Contacts of the helix formed by residues 173 - 189 (chain A) in PDB entry 4HYJ
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN 4.4 2.2 - - - +
172A LYS* 1.3 100.6 - - + +
174A ALA* 1.3 66.1 + - - +
175A PRO* 3.4 10.3 - - + -
176A ILE* 3.0 13.1 + - + -
177A ARG 2.9 18.9 + - - -
239A MET* 4.4 16.6 - - + -
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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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172A LYS 3.6 1.6 + - - -
173A PRO* 1.3 69.4 - - - +
175A PRO* 1.4 65.8 - - + +
177A ARG* 4.3 5.2 - - - -
178A ASP* 2.7 44.9 + - - +
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Residues in contact with PRO 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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173A PRO* 3.4 13.7 - - + -
174A ALA* 1.4 93.4 - - + +
176A ILE* 1.3 55.7 + - - +
178A ASP* 4.0 4.8 - - + +
179A ALA* 3.2 18.7 + - - +
235A ALA* 3.4 19.8 - - - +
238A THR* 4.5 23.1 - - - +
239A MET* 4.1 16.8 - - + -
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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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40A TYR* 4.3 28.3 - - + +
100A LEU* 3.8 33.0 - - + +
172A LYS* 3.7 34.5 - - + +
173A PRO* 3.0 14.6 + - + +
175A PRO* 1.3 77.9 - - - +
177A ARG* 1.3 64.6 + - - +
178A ASP 3.3 0.2 - - - -
179A ALA* 3.3 2.5 + - - +
180A LEU* 3.0 33.6 + - + +
235A ALA* 4.3 15.5 - - + +
236A VAL* 5.2 1.6 - - + -
239A MET* 4.3 19.1 - - + -
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Residues in contact with ARG 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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169A ALA* 3.2 38.0 - - + +
170A GLU* 4.8 5.2 - - - +
172A LYS* 3.8 5.6 - - - +
173A PRO 2.9 10.6 + - - +
174A ALA* 3.6 9.2 - - - +
176A ILE* 1.3 80.7 - - - +
178A ASP* 1.3 61.2 + - - +
180A LEU* 3.4 3.8 + - - +
181A LEU* 3.1 38.0 + - + +
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Residues in contact with ASP 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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174A ALA* 2.7 40.3 + - - +
175A PRO* 4.3 4.9 - - + +
177A ARG* 1.3 74.8 - - - +
179A ALA* 1.3 65.5 + - - +
181A LEU* 3.5 12.9 + - - +
182A LYS* 3.2 38.8 + - - +
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Residues in contact with ALA 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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100A LEU* 4.4 9.6 - - + -
175A PRO 3.2 19.7 + - - +
176A ILE 3.6 4.0 - - - +
177A ARG 3.3 0.2 - - - -
178A ASP* 1.3 73.7 - - - +
180A LEU* 1.3 60.6 + - - +
182A LYS* 3.0 8.1 + - - +
183A MET* 2.9 36.0 + - - +
231A ILE* 3.9 21.7 - - + +
235A ALA* 3.6 20.9 - - + -
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Residues in contact with LEU 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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97A PHE* 3.7 39.5 - - + +
100A LEU* 3.6 29.8 - - + -
101A LEU* 3.6 28.7 - - + -
165A VAL* 4.5 9.2 - - + -
169A ALA* 4.3 18.8 - - + -
172A LYS* 5.0 0.4 - - + -
176A ILE* 3.0 36.8 + - + +
177A ARG 3.6 4.5 - - - +
179A ALA* 1.3 74.7 - - - +
181A LEU* 1.3 60.7 + - - +
183A MET* 3.4 8.3 + - - +
184A ARG* 3.2 26.3 + - - +
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Residues in contact with LEU 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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165A VAL* 6.5 0.2 - - + -
166A THR* 4.2 20.4 - - + +
169A ALA* 4.7 7.0 - - + -
170A GLU* 5.1 13.9 - - - -
177A ARG* 3.1 25.5 + - + +
178A ASP* 3.9 12.1 - - - +
179A ALA 3.2 0.2 - - - -
180A LEU* 1.3 74.3 - - - +
182A LYS* 1.3 65.9 + - + +
184A ARG* 3.1 60.8 + - - +
