Contacts of the helix formed by residues 182 - 194 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ASN 3.5 6.7 + - - -
179A LEU* 3.1 13.8 + - - +
180A THR 3.1 2.8 - - - -
181A LYS* 1.3 80.0 - - - +
183A VAL* 1.3 63.3 + - - +
184A LYS* 3.2 24.3 + - - +
185A ASP* 2.6 27.5 + - - -
186A LEU* 3.0 18.2 + - - +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LYS* 6.3 1.6 - - - +
117A ARG* 4.3 18.2 - - - +
180A THR 5.8 0.9 - - - +
181A LYS 5.6 1.6 - - - +
182A SER* 1.3 73.0 - - - +
184A LYS* 1.3 73.1 + - - +
186A LEU* 3.7 9.6 - - + -
187A GLU* 2.8 50.2 + - - +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A SER* 3.2 20.3 - - - +
183A VAL* 1.3 113.7 - - - +
185A ASP* 1.3 64.9 + - - +
186A LEU 3.1 0.2 - - - -
187A GLU* 4.0 9.1 - - - +
188A LYS* 3.1 41.0 + - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLY 5.1 4.2 - - - +
168A ILE* 3.3 27.2 - - + +
179A LEU* 3.6 19.1 - - + +
182A SER* 2.6 35.4 + - - +
184A LYS* 1.3 78.6 - - - +
186A LEU* 1.3 57.5 + - - +
188A LYS* 3.8 19.1 - - - +
189A LEU* 3.2 20.1 + - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS 4.3 10.3 - - - +
103A LEU* 4.5 3.4 - - + -
117A ARG* 3.5 43.5 - - + +
121A ILE* 4.3 14.6 - - + -
179A LEU* 3.3 32.8 - - + +
180A THR* 3.7 28.5 - - - +
182A SER 3.0 9.8 + - - +
183A VAL* 3.0 17.7 + - + +
185A ASP* 1.3 77.1 - - - +
187A GLU* 1.3 59.7 + - - +
189A LEU* 3.1 9.3 + - + +
190A ASP* 3.0 30.5 + - - +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ARG* 3.5 20.6 + - - +
183A VAL* 2.8 35.6 + - + +
184A LYS* 4.1 6.9 - - - +
186A LEU* 1.3 70.2 - - - +
188A LYS* 1.3 66.0 + - - +
190A ASP* 3.4 5.8 + - - +
191A LYS* 3.2 23.6 + - - +
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 3.4 39.0 - - + +
167A GLY 5.8 0.4 - - - +
168A ILE* 4.3 3.4 - - + -
184A LYS* 3.1 35.3 + - - +
185A ASP* 3.6 21.9 + - - +
187A GLU* 1.3 76.6 - - - +
189A LEU* 1.3 62.7 + - - +
191A LYS* 3.6 5.9 + - - +
192A ALA* 3.2 22.9 + - - +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ARG* 5.4 1.3 - - + +
120A ASN* 4.1 22.0 - - + +
121A ILE* 3.7 29.6 - - + -
124A VAL* 4.2 9.2 - - + -
163A LEU* 3.6 29.6 - - + -
166A ALA* 5.4 0.2 - - - -
168A ILE* 4.4 8.5 - - + +
179A LEU* 4.3 13.0 - - + -
185A ASP 3.2 10.9 + - - +
186A LEU* 3.1 13.6 + - + +
188A LYS* 1.3 78.3 - - - +
190A ASP* 1.3 66.5 + - - +
192A ALA* 3.3 3.7 + - + +
193A LEU* 3.1 42.4 + - + +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP* 3.5 17.5 - - - +
114A ARG* 6.1 0.2 - - - -
116A ASP* 4.9 0.7 - - - +
117A ARG* 3.3 36.6 + - - +
120A ASN* 3.4 20.0 + - - +
186A LEU 3.0 14.5 + - - +
187A GLU* 3.4 10.0 + - + +
189A LEU* 1.3 78.8 - - - +
191A LYS* 1.3 60.9 + - - +
194A ASN* 2.4 43.6 + - - +
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A GLU 3.2 17.2 + - - +
188A LYS* 4.0 6.5 - - - +
189A LEU 3.3 0.2 - - - -
190A ASP* 1.3 77.5 - - - +
192A ALA* 1.3 63.2 + - - +
194A ASN* 4.9 1.5 - - - +
195A SER* 4.2 11.8 + - - -
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LYS* 3.2 41.5 + - + +
163A LEU* 5.2 2.0 - - + -
165A ARG* 5.9 1.1 - - + -
166A ALA* 4.4 7.6 - - + -
188A LYS 3.2 16.0 + - - +
189A LEU* 3.3 7.4 + - + +
191A LYS* 1.3 80.3 - - - +
193A LEU* 1.3 60.2 + - + +
195A SER* 2.5 30.1 + - - -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASN* 3.6 38.8 - - + +
123A ASP* 4.4 12.6 - - + +
124A VAL* 4.4 6.7 - - + -
159A TYR* 4.1 22.7 - - + +
162A LYS* 4.2 15.7 - - + -
163A LEU* 4.9 6.1 - - + -
189A LEU* 3.1 35.9 + - + +
192A ALA* 1.3 75.3 - - + +
194A ASN* 1.3 62.9 + - - +
195A SER 3.0 5.6 - - - -
196A ILE* 3.1 37.5 + - + +
212A ARG* 3.2 18.2 + - - +
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Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 3.7 17.4 + - - +
119A ARG* 3.0 32.6 + - - +
120A ASN* 3.8 5.2 + - - +
190A ASP* 2.4 45.1 + - - +
191A LYS* 4.9 1.8 - - - +
192A ALA 3.4 0.2 - - - -
193A LEU* 1.3 76.1 - - - +
195A SER* 1.3 61.7 + - - +
196A ILE 3.2 7.5 + - - +
197A PRO* 5.5 0.2 - - - +
212A ARG* 4.3 4.3 + - - +
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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