Contacts of the helix formed by residues 162 - 178 (chain A) in PDB entry 5KG2
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 GLN 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A THR* 3.5 17.6 - - + +
161A VAL* 1.3 82.3 - - + +
163A LYS* 1.3 62.7 + - - +
164A GLU* 4.6 9.1 - - - +
165A GLY* 3.5 17.5 + - - +
166A MET* 3.2 25.9 + - - +
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Residues in contact with LYS 163 (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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146A TYR* 4.0 25.0 + - - +
162A GLN* 1.3 71.7 - - - +
164A GLU* 1.3 77.3 + - + +
166A MET* 3.3 8.8 + - - +
167A ARG* 3.1 20.8 + - - +
234A ARG* 3.9 31.6 - - - +
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Residues in contact with GLU 164 (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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143A PRO 4.7 2.8 - - - +
146A TYR* 5.1 1.5 + - - -
162A GLN* 4.5 8.9 - - - +
163A LYS* 1.3 91.7 - - + +
165A GLY* 1.3 62.4 + - - +
167A ARG* 3.1 43.6 + - - +
168A LYS* 3.1 40.7 + - + +
234A ARG* 4.7 13.4 + - - +
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Residues in contact with GLY 165 (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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160A THR* 3.8 11.9 - - - -
162A GLN* 3.5 27.0 - - - +
163A LYS 3.1 0.8 - - - -
164A GLU* 1.3 77.0 - - - +
166A MET* 1.3 58.1 + - - +
168A LYS* 3.4 9.3 + - - +
169A GLN* 3.0 32.1 + - - +
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Residues in contact with MET 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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146A TYR* 5.4 2.2 - - + -
151A PRO* 3.5 35.5 - - + +
160A THR* 4.0 16.5 - - + +
161A VAL* 5.6 1.1 - - - -
162A GLN 3.2 16.7 + - - +
163A LYS* 3.3 9.8 + - - +
165A GLY* 1.3 73.7 - - - +
167A ARG* 1.3 66.0 + - - +
169A GLN* 3.2 19.9 + - - +
170A GLY* 3.0 19.2 + - - -
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Residues in contact with ARG 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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139A ALA 5.6 0.8 + - - -
142A LEU 2.9 24.4 + - - -
143A PRO* 3.2 24.2 + - - +
144A SER* 4.3 3.6 - - - +
145A THR 2.9 39.7 + - - +
146A TYR* 3.5 52.3 - - + +
147A ILE 5.5 1.0 + - - -
163A LYS 3.1 9.5 + - - +
164A GLU* 3.1 44.2 + - - +
165A GLY 3.3 0.2 - - - -
166A MET* 1.3 77.8 - - - +
168A LYS* 1.3 78.6 + - - +
170A GLY* 3.3 1.6 + - - -
171A LEU* 3.0 38.7 + - - +
234A ARG* 4.9 2.9 - - - +
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Residues in contact with LYS 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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139A ALA* 5.5 6.3 - - - +
140A ASP* 5.5 4.8 + - - -
164A GLU* 3.1 33.9 + - + +
165A GLY* 3.7 6.1 - - - +
166A MET 3.3 0.2 - - - -
167A ARG* 1.3 98.1 - - - +
169A GLN* 1.3 59.4 + - - +
171A LEU* 3.7 9.3 - - + +
172A PHE* 2.8 64.3 + - + -
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Residues in contact with GLN 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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151A PRO* 4.0 15.5 - - + +
160A THR* 3.0 32.8 + - - +
165A GLY 3.0 15.5 + - - +
166A MET* 3.2 31.0 + - - +
168A LYS* 1.3 75.6 - - - +
170A GLY* 1.3 63.4 + - - +
172A PHE* 3.3 11.0 + - + +
173A GLN* 3.0 28.4 + - + +
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Residues in contact with GLY 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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147A ILE* 4.5 6.3 - - - -
150A LEU* 3.7 16.0 - - - +
151A PRO* 3.5 27.5 - - - +
166A MET 3.0 11.5 + - - -
