Contacts of the helix formed by residues 168 - 180 (chain B) in PDB entry 1KYO
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 SER 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B LEU* 5.2 0.7 - - - -
166B ARG* 4.0 2.4 + - - +
167B VAL* 1.3 76.0 - - - +
169B LEU* 1.3 65.1 + - - +
170B GLN* 3.1 20.4 + - - +
171B ASP* 3.1 33.3 + - - +
172B ILE* 3.5 12.9 + - - +
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Residues in contact with LEU 169 (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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54B PHE* 3.6 37.2 - - + -
114B PHE* 3.2 25.4 - - + +
115B LYS 4.5 1.6 - - - +
116B PRO* 4.2 23.8 - - + -
119B LEU* 4.0 24.6 - - + +
168B SER* 1.3 73.6 - - - +
170B GLN* 1.3 62.1 + - - +
172B ILE* 3.6 9.5 + - + +
173B LYS* 3.4 37.1 + - - +
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Residues in contact with GLN 170 (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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168B SER* 3.0 10.2 + - - +
169B LEU* 1.3 76.8 - - - +
171B ASP* 1.3 60.4 + - - +
172B ILE 3.1 1.6 - - - -
173B LYS* 2.9 39.2 + - - +
174B ASP* 2.8 55.5 + - - +
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Residues in contact with ASP 171 (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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43B THR* 4.7 5.3 - - + +
44B LYS* 2.9 42.7 + - + +
47B VAL* 3.7 6.2 - - + +
166B ARG 4.1 0.2 - - - +
167B VAL* 3.7 14.8 - - + -
168B SER* 3.1 32.5 + - - +
170B GLN* 1.3 77.6 - - - +
172B ILE* 1.3 61.1 + - - +
174B ASP* 3.7 12.4 - - - +
175B PHE* 3.1 24.9 + - - +
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Residues in contact with ILE 172 (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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47B VAL* 3.9 8.2 - - + +
50B LEU* 4.4 16.8 - - + -
51B LEU* 4.2 21.5 - - + +
54B PHE* 3.8 29.8 - - + -
114B PHE* 3.8 14.8 - - + -
119B LEU* 3.7 30.5 - - + -
167B VAL* 4.2 12.1 - - + +
168B SER 3.6 16.8 - - - +
169B LEU* 3.6 13.0 - - - +
170B GLN 3.1 0.6 - - - -
171B ASP* 1.3 74.9 - - - +
173B LYS* 1.3 55.2 + - - +
175B PHE* 3.3 3.5 + - - +
176B ALA* 2.8 34.8 + - - +
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Residues in contact with LYS 173 (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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113B ALA 5.5 1.3 + - - +
114B PHE* 3.8 39.2 + - + -
169B LEU* 3.4 27.6 + - - +
170B GLN* 2.9 41.4 + - - +
172B ILE* 1.3 81.2 - - - +
174B ASP* 1.3 61.3 + - - +
176B ALA* 3.4 8.2 - - - +
177B ASP* 3.2 28.0 + - - +
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Residues in contact with ASP 174 (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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43B THR* 6.1 1.3 - - + -
170B GLN* 2.8 43.6 + - - +
171B ASP* 3.7 13.2 - - - +
173B LYS* 1.3 74.5 - - - +
175B PHE* 1.3 60.9 + - - +
176B ALA 3.0 1.6 - - - -
177B ASP* 2.8 24.9 + - - +
178B LYS* 3.0 17.4 + - + +
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Residues in contact with PHE 175 (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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37B GLY* 3.3 30.1 - - - -
41B TYR 3.3 26.0 - - - -
42B ALA* 3.5 14.1 - - - -
43B THR* 3.5 26.9 - - + +
47B VAL* 3.6 20.6 - - + -
48B ALA* 4.2 11.0 - - + -
51B LEU* 3.6 23.8 - - + -
171B ASP 3.1 16.0 + - - +
172B ILE 3.8 0.7 - - - +
174B ASP* 1.3 78.3 - - - +
176B ALA* 1.3 59.9 + - - +
178B LYS* 3.8 13.7 - - + -
179B VAL* 3.0 56.1 + - + +
215B LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 176 (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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51B LEU* 3.9 23.6 - - + -
114B PHE* 4.1 13.0 - - + -
172B ILE 2.8 17.6 + - - +
173B LYS* 3.4 12.6 - - - +
175B PHE* 1.3 79.1 - - - +
177B ASP* 1.3 57.9 + - - +
180B TYR* 2.9 46.7 + - + +
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Residues in contact with ASP 177 (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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173B LYS* 3.2 16.4 + - - +
174B ASP* 2.8 13.5 + - - +
176B ALA* 1.3 78.4 - - - +
178B LYS* 1.3 64.1 + - - +
179B VAL 3.4 0.3 + - - -
180B TYR* 3.9 2.9 + - - +
181B THR* 3.4 21.5 - - - +
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Residues in contact with LYS 178 (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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41B TYR 4.9 8.4 + - - -
43B THR* 5.5 9.3 - - - -
174B ASP* 3.0 14.7 + - + +
175B PHE* 3.9 17.7 - - + +
176B ALA 3.5 0.2 - - - -
177B ASP* 1.3 77.9 - - + +
179B VAL* 1.3 62.6 + - + +
181B THR* 3.4 17.7 + - - +
184B ASN* 4.1 8.1 + - - -
212B GLY* 5.8 0.7 - - - -
213B LYS 5.1 3.3 - - - +
215B LEU* 3.7 33.8 - - - +
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Residues in contact with VAL 179 (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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35B VAL* 3.1 32.7 - - + +
36B HIS 3.6 7.2 - - - +
37B GLY* 3.3 24.2 - - - -
41B TYR* 5.5 2.7 - - + -
51B LEU* 4.9 5.8 - - + -
87B ILE* 5.4 1.1 - - + -
175B PHE* 3.0 53.9 + - + +
176B ALA 4.4 0.7 - - - +
178B LYS* 1.3 81.1 - - + +
180B TYR* 1.3 64.4 + - + +
181B THR 3.1 7.8 + - - -
184B ASN* 3.8 15.6 - - - +
215B LEU* 5.6 4.0 - - + -
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Residues in contact with TYR 180 (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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35B VAL* 4.0 23.6 - - + -
51B LEU* 3.5 38.8 - - + +
55B ASN* 2.7 38.7 + - - -
87B ILE* 3.9 9.2 - - + +
89B LEU* 4.3 4.8 - - + +
108B VAL 6.0 0.2 - - - -
109B LEU* 3.3 61.0 - - + +
112B THR* 5.8 2.5 - - - -
114B PHE* 5.6 2.7 - + - -
176B ALA* 2.9 36.2 + - + +
177B ASP* 3.9 3.6 + - - +
178B LYS 3.7 0.2 - - - -
179B VAL* 1.3 68.9 - - + +
181B THR* 1.3 65.6 + - - +
185B LEU* 5.0 0.7 - - - -
209B LEU* 3.7 19.3 - - + +
210B PRO* 4.4 3.8 - - - +
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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