Contacts of the helix formed by residues 162 - 179 (chain A) in PDB entry 1KAS
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 ALA 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY* 4.1 18.7 + - - -
160A ALA 3.6 2.8 + - - -
161A THR* 1.3 75.5 - - - +
163A CYS* 1.3 63.4 + - - +
165A SER* 2.9 21.9 + - - -
342A LEU* 4.3 10.5 - - + -
343A GLY* 3.5 8.3 - - - -
400A PHE* 4.1 38.1 - - + +
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Residues in contact with CYS 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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161A THR 3.1 0.2 + - - -
162A ALA* 1.3 77.6 - - - +
164A THR* 1.3 58.7 + - - +
165A SER 3.4 0.7 - - - -
303A HIS* 3.6 16.6 - - + -
340A HIS* 3.2 28.9 - - - +
342A LEU* 3.7 21.7 - - - +
345A ALA* 4.6 1.9 - - - +
346A GLY 4.6 4.0 + - - -
397A SER* 3.0 19.3 + - - -
398A PHE 4.6 0.2 - - - -
399A GLY* 3.6 22.8 - - - +
400A PHE* 3.3 36.1 - - - -
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 2.8 20.1 + - - -
163A CYS* 1.3 71.0 - - - +
165A SER* 1.3 66.3 + - - +
166A GLY 3.3 2.0 - - - -
167A VAL* 3.0 6.9 + - + -
168A HIS* 2.8 53.5 + - + +
397A SER* 3.5 26.7 + - - +
399A GLY* 3.1 13.2 + - - -
403A THR 2.6 22.5 + - - -
404A ASN 3.9 1.3 - - - -
405A GLY* 3.7 9.9 - - - +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER 3.9 11.9 - - - -
159A ILE 3.7 12.4 + - - -
160A ALA* 3.7 2.8 - - - -
161A THR* 2.8 33.8 + - - +
162A ALA 2.9 18.0 + - - -
163A CYS 3.4 0.6 - - - -
164A THR* 1.3 76.3 - - - +
166A GLY* 1.3 64.6 + - - +
168A HIS* 3.8 0.6 - - - +
169A ASN* 2.8 35.9 + - - +
343A GLY* 3.5 16.4 - - - -
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Residues in contact with GLY 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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163A CYS 5.1 0.2 + - - -
164A THR 3.3 0.6 - - - -
165A SER* 1.3 79.2 - - - +
167A VAL* 1.3 60.1 + - - +
169A ASN* 4.1 0.9 - - - +
170A ILE* 3.2 31.7 + - - +
188A GLY 4.7 7.4 - - - -
343A GLY 3.2 17.6 + - - -
346A GLY* 4.0 10.0 - - - +
347A ALA* 3.7 22.0 - - - -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 3.0 8.8 + - + +
166A GLY* 1.3 73.3 - - - +
168A HIS* 1.3 64.6 + - - +
171A GLY 3.1 18.2 + - - -
260A PHE* 3.8 9.2 - - + -
346A GLY* 3.7 21.5 - - - +
395A CYS* 4.3 18.4 - - - +
397A SER* 3.7 24.0 - - - +
405A GLY* 3.7 33.2 - - - -
406A SER 3.9 4.0 - - - +
407A LEU* 3.6 26.9 - - + +
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Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.8 22.7 - - + -
161A THR* 3.0 35.7 - - + +
164A THR* 2.8 31.2 + - + +
165A SER 3.8 0.9 - - - +
167A VAL* 1.3 73.8 - - - +
169A ASN* 1.3 61.3 + - - +
171A GLY 3.6 0.3 + - - -
172A HIS* 3.0 39.6 + + + +
260A PHE* 3.9 15.6 - - - -
262A MET* 3.8 18.9 - - + +
403A THR* 3.1 21.6 + - - -
404A ASN 3.4 19.1 - - - -
405A GLY* 4.2 1.8 - - - -
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Residues in contact with ASN 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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103A ALA* 3.2 41.5 - - - +
105A GLY* 3.3 17.9 + - - +
157A ILE 4.6 0.2 - - - -
158A SER* 3.8 1.4 + - - -
159A ILE* 2.9 52.9 + - - +
165A SER 2.8 28.5 + - - +
166A GLY 4.1 1.6 - - - +
168A HIS* 1.3 75.3 - - - +
170A ILE* 1.3 66.1 + - - +
172A HIS* 3.3 1.2 + - - +
173A ALA* 2.9 25.5 + - - +
188A GLY 3.7 9.3 + - - +
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Residues in contact with ILE 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 GLY 3.2 18.6 + - - +
169A ASN* 1.3 77.6 - - - +
171A GLY* 1.3 60.6 + - - +
174A ALA* 3.2 17.8 + - - +
187A ALA* 3.9 20.0 - - + -
188A GLY* 4.3 6.5 - - - +
238A LEU* 4.2 22.4 - - + -
240A LEU* 3.2 16.3 - - + +
257A LEU* 3.8 17.3 - - + -
346A GLY 4.0 0.2 - - - +
347A ALA* 3.8 21.5 - - + -
350A SER* 3.5 26.7 - - - +
407A LEU* 3.6 18.2 - - + -
409A PHE* 4.8 2.7 - - + -
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Residues in contact with GLY 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 VAL 3.1 16.9 + - - -