167A ARG 3.7 2.9 - - - -
169A GLN* 1.3 75.3 - - - +
171A LEU* 1.3 57.9 + - - +
173A GLN* 3.3 3.5 + - - +
174A TRP* 3.0 28.1 + - - +
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Residues in contact with LEU 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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139A ALA* 4.0 26.9 - - + +
142A LEU* 3.6 51.6 - - + +
145A THR* 4.6 9.2 - - + +
147A ILE* 4.0 27.2 - - + +
167A ARG* 3.0 29.8 + - - +
168A LYS* 3.7 7.9 - - + +
170A GLY* 1.3 74.2 - - - +
172A PHE* 1.3 59.5 + - + +
174A TRP* 3.2 2.6 + - + +
175A LEU* 2.8 50.2 + - + +
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Residues in contact with PHE 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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139A ALA* 3.8 27.1 - - + -
168A LYS* 2.8 55.1 + - + +
169A GLN* 3.5 9.6 - - + +
170A GLY 3.2 0.2 - - - -
171A LEU* 1.3 79.1 - - + +
173A GLN* 1.3 62.9 + - + +
175A LEU* 3.3 6.6 + - + +
176A ASP* 3.0 35.5 + - - +
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Residues in contact with GLN 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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150A LEU* 3.7 15.8 - - + +
151A PRO* 3.3 21.8 - - - +
152A GLN* 3.1 39.0 + - - +
154A PRO 5.7 3.8 + - - -
169A GLN* 3.0 16.5 + - + +
170A GLY 3.7 7.0 - - - +
172A PHE* 1.3 76.4 - - + +
174A TRP* 1.3 62.0 + - - +
176A ASP* 4.0 4.6 - - - +
177A SER* 2.9 29.5 + - - -
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Residues in contact with TRP 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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142A LEU* 5.6 0.2 - - + -
147A ILE* 3.6 42.9 - - + +
150A LEU* 3.8 13.2 - - + +
170A GLY 3.0 14.5 + - - +
171A LEU* 3.4 8.5 - - + +
173A GLN* 1.3 77.7 - - - +
175A LEU* 1.3 79.2 + - + +
177A SER* 3.1 16.9 + - - -
178A LEU* 3.3 19.4 + - + +
187A ASP* 3.5 55.2 - - + -
191A THR* 2.9 22.5 + - + +
237A LEU* 3.9 17.8 - - + +
239A SER* 3.7 25.4 - - - -
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Residues in contact with LEU 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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137A ILE* 3.7 19.3 - - + +
138A SER 4.1 0.4 - - - -
139A ALA* 3.6 42.0 - - + +
142A LEU* 4.3 8.3 - - + -
171A LEU* 2.8 34.7 + - + +
172A PHE* 3.9 6.7 - - + +
174A TRP* 1.3 82.7 - - + +
176A ASP* 1.3 66.2 + - - +
178A LEU* 3.1 40.3 + - + +
191A THR* 4.2 12.3 - - + -
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Residues in contact with ASP 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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172A PHE* 3.0 24.2 + - - +
173A GLN* 4.0 5.4 - - - +
175A LEU* 1.3 80.5 - - - +
177A SER* 1.3 59.7 + - - +
178A LEU 3.6 4.0 + - - +
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Residues in contact with SER 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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173A GLN* 2.9 17.5 + - - +
174A TRP* 3.1 12.1 + - - -
176A ASP* 1.3 76.5 - - - +
178A LEU* 1.3 66.0 + - - +
179A GLN* 3.8 1.4 + - - +
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Residues in contact with LEU 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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137A ILE* 5.1 3.4 - - + +
174A TRP* 3.3 21.3 + - + +
175A LEU* 3.1 36.4 + - + +
176A ASP 3.3 3.7 - - - +
177A SER* 1.3 82.4 - - - +
179A GLN* 1.3 67.5 + - - +
180A ILE* 3.8 16.8 + - + +
185A SER* 5.8 0.4 - - - +
187A ASP* 4.0 24.5 - - + -
188A LEU* 4.1 20.4 - - + +
191A THR* 3.6 32.1 - - + +
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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