Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 5K6S
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LYS 4.6 8.7 - - - +
157A LYS 4.3 8.9 - - - +
158A TYR* 3.8 11.5 - - - +
159A ILE* 1.3 73.7 - - - +
161A GLN* 1.3 64.6 + - + +
162A LYS* 3.5 12.5 + - - +
163A PHE* 3.1 21.4 + - - +
164A VAL* 3.1 26.2 + - - +
196A LEU* 4.2 8.3 - - - -
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Residues in contact with GLN 161 (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 ASP* 1.3 75.8 - - - +
162A LYS* 1.3 60.8 + - - +
164A VAL* 3.4 1.5 + - - -
165A LEU* 2.8 30.9 + - - +
196A LEU* 4.1 13.1 - - + +
199A TYR* 3.4 64.7 + - + +
202A LYS* 5.6 0.4 - - - +
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Residues in contact with LYS 162 (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 ASP* 3.3 11.3 + - - +
161A GLN* 1.3 78.9 - - - +
163A PHE* 1.3 58.2 + - - +
165A LEU* 3.5 11.8 - - + +
166A GLN* 3.0 56.4 + - + +
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Residues in contact with PHE 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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96A VAL* 3.7 32.8 - - + -
99A PHE* 3.4 33.0 - + - -
100A ALA* 5.1 1.3 - - + -
104A PHE* 3.5 32.5 - + - -
141A PHE* 3.8 26.0 - + - -
158A TYR 4.3 2.7 - - - +
159A ILE* 3.7 19.1 - - + -
160A ASP* 3.1 27.8 + - - +
161A GLN 3.2 0.2 - - - -
162A LYS* 1.3 74.9 - - - +
164A VAL* 1.3 62.4 + - - +
166A GLN* 3.2 2.3 + - - -
167A LEU* 2.8 35.9 + - + +
189A ILE* 4.1 16.8 - - + -
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Residues in contact with VAL 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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159A ILE* 4.8 4.9 - - + -
160A ASP 3.1 14.0 + - - +
161A GLN* 3.7 8.3 - - - +
163A PHE* 1.3 78.6 - - + +
165A LEU* 1.3 62.4 + - - +
167A LEU* 3.3 8.5 + - - +
168A LEU* 3.0 33.1 + - + +
186A LEU* 4.3 13.7 - - + -
189A ILE* 4.3 15.7 - - + -
196A LEU* 3.9 26.9 - - + -
199A TYR* 4.7 10.1 - - + -
200A ILE* 3.8 26.9 - - + -
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Residues in contact with LEU 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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161A GLN 2.8 18.8 + - - +
162A LYS* 3.5 13.0 - - + +
163A PHE 3.2 0.2 - - - -
164A VAL* 1.3 78.2 - - - +
166A GLN* 1.3 65.8 + - + +
168A LEU* 3.1 18.4 + - + +
169A GLU* 3.2 33.6 + - - +
199A TYR* 3.8 15.9 - - - +
203A GLN* 3.7 27.6 - - + +
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Residues in contact with GLN 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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104A PHE* 3.3 55.3 + - + +
162A LYS* 3.0 50.1 + - + +
163A PHE* 4.7 0.7 - - - -
165A LEU* 1.3 76.1 - - + +
167A LEU* 1.3 64.2 + - - +
169A GLU* 3.4 25.7 + - + +
170A LEU* 3.7 11.6 + - - +
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Residues in contact with LEU 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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99A PHE* 3.8 31.9 - - + -
104A PHE* 3.6 6.0 - - + -
163A PHE* 2.8 21.1 + - + +
164A VAL* 3.5 7.9 - - - +
165A LEU 3.2 0.2 - - - -
166A GLN* 1.3 78.5 - - - +
168A LEU* 1.3 59.9 + - + +
170A LEU* 3.3 19.0 + - + +
171A PHE* 3.5 13.4 - - + -
182A LEU* 3.6 26.9 - - + +
185A THR* 4.0 15.3 - - + -
186A LEU* 4.2 24.9 - - + +
189A ILE* 3.7 29.2 - - + -
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Residues in contact with LEU 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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164A VAL* 3.0 27.6 + - + +
165A LEU* 3.1 13.4 + - + +
167A LEU* 1.3 74.0 - - - +
169A GLU* 1.3 65.4 + - - +
170A LEU 3.1 2.2 - - - -
171A PHE* 3.1 30.8 + - + +
172A ASP 4.3 1.0 + - - -
186A LEU* 3.6 32.1 - - + -
200A ILE* 5.0 2.2 - - + +
203A GLN* 3.7 32.3 - - + -
204A ILE* 4.7 7.6 - - + -
207A ILE* 4.2 24.7 - - + +
218A HIS* 4.4 6.9 + - - -
224A LEU* 4.0 12.6 - - + -
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Residues in contact with GLU 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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107A LEU* 3.6 9.7 - - + +
165A LEU* 3.2 36.9 + - + +
166A GLN* 3.5 20.0 - - + +
167A LEU 3.3 0.2 - - - -
168A LEU* 1.3 78.5 - - - +
170A LEU* 1.3 62.2 + - + +
171A PHE 3.3 0.7 + - - -
172A ASP* 3.3 20.3 + - - +
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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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103A MET* 3.5 41.5 - - + +
104A PHE* 4.1 13.7 - - + -
105A ARG* 4.0 19.5 - - - +
107A LEU* 4.0 22.7 - - + -
138A TYR* 3.7 19.1 - - - +
166A GLN 3.8 10.3 - - - +
167A LEU* 3.3 10.5 + - + +
168A LEU 3.1 1.0 - - - -
169A GLU* 1.3 75.2 - - + +
171A PHE* 1.3 55.2 + - - +
172A ASP 3.0 5.6 - - - -
173A SER* 3.0 29.7 + - - -
178A GLU* 4.5 1.8 - - - +
182A LEU* 3.2 25.3 - - + +
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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