Contacts of the helix formed by residues 175 - 191 (chain A) in PDB entry 1ZJA
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 THR 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 2.6 44.3 + - + +
126A TYR* 4.5 8.3 - - + -
172A ASN* 3.4 13.7 + - - +
173A TRP 3.1 0.4 - - - -
174A ASP* 1.3 77.3 - - - +
176A PRO* 1.3 69.8 - - + +
177A LYS* 4.0 6.7 - - + +
178A LEU* 3.1 20.0 + - + +
179A ARG* 3.1 22.6 + - - +
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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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174A ASP 3.2 11.7 - - - +
175A THR* 1.3 86.0 - - + +
177A LYS* 1.3 59.1 + - + +
179A ARG* 3.0 32.1 + - - +
180A GLU* 2.9 34.2 + - + +
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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
----------------------------------------------------------
126A TYR* 3.9 18.6 - - + +
175A THR* 3.3 7.1 + - + +
176A PRO* 1.3 79.9 - - + +
178A LEU* 1.3 61.2 + - - +
180A GLU* 3.4 9.2 + - + +
181A GLU* 3.1 26.7 + - - +
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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
----------------------------------------------------------
111A TRP* 3.9 23.1 - - + -
126A TYR* 3.7 53.3 - - + +
171A LEU* 4.0 16.2 - - + -
172A ASN 3.7 26.9 - - - +
173A TRP* 4.4 6.5 - - + +
175A THR* 3.1 13.8 + - - +
177A LYS* 1.3 75.0 - - - +
179A ARG* 1.3 70.4 + - + +
181A GLU* 3.0 3.0 + - + +
182A LEU* 2.9 42.9 + - + +
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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
----------------------------------------------------------
173A TRP* 2.8 67.0 + - + +
174A ASP* 3.7 18.2 + - - +
175A THR 3.1 8.7 + - - +
176A PRO* 3.0 33.3 + - - +
178A LEU* 1.3 78.9 - - - +
180A GLU* 1.3 63.1 + - + +
182A LEU* 3.1 7.7 + - - +
183A TYR* 3.0 45.6 + - + +
234A ARG* 6.0 1.8 - - - +
235A TYR* 3.7 22.4 + - - -
238A GLU* 2.7 36.9 + - - +
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO* 2.9 21.6 + - + +
177A LYS* 3.7 9.0 - - + +
178A LEU 3.1 0.2 - - - -
179A ARG* 1.3 79.2 - - + +
181A GLU* 1.3 62.0 + - + +
183A TYR* 3.2 20.1 + - - +
184A ALA* 3.0 23.9 + - - +
187A ARG* 4.7 8.1 + - - -
238A GLU* 5.3 1.6 - - - +
242A LYS* 3.4 31.1 - - - +
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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
----------------------------------------------------------
70A ARG* 4.8 1.6 + - - -
111A TRP* 3.6 40.4 + - + -
123A TYR* 3.9 8.8 + - - -
126A TYR* 2.6 30.1 + - + +
177A LYS 3.1 16.9 + - - +
178A LEU* 3.0 9.7 + - - +
180A GLU* 1.3 76.0 - - - +
182A LEU* 1.3 65.0 + - - +
184A ALA* 3.3 7.2 + - - +
185A MET* 3.0 22.2 + - - +
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Residues in contact with LEU 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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69A TYR* 5.0 2.2 - - + -
102A ILE* 3.9 37.2 - - + +
111A TRP* 4.1 26.2 - - + -
171A LEU* 4.3 7.9 - - + -
173A TRP* 3.6 35.0 - - + +
178A LEU* 2.9 38.7 + - + +
179A ARG* 3.6 7.9 - - - +
181A GLU* 1.3 77.5 - - - +
183A TYR* 1.3 67.4 - - + +
185A MET* 3.1 11.4 + - + +
186A LEU* 3.0 26.7 + - - +
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TRP* 3.8 19.2 - + - -
179A ARG* 3.0 34.6 + - + -
180A GLU* 3.2 17.7 + - - +
182A LEU* 1.3 78.8 - - + +
184A ALA* 1.3 64.4 + - - +
186A LEU* 3.1 8.4 + - + +
187A ARG* 3.0 38.0 + - - +
235A TYR 3.9 0.3 + - - -
238A GLU* 2.5 36.8 + - + +
239A MET* 3.6 36.3 + - + -
242A LYS* 3.8 31.0 - - + -
243A VAL* 3.5 26.7 - - + +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 3.5 20.2 + - - +
180A GLU 3.0 17.1 + - - +
