Contacts of the helix formed by residues 165 - 179 (chain A) in PDB entry 2K5U
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 GLY 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLN* 3.2 8.6 - - - +
157A ALA 4.3 3.6 - - - -
158A THR* 2.9 27.4 - - - +
163A GLY 3.3 1.6 + - - -
164A GLU* 1.3 74.1 - - - +
166A LEU* 1.3 58.3 + - - +
167A TYR* 3.4 3.3 - - - +
168A GLU* 4.0 10.4 - - - +
169A GLY* 3.0 24.2 + - - -
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Residues in contact with LEU 166 (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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33A VAL* 6.0 4.0 - - + -
36A LYS* 4.3 24.9 - - + -
124A PHE* 5.6 2.9 - - + -
126A ASN* 4.4 7.0 - - - +
158A THR* 3.3 29.6 - - + +
159A CYS 3.6 10.5 - - - +
160A ALA* 3.6 26.2 - - + +
163A GLY* 3.3 34.0 + - - +
165A GLY* 1.3 76.2 - - - +
167A TYR* 1.3 68.6 + - + +
169A GLY* 3.3 1.4 + - - -
170A LEU* 3.2 28.6 + - + +
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Residues in contact with TYR 167 (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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36A LYS* 5.3 11.4 - - + +
162A SER 5.0 2.0 + - - -
163A GLY* 3.1 39.0 - - - -
164A GLU* 5.3 0.4 - - - -
165A GLY 3.4 1.7 - - - +
166A LEU* 1.3 80.6 - - + +
168A GLU* 1.3 58.2 + - - +
170A LEU* 3.0 21.3 - - + +
171A GLU* 2.9 32.9 + - - +
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Residues in contact with GLU 168 (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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156A GLN* 4.5 7.9 - - - +
165A GLY* 3.8 13.4 + - - +
166A LEU 3.4 0.2 - - - -
167A TYR* 1.3 78.0 - - - +
169A GLY* 1.3 57.2 + - - +
171A GLU* 4.1 5.6 - - + +
172A TRP* 3.2 31.5 + - + +
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Residues in contact with GLY 169 (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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124A PHE* 3.9 19.5 - - - -
156A GLN* 4.0 11.0 + - - -
165A GLY 3.0 19.3 + - - -
166A LEU 3.8 1.6 - - - -
167A TYR 3.1 0.2 - - - -
168A GLU* 1.3 76.8 - - - +
170A LEU* 1.3 56.6 + - - +
172A TRP* 3.9 1.9 - - - +
173A LEU* 2.7 40.2 + - - +
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Residues in contact with LEU 170 (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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1A MYR 4.6 27.6 - - + +
124A PHE* 4.7 3.1 - - - -
166A LEU* 3.2 18.6 + - + +
167A TYR* 3.0 28.9 - - + +
169A GLY* 1.3 74.1 - - - +
171A GLU* 1.3 88.2 + - - +
173A LEU* 3.0 8.0 + - - +
174A SER* 2.7 41.3 + - - +
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Residues in contact with GLU 171 (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 TYR* 2.9 16.5 + - - +
168A GLU* 4.1 6.5 - - + +
170A LEU* 1.3 96.1 - - - +
172A TRP* 1.3 62.3 + - - +
174A SER* 3.2 15.9 + - - -
175A ASN* 3.3 14.4 + - - +
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Residues in contact with TRP 172 (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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154A PHE* 5.0 25.4 - + + -
156A GLN* 6.3 2.9 - - + -
168A GLU* 3.2 21.3 + - + +
169A GLY* 3.9 5.2 - - - +
171A GLU* 1.3 80.4 - - - +
173A LEU* 1.3 69.3 + - + +
175A ASN* 3.1 32.3 + - + +
176A SER* 3.4 11.0 + - - -
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Residues in contact with LEU 173 (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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1A MYR 4.5 12.8 - - + -
89A ILE* 4.7 8.5 - - + -
120A ALA* 6.1 3.4 - - + -
121A TRP 5.8 0.7 - - - -
122A LEU* 3.3 51.6 - - + -
124A PHE* 3.6 14.1 - - + -
156A GLN* 6.3 1.1 - - + -
169A GLY* 2.7 30.2 + - - +
170A LEU* 3.0 8.6 + - - +
172A TRP* 1.3 85.9 - - + +
174A SER* 1.3 62.1 + - - +
176A SER* 2.5 32.3 + - - +
177A LEU* 3.1 19.3 + - + +
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Residues in contact with SER 174 (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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1A MYR 4.1 27.6 - - - +
12A LEU* 4.2 28.2 - - - +
170A LEU* 2.7 21.6 + - - +
171A GLU* 3.3 16.8 + - - -
172A TRP 3.2 0.2 - - - -
173A LEU* 1.3 73.8 - - - +
175A ASN* 1.3 51.0 + - - +
177A LEU* 3.1 4.2 + - - +
178A LYS* 2.7 35.7 + - - +
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Residues in contact with ASN 175 (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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12A LEU* 5.8 0.4 - - - -
171A GLU 3.3 7.6 + - - +
172A TRP* 3.1 29.9 + - + +
174A SER* 1.3 79.8 - - - +
176A SER* 1.3 62.8 + - - +
178A LYS* 3.0 38.0 + - - +
179A ASN* 3.1 17.0 + - - +
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Residues in contact with SER 176 (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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154A PHE* 6.5 0.4 - - - -
172A TRP* 3.4 6.5 + - - -
173A LEU* 2.5 38.2 + - - +
175A ASN* 1.3 77.9 - - - +
177A LEU* 1.3 62.8 + - - +
179A ASN* 3.1 24.8 - - - +
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Residues in contact with LEU 177 (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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1A MYR 3.2 30.5 - - + -
12A LEU* 5.9 2.2 - - + -
14A GLY* 5.0 7.4 - - - -
18A MET* 4.2 41.1 - - + +
20A ILE* 4.6 9.0 - - + -
86A GLU 6.0 0.9 - - - +
120A ALA* 4.3 24.2 - - + -
173A LEU* 3.1 17.7 + - + +
174A SER* 3.1 9.0 + - - +
176A SER* 1.3 84.3 + - - +
178A LYS* 1.3 63.5 + - - +
179A ASN 3.4 0.9 - - - -
180A SER* 4.0 12.0 + - - -
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Residues in contact with LYS 178 (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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11A ASN* 3.6 34.1 - - + +
12A LEU* 3.7 43.0 - - + +
13A PHE 4.7 2.9 - - - +
14A GLY* 5.0 12.9 + - - +
174A SER 2.7 13.5 + - - +
175A ASN* 3.0 32.5 + - - +
177A LEU* 1.3 79.8 - - - +
179A ASN* 1.3 67.2 + - + +
180A SER* 3.7 3.8 + - - -
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Residues in contact with ASN 179 (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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175A ASN* 3.1 15.4 + - - +
176A SER* 3.1 17.3 - - - +
178A LYS* 1.3 82.6 - - + +
180A SER* 1.3 67.8 + - - +
181A THR* 4.0 4.0 + - - +
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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