Contacts of the helix formed by residues 175 - 187 (chain A) in PDB entry 5ITX
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLU* 2.9 21.4 + - - +
54A LYS* 3.5 1.7 - - - +
166A LEU* 3.3 13.3 - - - +
173A GLY 3.8 0.4 + - - -
174A ILE* 1.3 74.8 - - - +
176A ASN* 1.3 59.7 + - - -
179A ARG* 2.9 28.8 + - - +
298D G 3.0 22.7 - - - -
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Residues in contact with ASN 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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3A GLU* 2.9 4.0 + - - -
166A LEU* 3.7 3.2 - - + +
175A GLY* 1.3 70.3 - - - -
177A TYR* 1.3 66.4 + - - +
179A ARG* 2.8 50.0 + - - +
180A ALA* 3.5 8.8 + - - +
263A TYR* 3.7 9.6 - - - -
277A ARG* 3.8 16.7 - - - +
278A THR* 2.8 31.0 + - - +
279A ILE* 6.1 0.2 - - - -
297D CTG 2.9 34.1 + - - +
298D G 3.4 16.7 + - - +
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 2.8 27.6 + - - -
5A PRO* 3.5 6.4 - - - +
6A GLU* 2.4 30.1 + - - -
176A ASN* 1.3 78.6 - - - +
178A LEU* 1.3 90.9 + - + +
180A ALA* 3.2 5.7 + - - +
181A GLU* 3.1 22.3 + - - +
236A VAL* 3.3 15.8 - - - +
256A PHE* 3.7 25.4 - + - -
259A TRP* 3.9 14.1 - + - -
260A LEU* 4.3 4.5 - - + -
263A TYR* 3.7 32.8 - - + +
297D CTG 3.4 45.0 + - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.0 20.4 + - + +
5A PRO* 3.8 26.7 - - + -
173A GLY 3.9 13.5 - - - +
174A ILE* 4.0 10.5 - - + -
175A GLY 3.9 2.0 - - - +
177A TYR* 1.3 101.2 - - + +
179A ARG* 1.3 57.1 + - - +
181A GLU* 3.3 2.0 + - - +
182A ILE* 2.8 43.5 + - + +
232A VAL* 3.9 27.1 - - + -
233A PRO* 3.9 23.6 - - + -
236A VAL* 4.4 1.1 - - + -
259A TRP* 4.2 4.5 - - + -
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Residues in contact with ARG 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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162A CYS* 2.8 42.4 + - - -
163A GLU* 4.0 0.8 - - - +
165A LEU* 4.0 27.8 - - + -
166A LEU* 3.4 24.2 - - - +
174A ILE* 4.1 5.7 - - + +
175A GLY 2.9 15.6 + - - +
176A ASN* 2.8 34.5 + - - +
178A LEU* 1.3 75.7 - - - +
180A ALA* 1.3 67.3 + - - +
182A ILE* 4.5 2.0 - - - -
183A LEU* 2.9 30.4 + - + +
273A ASP* 2.6 30.5 + - - -
277A ARG* 3.3 15.0 + - - +
278A THR 3.3 15.4 + - - -
279A ILE* 3.6 23.7 - - + +
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Residues in contact with ALA 180 (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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176A ASN 3.8 7.6 - - - +
177A TYR 3.2 10.0 + - - +
179A ARG* 1.3 85.6 - - - +
181A GLU* 1.3 65.4 + - - +
183A LEU* 4.0 2.0 - - - +
184A TYR* 3.0 24.0 + - - +
262A CYS* 4.3 2.9 - - - -
263A TYR* 3.8 28.5 - - + +
279A ILE* 4.2 4.7 - - + -
280A TRP* 3.8 30.3 - - + +
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Residues in contact with GLU 181 (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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177A TYR* 3.1 14.4 + - + +
178A LEU* 3.8 5.6 - - - +
180A ALA* 1.3 79.9 - - - +
182A ILE* 1.3 61.4 + - - +
184A TYR* 3.4 5.5 + - - +
185A ARG* 3.2 35.4 + - - +
232A VAL* 4.3 8.3 - - + -
