Contacts of the helix formed by residues 163 - 173 (chain C) in PDB entry 1KBO
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 ASP 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A GLY* 3.1 22.2 + - - +
258A HIS* 2.9 25.8 + - - +
155C TYR 3.8 5.0 - - - +
156C SER* 3.9 3.0 - - - -
157C LEU* 3.5 22.8 - - + +
162C GLY* 1.3 69.9 - - - -
164C MET* 1.3 64.3 + - - +
165C ASN* 3.2 35.9 + - - +
166C VAL* 2.8 35.6 + - + +
167C ILE* 3.3 9.6 - - - +
263C ILE* 5.3 3.6 - - - +
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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
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103C LEU* 4.2 22.9 - - + -
146C ILE* 5.9 2.2 - - + -
148C THR* 4.5 4.9 - - + -
155C TYR* 3.1 34.6 + - + +
162C GLY 3.6 1.2 + - - -
163C ASP* 1.3 75.7 + - - +
165C ASN* 1.3 60.5 + - - +
166C VAL 3.0 0.2 - - - -
167C ILE* 3.2 22.9 + - - -
168C LEU* 3.1 50.9 + - + +
188C LEU* 4.2 7.4 - - + -
190C TYR* 3.4 43.1 - - + +
269C ILE* 3.8 11.4 - - + -
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Residues in contact with ASN 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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157C LEU* 5.8 0.6 - - - +
163C ASP* 3.0 30.4 + - - +
164C MET* 1.3 77.7 - - - +
166C VAL* 1.3 60.2 + - - +
168C LEU* 4.4 1.1 - - - -
169C TRP* 3.5 7.1 + - - +
255C VAL* 3.7 18.0 - - + +
263C ILE* 5.8 0.7 - - + -
264C PRO 5.7 0.2 - - - -
266C ASP* 2.7 42.1 + - - +
267C ASN 3.9 1.3 - - - -
268C GLN* 2.7 53.3 + - - +
269C ILE* 3.2 18.5 + - - +
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Residues in contact with VAL 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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166A VAL* 3.9 13.9 - - + +
169A TRP* 3.3 33.7 - - + +
170A PRO* 4.3 1.2 - - - +
255A VAL* 3.7 35.0 - - + +
256A GLY* 4.2 1.8 - - - -
258A HIS* 4.4 3.8 - - + +
163C ASP* 2.8 34.8 + - + +
165C ASN* 1.3 78.3 - - - +
167C ILE* 1.3 60.6 + - - +
169C TRP* 3.6 2.8 - - - +
170C PRO* 3.4 18.2 - - - +
255C VAL* 4.0 15.5 - - + -
263C ILE* 5.1 4.0 - - + -
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Residues in contact with ILE 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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169A TRP* 3.7 29.6 - - + +
170A PRO* 4.3 10.6 - - + +
103C LEU* 4.5 8.3 - - + -
106C PHE* 3.1 58.5 - - + +
107C GLY* 5.2 0.4 - - - -
155C TYR* 5.3 5.4 - - + -
161C HIS 4.8 3.4 - - - +
162C GLY 5.1 0.9 - - - -
163C ASP 3.3 19.3 - - - +
164C MET* 3.2 26.4 + - + +
166C VAL* 1.3 77.8 - - - +
168C LEU* 1.3 64.5 + - + +
170C PRO* 3.5 11.3 - - - +
171C ILE* 4.0 13.0 - - + +
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Residues in contact with LEU 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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103C LEU* 6.5 0.2 - - + -
144C LEU* 4.4 4.3 - - + -
146C ILE* 3.7 30.7 - - + -
164C MET* 3.1 39.4 + - + +
167C ILE* 1.3 75.8 - - + +
169C TRP* 1.3 65.8 + - - +
171C ILE* 3.4 11.1 + - + +
172C GLN* 2.9 46.7 + - - +
186C PRO* 4.3 4.9 - - + -
188C LEU* 4.3 8.3 - - + -
268C GLN* 4.1 18.4 - - + +
269C ILE* 3.4 31.4 - - + -
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Residues in contact with TRP 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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106A PHE* 5.6 1.6 - - - -
160A ILE 5.6 0.7 - - - -
161A HIS 4.2 20.7 + - - -
162A GLY* 4.8 1.7 - - - -
163A ASP 5.2 0.6 + - - -
166A VAL* 3.5 23.2 - - + +
167A ILE* 4.7 10.3 - - + +
165C ASN 3.5 12.8 + - - +
166C VAL 3.6 9.4 - - - +
167C ILE 3.3 0.2 - - - -
168C LEU* 1.3 78.0 - - - +
170C PRO* 1.4 73.7 - - + +
171C ILE 3.0 0.3 + - - -
173C SER* 2.7 71.3 + - - -
174C GLY 5.4 0.8 - - - +
222C PHE* 4.1 9.4 - + - -
223C ALA 6.3 0.2 - - - -
254C SER* 3.8 17.3 - - - -
255C VAL* 3.8 10.3 - - + -
256C GLY* 3.3 37.3 - - - -
257C HIS* 4.5 11.7 - + - -
267C ASN* 4.0 3.4 - - - -
268C GLN* 3.6 31.6 - - - +
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Residues in contact with PRO 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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105A TRP 5.6 0.4 - - - +
106A PHE* 3.9 30.5 - - + +
166A VAL 4.1 4.7 - - - +
167A ILE* 4.1 21.3 - - + +
170A PRO* 4.3 10.3 - - + -
166C VAL 3.4 11.7 - - - +
167C ILE 3.5 11.7 - - - +
169C TRP* 1.4 107.0 - - + +
171C ILE* 1.3 59.7 + - + +
174C GLY* 3.1 26.7 - - - +
175C ILE* 3.3 9.2 + - - +
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Residues in contact with ILE 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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101C PHE* 5.0 3.4 - - + -
103C LEU* 5.9 1.6 - - + -
106C PHE 5.0 0.4 - - - +
107C GLY* 4.4 10.5 - - - -
108C VAL* 3.8 37.2 - - + +
116C PHE* 5.7 4.5 - - + -
144C LEU* 3.5 34.3 - - + -
146C ILE* 5.8 1.3 - - + -
167C ILE* 4.0 18.8 - - + +
168C LEU* 3.5 12.3 - - + +
169C TRP 3.1 0.4 - - - -
170C PRO* 1.3 79.2 - - + +
172C GLN* 1.3 61.5 + - - +
175C ILE* 2.9 43.8 + - + +
176C LEU* 3.1 13.6 + - + +
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Residues in contact with GLN 172 (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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144C LEU* 3.5 35.0 - - + +
168C LEU* 2.9 20.3 + - + +
171C ILE* 1.3 78.8 - - - +
173C SER* 1.3 56.9 + - - +
176C LEU* 3.5 11.3 - - + +
177C HIS* 2.9 26.5 + - - +
183C VAL* 3.6 25.3 - - + +
186C PRO* 3.6 28.3 - - - +
220C LEU* 3.4 4.4 - - - +
222C PHE* 3.5 7.4 - - + -
268C GLN* 2.9 47.9 + - - +
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Residues in contact with SER 173 (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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161A HIS 5.3 0.9 + - - -
132C TYR* 3.9 15.8 + - - -
169C TRP* 2.7 67.6 + - - -
172C GLN* 1.3 74.1 - - - +
174C GLY* 1.3 65.7 + - - -
175C ILE 3.4 0.4 + - - -
177C HIS* 3.5 3.3 + - - +
178C PHE* 3.1 24.8 + - - +
222C PHE* 3.7 14.3 - - - -
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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