Contacts of the helix formed by residues 166 - 179 (chain A) in PDB entry 4II9
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 PRO 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A LEU 4.6 1.6 - - - +
165A TYR* 1.3 95.6 - - + +
167A SER* 1.3 68.8 + - - +
168A LYS* 3.2 7.4 - - + +
169A THR* 3.0 22.0 + - - +
170A LYS* 2.9 18.6 + - - +
310A LYS* 5.2 15.3 - - + -
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Residues in contact with SER 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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165A TYR 3.9 0.4 + - - -
166A PRO* 1.3 72.7 - - - +
168A LYS* 1.3 63.3 + - - +
170A LYS* 3.2 24.0 + - - +
171A SER* 3.0 25.7 + - - -
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Residues in contact with LYS 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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166A PRO* 3.2 6.7 - - + +
167A SER* 1.3 78.4 - - - +
169A THR* 1.3 63.7 + - - +
171A SER* 3.3 19.5 - - - -
172A LYS* 3.4 34.4 + - - +
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Residues in contact with THR 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 TYR* 3.7 27.4 - - + -
166A PRO* 3.0 23.4 + - - +
168A LYS* 1.3 76.6 - - - +
170A LYS* 1.4 67.1 + - - +
171A SER 3.1 1.3 - - - -
172A LYS* 3.0 14.8 + - + +
173A ILE* 3.0 30.7 + - + +
307A VAL* 3.7 33.8 + - + +
308A PHE* 5.7 0.2 - - + -
310A LYS* 4.4 10.6 + - - -
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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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162A LEU* 2.9 58.0 + - + +
163A ASP* 4.4 7.3 + - - +
165A TYR* 3.0 21.1 + - + +
166A PRO 2.9 16.5 + - - +
167A SER* 3.2 26.4 + - - +
169A THR* 1.4 74.8 - - - +
171A SER* 1.3 54.3 + - - +
173A ILE* 3.2 2.3 + - - -
174A LYS* 2.8 52.7 + - + +
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Residues in contact with SER 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 SER 3.0 11.7 + - - -
168A LYS* 3.3 14.5 - - - -
169A THR 3.1 0.2 - - - -
170A LYS* 1.3 77.2 - - - +
172A LYS* 1.3 63.2 + - - +
174A LYS* 3.3 9.8 + - - +
175A ARG* 3.1 24.8 + - - +
178A ARG* 4.9 5.5 + - - +
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Residues in contact with LYS 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 LYS* 3.5 38.5 - - - +
169A THR* 3.0 15.9 + - - +
171A SER* 1.3 79.3 - - - +
173A ILE* 1.3 61.1 + - + +
175A ARG* 3.6 9.0 + - - +
176A PRO* 3.3 18.5 - - - +
266A TYR* 5.0 1.6 - - + +
269A TYR* 3.6 30.4 + - + +
307A VAL* 4.3 33.0 - - + +
310A LYS* 5.5 4.0 - - - +
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Residues in contact with ILE 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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161A THR* 4.3 5.8 - - + -
162A LEU* 3.9 18.8 - - + -
165A TYR* 3.7 35.2 - - + -
169A THR* 3.0 24.0 + - + +
170A LYS 3.8 5.8 - - - +
172A LYS* 1.3 74.4 - - + +
174A LYS* 1.4 66.3 + - - +
176A PRO* 3.3 9.7 - - - +
177A PHE* 3.2 20.0 - - + -
269A TYR* 4.7 7.6 - - + +
273A SER* 3.5 32.5 - - - +
307A VAL* 5.5 0.7 - - + -
308A PHE* 4.0 26.0 - - + -
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Residues in contact with LYS 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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162A LEU* 3.8 31.4 - - + +
170A LYS* 2.8 38.3 + - + +
171A SER* 3.8 7.9 - - - +
173A ILE* 1.4 74.4 - - - +
175A ARG* 1.3 64.2 + - - +
177A PHE* 3.2 12.8 + - - +
178A ARG* 3.0 40.6 + - - +
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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 SER 3.1 15.4 + - - +
172A LYS* 3.7 7.9 - - - +
173A ILE 3.2 1.2 - - - -
174A LYS* 1.3 76.6 - - - +
176A PRO* 1.4 71.2 - - + +
178A ARG* 3.1 22.3 + - - +
179A ASP* 2.9 42.2 + - - +
266A TYR* 2.9 52.1 + - + -
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Residues in contact with PRO 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 LYS 3.3 17.0 - - - +
173A ILE 3.3 13.7 - - - +
175A ARG* 1.4 88.6 - - + +
177A PHE* 1.3 59.8 + - + +
179A ASP* 3.1 10.1 + - + +
180A GLY 3.3 0.3 + - - -
181A VAL* 2.9 39.7 + - + +
265A TYR 3.3 24.5 - - - +
266A TYR* 3.5 27.6 - - + +
269A TYR* 4.3 1.6 - - + -
270A ALA* 3.9 21.1 - - + +
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Residues in contact with PHE 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 ILE* 3.2 29.4 - - + -
174A LYS* 3.2 9.0 + - - +
176A PRO* 1.3 73.7 - - + +
178A ARG* 1.3 65.5 + - - +
180A GLY* 3.0 14.4 + - - -
181A VAL 3.5 19.2 - - - +
182A GLU* 5.2 0.9 - - - -
183A VAL* 4.3 15.3 - - + -
270A ALA* 3.4 42.6 - - + -
273A SER* 4.1 17.3 - - - -
274A GLU* 4.4 14.6 - - + -
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Residues in contact with ARG 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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171A SER* 4.9 5.7 + - - +
174A LYS* 3.0 36.2 + - - +
175A ARG* 3.5 31.7 - - - +
177A PHE* 1.3 77.6 - - - +
179A ASP* 1.3 68.7 + - - +
180A GLY 3.2 3.9 + - - -
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Residues in contact with ASP 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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175A ARG* 2.9 42.7 + - - +
176A PRO* 3.1 8.7 + - + +
177A PHE 3.1 0.2 - - - -
178A ARG* 1.3 90.4 - - - +
180A GLY* 1.3 51.7 + - - +
181A VAL* 3.5 0.7 - - - -
235A ARG* 2.8 36.8 + - - -
265A TYR* 4.2 22.6 - - + +
266A TYR* 5.6 0.3 - - - -
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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