Contacts of the helix formed by residues 159 - 177 (chain A) in PDB entry 3KAS
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 SER 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A PRO 4.2 3.6 + - - -
155A ARG* 3.6 2.8 - - - -
156A GLU* 2.6 37.8 + - - -
157A ALA 3.2 2.6 + - - -
158A GLY* 1.3 84.1 - - - +
160A GLN* 1.3 59.2 + - - +
161A LYS* 3.7 3.5 + - - -
162A ASP* 3.2 14.6 + - - +
163A GLU* 2.9 25.2 + - - +
382A LYS* 6.1 2.0 - - - +
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Residues in contact with GLN 160 (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 SER* 1.3 74.1 - - - +
161A LYS* 1.3 55.1 + - + +
163A GLU* 3.1 31.7 + - - +
164A ASN* 2.6 53.9 + - - +
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Residues in contact with LYS 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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150A ASN* 2.5 40.6 + - - +
151A SER* 3.6 21.0 - - - +
152A TYR* 4.2 8.2 - - - +
154A PRO* 3.3 52.0 - - + +
155A ARG* 4.1 3.3 - - + +
159A SER* 3.3 2.8 + - - +
160A GLN* 1.3 75.2 - - + +
162A ASP* 1.3 65.7 + - - +
164A ASN* 3.0 8.4 + - - +
165A LEU* 2.9 23.9 + - - +
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Residues in contact with ASP 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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155A ARG* 3.7 14.1 - - - +
156A GLU 3.4 22.2 - - - +
157A ALA* 4.1 3.8 - - - -
158A GLY* 3.1 14.9 + - - +
159A SER* 3.2 9.3 + - - +
161A LYS* 1.3 76.5 - - - +
163A GLU* 1.3 58.7 + - - +
165A LEU* 3.2 4.5 + - - +
166A ALA 2.9 15.1 + - - -
385A LYS 5.5 0.2 - - - +
386A ILE* 5.3 0.7 - - - -
387A LEU 5.3 2.4 + - - -
409A ARG* 2.4 48.6 + - - +
410A ASP* 3.9 17.2 - - - +
454A SER* 3.0 22.4 + - - -
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Residues in contact with GLU 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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158A GLY* 4.7 7.0 - - - +
159A SER 2.9 15.2 + - - +
160A GLN* 3.1 32.7 + - - +
162A ASP* 1.3 74.4 - - - +
164A ASN* 1.3 66.7 + - - +
166A ALA* 3.4 6.5 + - - +
167A LEU* 3.0 35.3 + - + +
385A LYS* 4.5 23.4 + - - +
387A LEU* 4.8 17.5 - - + -
409A ARG* 4.8 0.2 - - - +
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Residues in contact with ASN 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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151A SER* 3.4 31.9 + - - +
152A TYR* 4.1 10.3 - - + -
160A GLN* 2.6 37.2 + - - +
161A LYS* 3.3 12.9 - - - +
163A GLU* 1.3 74.5 - - - +
165A LEU* 1.3 64.8 - - - +
167A LEU* 2.9 17.1 + - - +
168A TYR* 2.9 20.4 + - - +
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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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147A LEU* 3.2 36.3 - - + -
152A TYR* 3.9 20.8 - - + -
155A ARG* 3.4 33.9 - - - +
161A LYS 2.9 12.6 + - - +
162A ASP 3.7 7.0 - - - +
164A ASN* 1.3 75.9 - - - +
166A ALA* 1.3 55.8 + - - +
168A TYR* 3.0 18.7 + - + +
169A VAL* 2.7 42.4 + - + +
409A ARG* 3.6 26.7 - - + +
423A THR* 4.8 5.8 - - + +
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Residues in contact with ALA 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 ASP 2.9 10.5 + - - +
163A GLU* 3.5 10.5 - - - +
164A ASN 3.2 0.2 - - - -
165A LEU* 1.3 76.1 - - - +
167A LEU* 1.3 56.6 + - - +
169A VAL* 3.6 1.2 + - - +
170A GLU* 3.0 29.0 + - - +
387A LEU* 4.5 17.0 - - + -
389A ILE* 3.6 18.0 - - + +
409A ARG* 3.3 38.9 - - - +
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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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163A GLU* 3.0 30.6 + - + +
164A ASN* 2.9 17.5 + - - +
166A ALA* 1.3 74.3 - - + +
168A TYR* 1.3 60.7 + - - +
170A GLU* 3.4 13.2 + - - +
171A ASN* 2.9 28.4 + - - +
183A ARG* 3.1 31.6 - - - +
387A LEU* 5.6 3.8 - - + -