181A GLU* 3.7 7.0 - - - +
183A TYR* 1.3 78.4 - - - +
185A MET* 1.3 60.2 + - - +
187A ARG* 3.4 21.4 + - - +
188A PHE* 3.1 17.2 + - - +
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Residues in contact with MET 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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55A TYR* 5.7 2.7 - - - -
69A TYR* 3.3 47.3 - - + +
70A ARG* 3.7 17.9 - - - +
100A VAL* 4.5 3.8 - - + -
102A ILE* 3.5 32.5 - - + -
111A TRP* 5.8 2.7 - - + -
181A GLU 3.0 13.2 + - - +
182A LEU* 3.1 16.8 + - + +
184A ALA* 1.3 74.3 - - - +
186A LEU* 1.3 86.2 + - + +
188A PHE* 3.1 17.3 + - - +
189A TRP* 3.4 23.0 + - + +
197A MET* 5.9 0.2 - - - -
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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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100A VAL* 3.7 29.8 - - + -
102A ILE* 4.7 4.3 - - + -
182A LEU 3.0 18.6 + - - +
183A TYR* 3.1 8.9 + - + +
185A MET* 1.3 89.3 - - + +
187A ARG* 1.3 58.4 + - - +
189A TRP 3.2 2.6 + - - -
190A LEU* 2.9 33.0 + - + +
197A MET* 3.6 24.9 - - + +
199A PHE* 4.4 1.3 - - + -
239A MET* 3.7 36.6 - - + -
243A VAL* 3.9 18.8 - - + -
244A PHE* 4.0 11.9 - - + -
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Residues in contact with ARG 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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180A GLU* 4.7 10.5 + - - -
183A TYR* 3.0 29.5 + - - +
184A ALA* 3.6 35.1 - - - +
186A LEU* 1.3 76.6 - - - +
188A PHE* 1.3 54.9 + - - +
190A LEU* 4.2 4.7 - - - -
191A ASP* 2.7 45.1 + - - +
242A LYS* 3.0 37.0 + - - +
243A VAL* 4.3 6.5 - - + +
246A HIS* 5.6 0.6 - - - -
247A TYR* 3.6 31.1 - - + +
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Residues in contact with PHE 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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70A ARG* 3.7 56.3 - - + +
79A MET* 4.1 9.9 - - + -
184A ALA 3.1 11.9 + - - +
185A MET 3.1 11.7 + - - +
187A ARG* 1.3 78.4 - - - +
189A TRP* 1.3 100.6 + + - +
191A ASP* 3.6 9.7 + - - +
192A LYS* 3.3 38.5 + - + +
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Residues in contact with TRP 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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54A HIS* 3.4 28.0 - + - -
55A TYR* 3.6 29.4 - + - -
69A TYR 2.7 30.1 + - - -
70A ARG* 4.2 7.2 - - - -
71A GLU 4.5 1.1 - - - -
72A VAL* 4.5 4.9 - - + -
79A MET* 3.8 19.7 - - + -
82A PHE* 3.6 31.2 - + - -
98A VAL* 5.1 3.4 - - + -
185A MET* 3.4 34.7 + - - +
186A LEU* 3.2 6.4 + - - +
188A PHE* 1.3 90.2 - + - +
190A LEU* 1.3 66.1 + - - +
192A LYS* 3.1 34.3 + - + +
194A VAL* 3.4 22.1 - - + +
197A MET* 4.1 14.1 - - + -
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Residues in contact with LEU 190 (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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186A LEU 2.9 20.2 + - - +
187A ARG* 3.9 0.7 - - - +
189A TRP* 1.3 71.0 - - - +
191A ASP* 1.3 58.0 + - - +
192A LYS 3.0 4.9 - - - -
193A GLY* 2.9 21.3 + - - -
194A VAL* 3.9 16.0 + - + +
197A MET* 3.7 21.8 - - + -
243A VAL* 3.5 31.4 - - + -
244A PHE* 3.7 13.2 - - + -
247A TYR* 3.5 40.9 - - + -
249A ALA* 3.5 31.4 - - + -
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Residues in contact with ASP 191 (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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187A ARG* 2.7 34.5 + - - +
188A PHE* 3.9 8.0 + - - +
190A LEU* 1.3 73.1 - - - +
192A LYS* 1.3 59.2 + - + +
193A GLY 3.3 1.6 + - - -
247A TYR* 2.6 30.5 + - - -
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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