Contacts of the helix formed by residues 182 - 194 (chain C) in PDB entry 4KYI
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 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C ASN 3.9 6.0 + - - -
179C LEU* 3.1 16.7 + - - +
180C THR 3.2 2.2 - - - -
181C LYS* 1.3 81.2 - - - +
183C VAL* 1.3 63.2 + - - +
184C LYS* 3.2 21.5 + - - +
185C ASP* 3.9 15.3 + - - +
186C LEU* 3.1 15.3 + - - +
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Residues in contact with VAL 183 (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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102C LYS* 5.8 6.1 - - - +
117C ARG* 4.4 18.8 - - - +
180C THR 5.8 2.0 - - - +
181C LYS 5.7 1.1 - - - +
182C SER* 1.3 73.0 + - - +
184C LYS* 1.3 75.4 + - - +
186C LEU* 3.5 10.3 - - + +
187C GLU* 2.9 47.1 + - + +
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Residues in contact with LYS 184 (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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182C SER* 3.1 16.0 - - - +
183C VAL* 1.3 100.1 - - - +
185C ASP* 1.3 65.4 + - - +
187C GLU* 3.2 25.4 + - - +
188C LYS* 3.4 22.1 + - - +
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Residues in contact with ASP 185 (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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167C GLY 4.4 12.1 - - - +
168C ILE* 3.4 25.1 - - + +
179C LEU* 3.3 23.1 - - + +
182C SER* 3.5 15.9 + - - +
184C LYS* 1.3 82.0 - - - +
186C LEU* 1.3 60.2 + - - +
187C GLU 3.3 0.4 - - - -
188C LYS* 4.0 23.2 + - - -
189C LEU* 3.5 2.6 + - - +
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Residues in contact with LEU 186 (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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102C LYS* 4.5 7.6 - - + +
103C LEU* 4.5 8.7 - - + -
117C ARG* 3.9 35.0 - - + +
121C ILE* 4.0 13.9 - - + -
179C LEU* 3.7 21.3 - - + +
180C THR* 4.1 24.7 - - + +
182C SER 3.1 15.6 + - - +
183C VAL* 3.5 12.8 - - + +
184C LYS 3.1 0.4 - - - -
185C ASP* 1.3 76.9 - - - +
187C GLU* 1.3 63.4 + - - +
189C LEU* 3.5 32.1 - - + +
190C ASP* 3.5 15.2 - - - +
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Residues in contact with GLU 187 (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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117C ARG* 3.9 19.9 + - - +
183C VAL* 2.9 31.9 + - + +
184C LYS* 3.5 14.4 - - - +
186C LEU* 1.3 76.4 - - - +
188C LYS* 1.3 63.0 + - - +
189C LEU 3.2 0.4 - - - -
190C ASP* 3.3 13.6 + - - +
191C LYS* 3.4 13.2 + - - +
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Residues in contact with LYS 188 (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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166C ALA* 3.2 39.6 - - + +
168C ILE* 4.1 6.5 - - + -
184C LYS* 3.4 20.4 + - - +
185C ASP* 4.1 26.3 + - - +
186C LEU 3.4 0.2 - - - -
187C GLU* 1.3 74.6 - - + +
189C LEU* 1.3 66.2 + - - +
191C LYS* 3.4 6.5 + - - +
192C ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 189 (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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117C ARG* 5.1 1.6 - - + +
120C ASN* 4.3 14.3 + - + -
121C ILE* 3.6 32.8 - - + -
124C VAL* 3.6 27.1 - - + -
163C LEU* 3.8 14.8 - - + -
168C ILE* 3.6 12.1 - - + +
179C LEU* 3.9 11.4 - - + -
185C ASP 3.5 12.9 + - - +
186C LEU* 3.5 23.8 - - + +
188C LYS* 1.3 80.4 - - - +
190C ASP* 1.3 61.9 + - - +
192C ALA* 3.8 2.7 - - - +
193C LEU* 3.1 37.5 + - + +
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Residues in contact with ASP 190 (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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105C ASP* 5.2 1.0 - - - +
116C ASP* 4.5 3.4 - - - -
117C ARG* 2.9 56.7 + - - +
120C ASN* 2.8 24.7 + - - +
186C LEU 3.5 6.8 + - - +
187C GLU* 3.3 7.9 + - - +
188C LYS 3.2 0.6 - - - -
189C LEU* 1.3 74.6 - - - +
191C LYS* 1.3 59.3 + - - +
193C LEU 3.0 1.7 + - - -
194C ASN* 2.6 51.7 + - - +
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Residues in contact with LYS 191 (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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187C GLU 3.4 9.9 + - - +
188C LYS* 4.0 8.7 - - - +
190C ASP* 1.3 78.8 - - - +
192C ALA* 1.3 62.2 + - - +
194C ASN* 4.4 6.8 - - - +
195C SER* 3.6 17.8 + - - -
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Residues in contact with ALA 192 (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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162C LYS* 3.2 46.1 - - + +
163C LEU* 4.5 8.7 - - + -
166C ALA* 4.5 8.9 - - + +
188C LYS 2.9 18.6 + - - +
189C LEU* 3.8 4.7 - - - +
191C LYS* 1.3 76.9 - - - +
193C LEU* 1.3 56.9 + - - +
195C SER* 2.3 27.6 + - - -
196C ILE* 4.2 0.9 - - - +
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Residues in contact with LEU 193 (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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120C ASN* 3.3 48.2 - - + +
123C ASP* 4.6 8.5 - - + -
124C VAL* 4.1 7.0 - - + +
159C TYR* 4.5 22.7 - - + +
162C LYS* 4.6 2.9 - - + -
163C LEU* 4.2 15.7 - - + -
189C LEU* 3.1 29.3 + - + +
190C ASP 3.0 2.0 + - - -
192C ALA* 1.3 77.9 - - - +
194C ASN* 1.3 61.6 + - - +
195C SER 3.1 5.2 - - - -
196C ILE* 3.1 34.6 + - + +
212C ARG* 3.1 22.1 + - - +
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Residues in contact with ASN 194 (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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116C ASP* 4.0 17.9 + - - +
119C ARG* 3.9 13.8 + - - +
120C ASN* 3.2 18.2 + - - -
190C ASP* 2.6 46.0 + - - +
191C LYS* 4.0 6.3 - - - +
193C LEU* 1.3 68.7 - - - +
195C SER* 1.3 56.6 + - - +
196C ILE 3.1 14.5 + - - +
212C ARG* 5.0 2.0 - - - +
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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