259A TRP* 3.9 25.7 - - + +
260A LEU* 3.4 27.6 - - + +
261A ARG* 2.8 29.9 + - - +
262A CYS* 3.0 7.0 + - - -
263A TYR* 2.8 32.4 + - - +
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Residues in contact with ILE 182 (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* 4.8 7.6 - - + -
174A ILE* 3.8 33.2 - - + -
178A LEU* 2.8 31.3 + - + +
179A ARG* 3.9 4.3 - - - +
181A GLU* 1.3 71.3 - - - +
183A LEU* 1.3 66.1 + - + +
185A ARG* 3.2 14.2 + - - +
186A LEU* 3.5 8.3 + - - +
225A LEU* 3.3 33.6 - - + +
228A LEU* 4.2 17.9 - - + +
229A CYS* 4.1 19.7 - - - -
232A VAL* 4.1 27.6 - - + -
233A PRO* 4.9 2.9 - - + -
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Residues in contact with LEU 183 (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 ILE* 4.0 16.4 - - + -
162A CYS* 3.9 33.9 - - + +
165A LEU* 3.9 20.0 - - + -
179A ARG 2.9 21.3 + - - +
180A ALA* 4.0 2.7 - - - +
182A ILE* 1.3 76.1 - - - +
184A TYR* 1.3 63.2 + - - +
186A LEU* 3.1 4.1 + - - -
187A LYS* 3.0 19.1 + - - -
188A ILE* 3.3 45.0 + - + +
190A PRO* 4.0 16.6 - - + -
225A LEU* 4.6 6.1 - - + -
279A ILE* 4.4 6.5 - - + -
280A TRP 5.9 1.1 - - - +
281A PHE* 6.2 2.9 - - + -
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Residues in contact with TYR 184 (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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180A ALA 3.0 17.9 + - - +
181A GLU* 3.8 5.8 - - - +
182A ILE 3.1 0.2 - - - -
183A LEU* 1.3 79.7 - - - +
185A ARG* 1.3 62.6 + - + +
187A LYS* 2.6 65.1 + - + +
261A ARG* 3.7 39.0 + - + +
262A CYS* 3.7 26.0 - - + -
268A MET* 3.5 25.0 - - + +
281A PHE* 5.6 1.8 - - - +
282A GLN* 3.7 32.8 + - + +
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Residues in contact with ARG 185 (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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181A GLU* 3.2 20.8 + - - +
182A ILE 3.2 8.5 + - - +
184A TYR* 1.3 85.3 - - + +
186A LEU* 1.3 66.0 + - - +
187A LYS* 3.7 5.7 + - - +
228A LEU* 4.1 19.6 - - + +
232A VAL* 4.3 19.3 - - + +
235A GLU* 2.8 42.2 + - - -
259A TRP* 3.6 24.7 + - - +
261A ARG* 3.5 48.8 - - - +
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Residues in contact with LEU 186 (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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182A ILE 3.5 4.5 + - - +
183A LEU 3.1 4.7 + - - +
185A ARG* 1.3 81.3 - - - +
187A LYS* 1.3 70.0 + - - +
188A ILE* 3.1 31.1 + - + +
222A ASN* 6.3 0.4 - - - -
223A PRO* 3.5 23.3 - - + +
224A ASP* 3.9 5.4 - - - -
225A LEU* 3.6 35.4 - - + +
228A LEU* 3.5 17.9 - - + -
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Residues in contact with LYS 187 (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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183A LEU 3.0 7.0 + - - -
184A TYR* 2.6 64.0 + - + +
185A ARG* 4.7 5.6 - - - +
186A LEU* 1.3 79.8 - - - +
188A ILE* 1.3 60.4 + - - +
189A PRO* 3.5 8.5 - - - +
282A GLN* 3.7 24.0 + - + +
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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