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Residues in contact with TYR 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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143A THR* 5.5 4.4 - - + +
146A LEU* 3.7 32.7 - - + +
147A LEU* 4.7 3.8 - - + -
152A TYR* 3.8 24.9 - + + +
164A ASN 2.9 11.2 + - - +
165A LEU* 3.4 23.6 - - + +
167A LEU* 1.3 74.0 - - - +
169A VAL* 1.3 71.2 + - + +
171A ASN* 3.1 8.9 + - + +
172A GLN* 2.9 59.9 + - + +
427A LEU* 3.9 18.3 - - + +
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Residues in contact with VAL 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 LEU* 2.7 35.6 + - + +
166A ALA* 3.9 5.2 - - - +
168A TYR* 1.3 77.5 - - + +
170A GLU* 1.3 57.6 + - - +
172A GLN* 3.3 2.8 + - - +
173A PHE* 3.0 57.9 + - + -
389A ILE* 4.1 8.5 - - + -
409A ARG* 4.3 7.4 - - - -
423A THR* 4.0 26.0 - - + -
426A LEU* 5.2 1.6 - - + -
427A LEU* 4.2 15.3 - - + -
452A SER* 4.1 14.4 - - - +
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Residues in contact with GLU 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 ALA 3.0 19.5 + - - +
167A LEU* 3.6 14.7 - - - +
169A VAL* 1.3 77.7 - - - +
171A ASN* 1.3 62.3 + - - +
173A PHE* 3.4 5.2 + - - +
174A ARG* 3.1 46.8 + - - +
181A VAL* 4.0 16.9 - - + +
182A TRP 5.5 1.0 - - - +
183A ARG* 3.4 43.2 + - + +
389A ILE* 3.9 21.5 - - + -
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Residues in contact with ASN 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 LEU 2.9 17.8 + - - +
168A TYR* 3.1 9.1 + - + +
170A GLU* 1.3 78.1 + - - +
172A GLN* 1.3 59.1 + - + +
174A ARG* 2.9 20.2 + - - +
175A GLU* 2.9 52.4 + - - +
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Residues in contact with GLN 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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168A TYR* 2.9 56.0 + - + +
169A VAL 3.4 8.7 - - - +
171A ASN* 1.3 77.2 + - + +
173A PHE* 1.3 57.7 + - - +
175A GLU* 3.1 30.1 + - - +
176A PHE* 2.9 57.4 + - + -
427A LEU* 3.8 19.5 - - + +
428A LYS* 5.4 5.4 + - - -
431A GLN* 5.7 0.3 + - - -
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A VAL* 3.0 29.6 + - + -
170A GLU 3.6 8.5 - - - +
172A GLN* 1.3 75.7 - - - +
174A ARG* 1.3 63.1 + - - +
176A PHE* 3.1 27.4 + + - +
177A LYS 3.2 8.5 + - - -
178A LEU* 3.6 22.2 + - + +
181A VAL* 4.1 12.1 - - + -
389A ILE* 3.9 21.5 - - + -
390A PHE 3.9 4.9 - - - -
391A GLY* 3.7 30.7 - - - -
426A LEU* 4.2 15.3 - - + -
427A LEU* 4.0 17.5 - - + -
430A ALA* 3.7 20.2 - - + -
450A PHE* 3.9 22.7 - - + -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A GLU* 3.1 40.5 + - - +
171A ASN* 2.9 19.7 + - - +
173A PHE* 1.3 75.5 - - - +
175A GLU* 1.3 62.4 + - + +
177A LYS* 3.1 18.0 + - - +
178A LEU 5.4 0.2 - - - +
181A VAL* 3.7 43.9 + - + +
182A TRP* 5.3 1.4 - - - +
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Residues in contact with GLU 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 ASN* 2.9 38.4 + - - +
172A GLN* 3.1 28.2 + - - +
174A ARG* 1.3 72.5 - - + +
176A PHE* 1.3 67.0 + - + +
177A LYS* 3.0 20.4 + - - +
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Residues in contact with PHE 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 GLN* 2.9 58.9 + - + -
173A PHE* 3.1 24.9 + + - +
175A GLU* 1.3 77.8 - - + +
177A LYS* 1.3 63.6 + - - +
178A LEU* 4.0 12.6 - - + -
427A LEU* 3.4 25.6 - - + -
428A LYS* 5.5 1.6 - - - -
430A ALA* 4.0 4.0 - - + -
431A GLN* 3.5 54.7 - - + -
434A SER* 2.6 33.0 + - - -
438A LEU* 4.1 3.5 - - - +
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Residues in contact with LYS 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 PHE 3.2 0.6 + - - -
174A ARG* 3.1 16.1 + - - +
175A GLU 3.0 17.2 - - - +
176A PHE* 1.3 82.2 - - - +
178A LEU* 1.3 67.3 + - - +
179A SER* 3.8 0.7 + - - -
434A SER* 3.7 4.7 + - - -
438A LEU* 4.1 22.7 - - + +
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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
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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