Contacts of the strand formed by residues 163 - 171 (chain C) in PDB entry 1KPH
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 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C LYS* 4.0 15.7 - - + +
60C LEU* 3.8 21.4 - - + +
132C ARG* 3.5 28.4 - - - +
133C ILE 3.2 20.6 + - - -
158C LEU* 3.8 7.0 - - - +
161C ASP 3.6 4.9 - - - +
162C GLY* 1.3 80.8 - - - +
164C MET* 1.3 68.1 + - - +
165C LEU* 5.7 0.2 - - + -
284C THR* 4.2 14.8 - - + -
285C CYS 3.5 11.4 - - - +
286C GLN* 3.4 25.1 - - - +
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Residues in contact with MET 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 4.1 1.8 - - - -
133C ILE* 3.2 30.5 - - + +
135C SER* 5.4 1.3 - - - +
150C PHE* 3.7 38.8 - - + -
151C PHE* 4.0 25.6 - - + -
154C ALA* 3.7 20.2 - - + -
158C LEU* 4.2 10.5 - - + +
163C VAL* 1.3 77.1 - - - +
165C LEU* 1.3 71.6 + - - +
166C LEU* 4.5 7.0 - - + -
220C PHE* 4.1 8.7 - - + -
283C PHE 3.5 0.9 - - - +
284C THR* 3.8 1.2 - - - -
285C CYS* 2.8 51.5 + - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 3.7 39.3 - - + +
59C LYS* 3.6 28.5 - - + -
60C LEU* 3.7 18.9 - - + +
133C ILE 2.9 10.0 + - - +
134C VAL* 3.5 8.8 - - + -
135C SER 3.1 25.5 + - - +
136C ILE* 4.9 0.2 - - + -
163C VAL* 5.5 0.4 - - + -
164C MET* 1.3 74.9 - - - +
166C LEU* 1.3 58.5 + - - +
167C HIS* 4.0 22.4 - - + +
282C GLN* 4.1 13.0 - - + -
283C PHE 3.7 15.5 - - - +
284C THR* 3.9 9.4 - - + +
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C SER* 3.7 23.3 - - - +
139C PHE* 4.1 34.1 - - + -
150C PHE* 4.3 11.9 - - + -
151C PHE* 3.5 37.5 - - + -
164C MET* 3.8 7.8 + - + -
165C LEU* 1.3 71.6 - - - +
167C HIS* 1.3 61.3 + - - +
168C THR* 4.5 9.0 - - + -
211C VAL* 4.2 15.5 - - + -
282C GLN* 3.4 0.3 - - - -
283C PHE* 2.6 51.4 + - + +
285C CYS* 4.5 7.9 - - - -
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Residues in contact with HIS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C CYS* 4.1 12.6 - - + -
52C LYS* 4.2 4.6 - - + +
135C SER 2.8 16.8 + - - +
136C ILE* 3.6 31.6 - - + +
137C GLY 2.9 25.6 + - - -
138C ALA 4.8 0.3 + - - -
139C PHE* 5.2 0.5 - - - +
165C LEU* 3.9 11.2 + - + -
166C LEU* 1.3 74.1 - - - +
168C THR* 1.3 65.6 + - - +
228C LEU* 3.9 19.5 - - + -
280C VAL* 3.5 12.4 - - + +
281C ASN 3.3 5.2 - - - -
282C GLN* 3.0 30.9 + - + +
3902C CO3 2.6 36.2 + - - -
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PHE* 3.8 33.2 - - + +
140C GLU* 3.2 21.8 + - - +
166C LEU* 4.5 7.2 - - + -
167C HIS* 1.3 78.2 - - - +
169C ILE* 1.3 77.8 + - - +
170C THR* 3.9 5.5 - - + +
206C PRO* 4.4 0.6 - - + +
211C VAL* 4.6 5.8 - - + -
280C VAL* 4.1 1.8 - - - -
281C ASN* 2.9 29.0 + - - +
283C PHE* 3.8 26.5 - - + -
3902C CO3 3.8 4.7 - - - -
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Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLU* 2.9 19.6 + - - +
168C THR* 1.3 88.7 + - - +
170C THR* 1.3 68.1 + - - +
205C LEU* 3.5 30.7 - - + +
206C PRO* 3.6 12.5 - - - +
232C TYR* 4.0 10.1 - - + -
273C PHE* 4.3 10.3 - - + -
278C ILE* 4.7 2.2 - - + -
279C ASP 3.3 15.7 - - - +
280C VAL* 3.9 3.4 - - + +
3901C 10A 3.6 48.0 - - + -
3902C CO3 3.5 27.6 - - - +
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C THR* 3.9 11.9 - - + +
169C ILE* 1.3 86.4 - - - +
171C GLY* 1.3 59.8 + - - +
205C LEU* 4.6 0.7 - - - -
206C PRO* 3.2 14.6 - - - +
207C SER 4.5 0.9 - - - -
208C ILE* 3.8 29.9 - - + +
211C VAL* 4.7 3.4 - - + -
278C ILE* 3.7 1.4 - - - -
279C ASP* 2.7 42.3 + - - +
281C ASN* 3.2 23.0 + - - +
283C PHE* 4.3 16.8 - - + -
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C THR* 1.3 75.6 - - - +
172C LEU* 1.3 69.7 + - - +
173C HIS* 4.0 4.7 + - - -
188C PHE* 5.9 0.7 - - - -
205C LEU* 4.0 23.0 - - - +
206C PRO 3.1 9.6 + - - +
207C SER* 4.0 20.4 + - - -
277C TYR 4.2 6.3 - - - -
278C ILE* 4.3 2.5 - - - -
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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