +
139A ASP 4.1 1.2 + - - -
140A ARG* 3.7 22.8 - - - +
141A ILE* 3.1 25.6 + - - +
173A THR* 5.1 1.7 - - - +
176A ASP 3.6 11.8 + - - +
177A GLY* 1.3 79.1 - - - +
179A MET* 1.3 60.3 + - - +
235A TRP* 4.4 4.4 - - - -
238A GLU* 4.2 20.6 + - - +
299A THR* 4.3 5.6 - - + +
300A LEU 3.4 7.6 - - - +
301A VAL* 3.5 26.3 - - + +
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Residues in contact with MET 179 (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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68A LEU* 4.1 2.9 - - - -
79A ILE* 4.5 0.2 - - + -
141A ILE* 3.4 48.9 - - + -
143A SER* 5.8 2.0 - - - +
165A PHE* 3.9 33.2 - - + -
166A PHE* 4.4 4.9 - - + -
169A PHE* 3.8 17.7 - - + -
178A ARG* 1.3 75.3 - - - +
180A LEU* 1.3 70.4 + - - +
181A LEU* 3.6 7.3 + - + +
235A TRP* 4.2 17.7 - - + -
298A PHE 3.3 2.4 - - - +
299A THR* 3.8 1.7 - - - +
300A LEU* 2.9 57.9 + - + +
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Residues in contact with LEU 180 (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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64A ALA* 3.8 36.8 - - + +
67A LYS* 3.7 17.3 - - + -
68A LEU* 3.7 17.8 - - + +
141A ILE 2.9 12.2 + - - +
142A VAL* 3.7 6.0 - - + -
143A SER* 3.1 26.7 + - - +
144A LEU* 4.2 2.9 - - + -
179A MET* 1.3 74.9 - - - +
181A LEU* 1.3 59.8 + - - +
182A HIS* 4.0 14.1 - - + -
297A GLN* 4.0 21.3 - - + -
298A PHE 3.4 15.5 - - - +
299A THR* 3.6 22.2 - - + +
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Residues in contact with LEU 181 (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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143A SER* 4.2 17.5 - - - +
147A PHE* 3.6 44.0 - - + -
165A PHE* 4.7 8.1 - - + -
166A PHE* 3.5 37.2 - - + -
179A MET* 3.6 5.9 + - + -
180A LEU* 1.3 72.7 - - - +
182A HIS* 1.3 62.1 + - - +
183A THR* 4.6 3.6 - - + -
226A VAL* 4.2 15.7 - - + -
296A CYS 3.3 3.1 - - - +
297A GLN* 3.2 1.4 - - - -
298A PHE* 2.7 54.6 + - + +
300A LEU* 4.5 8.7 - - + -
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Residues in contact with HIS 182 (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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42A SER* 4.2 2.2 - - - -
43A CYS 3.8 20.0 + - - -
60A LYS* 4.0 11.7 - - + -
143A SER 2.9 20.0 + - - +
144A LEU* 3.4 19.7 - - + +
145A GLY* 3.0 32.3 + - - -
146A ALA 4.6 1.4 + - - -
147A PHE* 4.6 2.9 - - - +
180A LEU* 3.7 7.1 + - + -
181A LEU* 1.3 71.6 - - - +
183A THR* 1.3 63.4 + - - +
243A ILE* 4.2 5.6 - - + -
295A VAL* 3.9 16.2 - - + +
296A CYS 3.5 4.9 - - - -
297A GLN* 2.7 31.5 + - + +
902A CO3 2.7 35.5 + - - -
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Residues in contact with THR 183 (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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147A PHE* 3.6 37.4 - - + +
148A GLU* 3.3 17.9 - - - +
181A LEU* 4.6 3.6 - - + -
182A HIS* 1.3 76.6 - - - +
184A ILE* 1.3 81.2 + - - +
185A THR* 3.7 11.1 - - + +
221A PRO* 4.1 4.5 - - + +
226A VAL* 5.0 0.4 - - + -
295A VAL* 3.5 2.7 - - - +
296A CYS 3.0 29.5 + - - -
298A PHE* 4.0 20.9 - - + -
902A CO3 3.6 10.5 - - - -
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Residues in contact with ILE 184 (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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148A GLU* 3.0 15.2 + - + +
183A THR* 1.3 88.0 + - - +
185A THR* 1.3 73.5 + - - +
220A LEU* 3.7 31.2 - - + -
221A PRO* 3.5 12.6 - - - +
247A TYR* 4.1 3.4 - - + -
288A PHE* 4.0 21.8 - - + -
293A THR* 4.3 3.1 - - + -
294A ASP 3.2 12.8 - - - +
295A VAL* 4.3 1.8 - - + +
901A 10A 3.7 44.0 - - + -
902A CO3 3.3 30.1 - - - +
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Residues in contact with THR 185 (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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183A THR* 3.7 22.9 - - + +
184A ILE* 1.3 84.4 - - - +
186A ILE* 1.3 68.1 + - - +
220A LEU* 4.8 0.9 - - - -
221A PRO* 3.2 17.5 - - + +
222A ARG 5.4 0.4 - - - -
223A ILE* 4.6 16.4 - - + +
293A THR* 3.5 6.4 - - - -
294A ASP* 2.7 54.1 + - - +
296A CYS* 4.3 15.6 - - + +
298A PHE* 4.5 9.4 - - + -
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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