Contacts of the helix formed by residues 161 - 170 (chain A) in PDB entry 6K71
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ALA* 4.5 1.6 - - - -
152A VAL* 3.5 19.2 - - - +
153A THR 3.2 25.8 - - - -
154A GLU* 3.0 13.8 + - - +
160A SER* 1.3 77.2 - - - +
162A LYS* 1.3 59.6 + - - +
163A LYS 3.2 2.7 - - - -
164A MET 3.3 2.9 + - - -
165A ALA 3.0 21.5 + - - -
177A VAL* 5.7 1.8 - - - -
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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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154A GLU* 5.3 4.2 - - + +
159A LEU* 5.4 11.9 - - + -
160A SER 3.7 1.8 - - - +
161A GLY* 1.3 76.5 - - - +
163A LYS* 1.3 57.3 + - - +
165A ALA* 3.3 10.6 - - + +
166A LYS* 3.0 30.5 + - - +
177A VAL* 5.4 18.8 - - + -
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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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130A TYR* 3.9 34.2 - - + -
159A LEU* 4.4 26.6 + - + +
160A SER* 3.5 19.3 - - - +
162A LYS* 1.3 76.6 - - - +
164A MET* 1.3 61.5 + - - +
166A LYS* 3.4 12.9 - - + +
167A ALA* 2.9 30.4 + - - +
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Residues in contact with MET 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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127A THR* 3.7 16.4 - - - -
128A HIS 3.2 16.4 - - - +
129A ALA 3.3 26.0 - - - +
130A TYR* 3.7 26.2 - - + +
131A SER 3.9 7.2 - - - +
134A VAL* 3.6 23.1 - - + -
135A LEU* 5.0 2.2 - - + +
152A VAL* 3.7 15.3 - - + -
161A GLY 3.3 9.6 + - - +
163A LYS* 1.3 80.2 - - - +
165A ALA* 1.3 65.9 + - - +
167A ALA* 4.3 5.4 - - + -
168A LEU* 2.9 49.2 + - + +
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Residues in contact with ALA 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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152A VAL* 3.7 13.4 - - + +
161A GLY 3.0 14.2 + - - +
162A LYS* 3.2 17.0 + - + +
164A MET* 1.3 75.5 - - - +
166A LYS* 1.3 56.9 + - - +
168A LEU 3.8 0.3 - - - -
169A CYS* 2.9 32.4 + - - +
175A VAL* 3.7 24.3 - - + +
177A VAL* 5.2 9.0 - - + -
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Residues in contact with LYS 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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162A LYS 3.0 15.9 + - - +
163A LYS* 3.4 16.8 - - + +
165A ALA* 1.3 74.6 - - - +
167A ALA* 1.3 72.5 + - - +
169A CYS* 3.3 14.2 + - - -
170A HIS* 3.0 22.5 + - - +
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Residues in contact with ALA 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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130A TYR* 4.9 14.8 - - + -
135A LEU* 4.8 10.2 - - + +
163A LYS 2.9 21.9 + - - +
164A MET* 3.2 5.6 + - - +
166A LYS* 1.3 84.3 - - + +
168A LEU* 1.3 60.9 + - + +
170A HIS* 3.3 19.4 + - - +
171A LEU* 4.2 6.8 - - - +
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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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127A THR* 5.9 0.9 - - + -
134A VAL 5.1 0.9 - - - +
135A LEU* 4.5 26.2 - - + -
138A LEU* 4.9 15.5 - - + -
150A VAL* 3.7 22.2 - - + -
152A VAL* 5.9 0.9 - - + -
164A MET* 2.9 46.2 + - + +
165A ALA 3.8 0.2 - - - -
167A ALA* 1.3 79.6 - - + +
169A CYS* 1.3 57.8 + - - +
170A HIS 3.2 0.7 - - - +
171A LEU* 3.4 39.9 + - + +
173A VAL* 4.2 5.6 - - + +
175A VAL* 3.6 26.4 - - + +
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Residues in contact with CYS 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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165A ALA 2.9 19.2 + - - +
166A LYS* 3.3 25.3 + - - -
168A LEU* 1.3 74.9 - - - +
170A HIS* 1.3 59.0 + - - +
171A LEU 3.1 5.7 + - - +
172A ASN* 3.8 9.1 + - - +
173A VAL 4.3 8.9 - - - +
175A VAL* 3.9 15.4 - - + +
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Residues in contact with HIS 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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166A LYS 3.0 11.9 + - - +
167A ALA* 3.3 21.5 + - - +
168A LEU 3.2 0.2 - - - -
169A CYS* 1.3 77.5 - - - +
171A LEU* 1.3 57.0 + - + +
172A ASN 3.7 1.4 + - - -
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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