Contacts of the helix formed by residues 160 - 166 (chain B) 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 PRO 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ARG 5.1 0.7 - - - -
159B PHE* 1.3 92.9 - - + +
161B ASN* 1.3 65.2 + - - +
162B LEU* 3.2 3.7 + - - -
163B LEU* 3.4 11.7 + - + +
164B VAL* 3.5 10.0 + - + +
183B LEU* 4.4 1.1 - - + -
186B VAL* 3.3 33.4 - - + +
187B ILE* 4.2 18.4 - - + -
190B ALA* 5.6 2.2 - - + -
345B ILE* 6.5 0.9 - - + -
346B LEU* 5.2 4.3 - - + -
349B TYR* 3.2 41.0 - - + +
467B LEU* 4.8 1.3 - - + -
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Residues in contact with ASN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG 4.7 3.4 + - - -
35B ASP 3.0 29.0 + - - +
36B GLY 3.5 15.4 + - - -
37B LEU* 3.6 13.3 - - - +
98B LEU* 3.9 6.5 - - - +
130B LEU* 4.0 22.2 - - + -
159B PHE* 3.2 26.4 + - + -
160B PRO* 1.3 73.3 - - - +
162B LEU* 1.3 64.7 + - - +
164B VAL* 3.0 1.6 + - - -
165B ASN* 3.0 56.1 + - - +
166B GLY 4.0 1.0 + - - -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 4.5 3.8 - - + -
32B ASP 4.2 3.8 - - - +
33B ILE* 4.0 30.7 - - - +
34B ARG 5.0 1.9 + - - +
35B ASP 4.3 0.2 - - - -
36B GLY* 3.6 30.2 - - - +
160B PRO 3.2 2.3 + - - +
161B ASN* 1.3 76.0 - - - +
163B LEU* 1.3 57.9 + - - +
166B GLY* 3.0 31.7 + - - +
167B SER* 4.4 6.3 - - - -
178B ILE* 3.3 37.6 - - + +
331B ALA* 4.2 10.1 - - + -
345B ILE* 4.2 28.0 - - + -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO* 3.4 4.2 + - + +
161B ASN 3.2 0.4 - - - -
162B LEU* 1.3 77.3 - - - +
164B VAL* 1.3 65.5 + - - +
165B ASN 3.4 0.5 + - - -
178B ILE* 4.7 7.9 - - + -
179B PRO 3.4 7.6 - - - +
181B HIS* 2.9 47.7 + - + +
186B VAL* 3.8 37.5 - - + -
208B LEU* 5.0 4.9 - - + -
329B MET* 5.1 3.1 - - - -
342B ILE* 3.8 26.9 - - + -
345B ILE* 3.7 40.4 - - + +
346B LEU* 3.9 12.3 - - + -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG* 3.2 16.3 - - + +
96B GLU* 4.0 25.8 - - + -
159B PHE* 4.0 15.5 - - + -
160B PRO* 3.5 21.8 - - + +
161B ASN 3.0 5.2 + - - +
163B LEU* 1.3 76.6 - - - +
165B ASN* 1.3 57.6 + - - +
180B PRO* 3.2 0.7 - - - +
181B HIS 3.1 30.8 + - - +
183B LEU* 3.9 42.8 - - + -
186B VAL* 4.3 7.4 - - + -
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 5.5 2.1 + - - -
93B LYS 4.5 6.8 - - - +
94B ASN* 3.5 25.8 + - - +
95B ARG* 2.9 9.2 + - - -
96B GLU* 2.8 54.4 + - - +
98B LEU* 3.9 13.9 - - - +
159B PHE* 4.8 2.2 - - - -
161B ASN* 3.0 37.6 + - - +
164B VAL* 1.3 76.5 - - - +
166B GLY* 1.3 65.4 + - - +
180B PRO* 4.0 11.3 - - - +
261B TYR* 4.6 4.0 + - - -
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY 4.4 10.0 - - - +
94B ASN* 5.7 0.2 + - - -
161B ASN* 5.0 0.9 + - - +
162B LEU* 3.0 23.6 + - - +
163B LEU 3.7 1.4 + - - -
164B VAL 3.6 1.4 - - - -
165B ASN* 1.3 86.0 - - - +
167B SER* 1.3 64.0 + - - -
178B ILE* 3.1 22.4 - - - -
179B PRO 3.9 5.8 - - - -
180B PRO* 4.2 0.4 - - - -
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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