170A ILE* 1.3 78.0 - - - +
172A HIS* 1.3 55.3 + - - +
174A ALA* 3.3 8.3 + - - +
175A ARG* 2.9 29.6 + - - +
257A LEU* 4.6 0.2 - - - -
260A PHE* 3.8 25.9 - - - +
407A LEU* 3.9 13.9 - - - +
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Residues in contact with HIS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 4.3 11.0 - - + -
159A ILE* 3.6 24.2 - - + -
168A HIS* 3.0 30.8 + + + +
169A ASN 4.2 1.8 - - - +
171A GLY* 1.3 74.6 - - - +
173A ALA* 1.3 59.6 + - - +
175A ARG* 3.7 16.5 - - + +
176A ILE* 2.8 38.3 + - + +
260A PHE* 3.6 15.2 - + - -
262A MET* 3.3 33.6 - - + -
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Residues in contact with ALA 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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103A ALA* 3.8 11.8 - - + +
169A ASN 2.9 17.7 + - - +
170A ILE 3.5 6.3 - - - +
172A HIS* 1.3 78.6 - - - +
174A ALA* 1.3 55.7 + - - +
176A ILE* 3.4 5.2 + - - +
177A ILE* 2.9 33.5 + - - +
185A MET* 3.7 21.7 - - + +
187A ALA* 3.8 13.9 - - + -
240A LEU* 3.7 15.5 - - + -
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Residues in contact with ALA 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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5A VAL* 3.7 26.0 - - + +
170A ILE 3.2 2.4 + - - +
171A GLY* 3.5 8.5 - - - +
172A HIS 3.2 0.2 - - - -
173A ALA* 1.3 77.5 - - - +
175A ARG* 1.3 57.6 + - + +
177A ILE* 3.2 2.6 + - - +
178A ALA* 2.7 37.5 + - - +
240A LEU* 4.0 1.3 - - + +
257A LEU* 3.5 35.2 - - + -
260A PHE* 6.4 0.7 - - + -
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Residues in contact with ARG 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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171A GLY 2.9 21.0 + - - +
172A HIS* 3.3 26.3 + - + +
174A ALA* 1.3 73.9 - - - +
176A ILE* 1.3 66.0 + - + +
178A ALA* 3.1 8.7 + - - +
179A TYR* 2.9 25.3 + - - +
259A GLY 5.2 0.2 - - - -
260A PHE* 3.0 49.4 + - + +
262A MET* 4.8 10.7 - - - +
289A ASP* 3.1 28.2 + - - -
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Residues in contact with ILE 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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155A PRO* 3.8 24.2 - - + -
157A ILE* 4.1 28.0 - - + -
172A HIS* 2.8 26.2 + - + +
173A ALA* 3.5 4.3 - - - +
175A ARG* 1.3 74.3 - - + +
177A ILE* 1.3 63.7 + - - +
179A TYR* 3.1 12.8 + - - +
180A GLY 3.2 9.4 + - - -
181A ASP* 3.3 32.6 + - + +
182A ALA* 3.9 9.9 - - + -
185A MET* 3.7 23.3 - - + -
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Residues in contact with ILE 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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3A ARG* 3.3 13.3 + - + -
4A ARG 4.9 0.2 - - - +
5A VAL* 3.5 21.1 - - + -
173A ALA 2.9 20.4 + - - +
174A ALA 3.6 3.4 - - - +
176A ILE* 1.3 70.7 - - - +
178A ALA* 1.3 64.5 + - - +
180A GLY 3.2 10.9 + - - -
182A ALA 3.5 21.3 - - - +
183A ASP 3.5 19.3 - - - +
185A MET* 3.6 24.7 - - + +
240A LEU* 3.3 41.5 - - + +
241A GLU* 3.9 0.9 - - - +
242A GLU* 4.0 19.7 - - + +
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Residues in contact with ALA 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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2A LYS* 6.0 4.5 - - - -
3A ARG* 3.8 40.8 + - - +
5A VAL* 4.6 3.6 - - + -
174A ALA 2.7 21.1 + - - +
175A ARG* 3.6 8.1 - - - +
177A ILE* 1.3 72.9 - - - +
179A TYR* 1.3 59.2 + - - +
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Residues in contact with TYR 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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3A ARG* 5.0 1.1 - - - -
175A ARG 2.9 16.3 + - - +
176A ILE* 3.1 8.5 + - - +
178A ALA* 1.3 75.7 - - - +
180A GLY* 1.3 56.6 + - - +
181A ASP* 3.6 28.7 - - - +
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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
------------------------------------------------------------
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