Contacts of the helix formed by residues 163 - 175 (chain A) in PDB entry 4N0N
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLY 3.3 2.2 + - - -
162A SER* 1.3 77.6 - - - +
164A LYS* 1.3 65.1 + - - +
165A THR 3.3 2.7 - - - -
166A PHE* 3.2 13.4 + - - +
167A HIS* 3.0 28.3 + - - -
295A HIS* 4.1 9.6 - - - -
296A ARG* 4.8 5.6 - - - -
508A SO4 3.0 15.0 + - - -
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Residues in contact with LYS 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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158A GLY* 2.7 38.2 + - - +
159A PRO 3.2 11.9 + - - -
162A SER* 3.4 10.5 - - - +
163A GLY* 1.3 75.9 - - - +
165A THR* 1.3 58.7 + - - +
167A HIS* 3.3 1.0 + - - -
168A LEU* 2.9 30.3 + - - +
240A ASP* 4.9 2.2 - - - +
241A GLU* 3.1 40.4 - - - +
262A TYR* 3.8 16.8 - - + -
263A GLY* 3.8 24.9 - - - +
264A ASP* 4.8 0.2 - - - -
267A GLN* 3.8 12.1 - - - +
291A LEU* 4.0 11.7 - - + -
508A SO4 3.1 31.8 + - - +
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Residues in contact with THR 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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163A GLY 3.3 0.4 - - - -
164A LYS* 1.3 74.4 - - - +
166A PHE* 1.3 61.2 + - - +
168A LEU* 3.7 3.3 - - + +
169A VAL* 2.9 31.2 + - + +
191A ASP* 3.7 22.9 + - - +
192A CYS* 3.7 29.8 - - - -
195A LYS* 4.0 15.7 - - + -
240A ASP* 2.9 25.5 + - - +
241A GLU* 4.6 6.8 + - - +
508A SO4 4.9 3.7 + - - -
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Residues in contact with PHE 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 GLY* 3.2 14.4 + - - +
165A THR* 1.3 78.6 - - - +
167A HIS* 1.3 86.3 + + - +
169A VAL* 3.5 3.3 + - - +
170A LYS* 3.2 57.8 + - + +
195A LYS* 4.1 22.1 - - + +
295A HIS* 5.4 6.5 - + - -
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Residues in contact with HIS 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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162A SER 3.4 17.7 + - - -
163A GLY* 3.0 29.0 + - - +
164A LYS 3.9 0.7 - - - +
166A PHE* 1.3 91.7 - + - +
168A LEU* 1.3 66.3 + - - +
170A LYS* 3.2 15.6 + - - +
171A ASP* 3.1 25.5 + - - +
262A TYR* 3.8 22.9 - - + +
291A LEU* 3.9 22.8 - - + +
295A HIS* 3.8 17.1 - + - -
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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 LYS 2.9 17.4 + - - +
165A THR* 3.7 5.4 - - - +
167A HIS* 1.3 75.9 - - - +
169A VAL* 1.3 70.6 + - + +
171A ASP* 3.1 6.5 + - - +
172A VAL* 3.0 24.3 + - - +
181A LEU* 3.4 37.5 - - + -
192A CYS* 4.7 8.1 - - - -
238A PHE* 4.2 9.9 - - + -
239A VAL 3.4 41.3 - - - +
240A ASP* 3.6 14.1 - - + +
262A TYR* 3.9 30.2 - - + -
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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 THR* 2.9 27.4 + - + +
166A PHE* 3.9 4.9 - - - +
167A HIS 3.3 0.2 - - - -
168A LEU* 1.3 86.7 - - + +
170A LYS* 1.3 62.9 + - + +
172A VAL* 3.3 6.0 + - - +
173A LEU* 3.0 41.4 + - + +
181A LEU* 4.6 9.2 - - + -
192A CYS* 4.6 10.1 - - - +
195A LYS* 4.1 34.3 - - + +
196A LEU* 3.8 15.5 - - + -
199A ALA* 5.4 0.2 - - + -
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Residues in contact with LYS 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 PHE* 3.2 47.9 + - + +
167A HIS* 3.6 18.1 - - - +
168A LEU 3.2 0.2 - - - -
169A VAL* 1.3 78.3 - - + +
171A ASP* 1.3 63.1 + - - +
173A LEU* 3.3 11.1 + - + +
174A ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 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 HIS 3.1 10.1 + - - +
168A LEU 3.1 10.3 + - - +
170A LYS* 1.3 77.3 - - - +
172A VAL* 1.3 62.7 + - - +
174A ALA* 3.2 19.4 + - - +
175A VAL* 3.6 11.1 - - - +
238A PHE* 3.6 19.7 - - + -
260A LYS* 2.7 27.2 + - - +
262A TYR* 2.5 34.1 + - - -
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Residues in contact with VAL 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 LEU* 3.0 18.7 + - + +
169A VAL* 3.7 9.0 - - - +
170A LYS 3.3 0.2 - - - -
171A ASP* 1.3 75.8 - - - +
173A LEU* 1.3 61.9 + - - +
175A VAL* 3.3 21.8 + - - +
179A ALA* 4.5 9.9 - - + +
181A LEU* 2.9 35.4 - - + -
196A LEU* 4.3 7.0 - - + -
223A ILE* 3.7 43.5 - - + +
238A PHE* 3.5 24.2 - - + -
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Residues in contact with LEU 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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169A VAL* 3.0 34.8 + - + +
170A LYS* 3.8 10.3 - - + +
171A ASP 3.3 0.2 - - - -
172A VAL* 1.3 77.2 - - - +
174A ALA* 1.3 59.7 + - - +
175A VAL 3.3 4.5 + - - +
196A LEU* 3.9 20.9 - - + -
199A ALA* 3.5 31.9 - - + +
201A ALA* 3.9 21.1 - - + +
223A ILE* 4.4 7.2 - - + -
504A SO4 5.4 0.9 - - - +
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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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170A LYS 3.1 11.3 + - - +
171A ASP* 3.2 14.1 + - - +
173A LEU* 1.3 76.8 - - - +
175A VAL* 1.3 64.0 + - + +
176A VAL* 3.7 8.1 + - - +
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Residues in contact with VAL 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 ASP 3.6 11.9 - - - +
172A VAL 3.3 17.5 + - - +
173A LEU 4.2 5.4 - - - +
174A ALA* 1.3 79.3 - - + +
176A VAL* 1.3 78.3 + - - +
177A GLY 4.0 5.9 + - - +
178A SER 3.9 12.8 - - - +
179A ALA* 4.2 5.6 - - + -
236A GLU* 3.6 29.2 - - + -
238A PHE* 3.9 24.5 - - + -
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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