185A LEU* 4.0 8.3 - - - +
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Residues in contact with LYS 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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178A ASP* 3.2 27.0 + - - +
179A ALA* 3.0 8.0 + - - +
181A LEU* 1.3 74.6 - - + +
183A MET* 1.3 66.9 + - - +
185A LEU* 3.0 31.0 + - + +
186A PHE* 3.7 9.5 - - + -
231A ILE* 4.1 32.8 - - + +
307A LFA 4.7 12.8 - - + +
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Residues in contact with MET 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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96A LYS* 3.7 32.5 - - + +
97A PHE* 3.6 23.1 - - + -
100A LEU* 3.6 25.4 - - + -
179A ALA 2.9 21.4 + - - +
180A LEU* 3.6 2.7 - - - +
182A LYS* 1.3 77.2 - - - +
184A ARG* 1.3 62.9 + - - +
186A PHE* 3.0 28.4 + - - +
187A ILE* 3.6 9.2 + - - +
228A PHE* 3.5 34.7 - - + +
231A ILE* 3.8 15.9 - - + -
232A ALA* 3.8 17.7 - - + -
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Residues in contact with ARG 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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97A PHE* 3.9 11.4 - - + -
161A LEU* 3.6 24.6 - - + +
162A PHE* 3.2 46.2 + - + +
165A VAL* 5.0 2.5 - - + -
166A THR* 2.9 36.4 + - - +
180A LEU 3.2 13.9 - - - +
181A LEU* 3.1 45.0 + - - +
182A LYS 3.1 0.2 - - - -
183A MET* 1.3 77.7 - - - +
185A LEU* 1.3 62.0 + - - +
187A ILE* 3.1 7.3 + - - +
188A LEU* 3.0 25.3 + - - +
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Residues in contact with LEU 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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162A PHE* 4.3 19.3 - - + -
181A LEU 4.0 11.7 - - - +
182A LYS* 3.0 19.2 + - + +
184A ARG* 1.3 77.4 - - + +
186A PHE* 1.3 58.2 + - - +
188A LEU* 3.7 15.3 - - + +
189A ILE* 2.7 49.3 + - + +
307A LFA 4.4 29.8 - - + +
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Residues in contact with PHE 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 LYS* 3.7 15.5 - - + -
183A MET* 3.0 16.0 + - - +
185A LEU* 1.3 77.9 - - - +
187A ILE* 1.3 54.5 + - + +
190A GLY* 2.8 12.3 + - - +
191A TRP* 2.7 37.4 + - + +
223A THR* 3.3 41.7 - - + -
224A ASN* 3.7 14.6 - - - +
227A GLY* 4.0 8.1 - - - -
228A PHE* 3.6 35.7 - + + -
231A ILE* 3.8 24.5 - - + -
307A LFA 3.6 31.9 - - + -
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Residues in contact with ILE 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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94A LEU* 4.0 9.2 - - + -
97A PHE* 3.9 11.0 - - + -
154A TRP* 3.1 23.9 + - - +
157A ILE* 3.9 17.9 - - + -
158A ILE* 4.0 14.4 - - + -
161A LEU* 3.6 23.8 - - + -
183A MET 3.7 5.4 - - - +
184A ARG 3.1 7.2 + - - +
186A PHE* 1.3 77.3 - - + +
188A LEU* 1.3 61.1 + - - +
191A TRP* 3.2 47.1 - - + +
228A PHE* 3.6 31.4 - - + -
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Residues in contact with LEU 188 (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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154A TRP* 3.7 7.4 - - + -
158A ILE* 4.1 28.7 - - + -
162A PHE* 3.9 28.9 - - + -
184A ARG 3.0 15.2 + - - +
185A LEU* 4.1 11.2 - - + +
187A ILE* 1.3 80.7 - - - +
189A ILE* 1.3 73.8 + - + +
192A ALA* 3.6 15.6 - - - +
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Residues in contact with ILE 189 (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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185A LEU* 2.7 39.1 + - + +
188A LEU* 1.3 87.1 - - + +
190A GLY* 1.3 66.3 + - - +
191A TRP 3.3 0.9 - - - -
192A ALA* 3.1 20.0 + - - +
193A ILE* 4.0 1.2 + - - +
307A LFA 3.9 56.1 - - + +
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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