Contacts of the helix formed by residues 170 - 185 (chain J) in PDB entry 1ZUM
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 PHE 170 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106J GLU* 4.4 0.4 - - - -
112J LYS* 3.2 27.6 - - - +
121J ASP* 3.5 10.1 - - - +
124J MET* 5.5 3.4 - - + -
167J PRO 4.7 0.7 - - - -
169J ASN* 1.3 102.0 + - - +
171J PRO* 1.3 59.9 - - - +
172J LEU 3.4 1.8 - - - -
173J LEU* 3.3 26.8 + - + -
174J MET* 2.8 50.6 + - + +
296J PHE* 3.9 32.5 - + - -
297J ASN* 3.4 24.2 - - + -
300J GLN 3.7 4.3 - - - -
301J CYS* 4.3 18.2 - - + -
302J CYS* 5.4 0.9 - - - -
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Residues in contact with PRO 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J GLU* 3.3 29.8 - - + +
110J ASN* 4.0 7.9 - - + +
112J LYS* 4.7 1.1 - - - +
166J ILE* 4.0 8.6 - - + +
167J PRO 4.2 9.9 - - - +
168J TRP 3.3 18.8 - - - +
169J ASN 3.6 2.9 - - - +
170J PHE* 1.3 87.4 - - - +
172J LEU* 1.3 61.1 + - - +
174J MET* 4.1 0.2 - - - +
175J GLN* 3.3 20.7 + - - +
197J THR* 3.4 35.4 - - + +
200J THR* 3.7 9.0 - - - +
201J ALA* 5.2 4.4 - - + +
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Residues in contact with LEU 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J ILE* 5.9 0.7 - - + -
102J LEU* 4.2 18.6 - - + +
106J GLU* 3.0 22.1 + - - +
121J ASP* 5.6 2.2 - - + -
122J LEU* 3.7 31.9 - - + -
125J VAL* 3.7 24.9 - - + +
171J PRO* 1.3 72.6 - - - +
173J LEU* 1.3 60.8 + - - +
175J GLN* 3.3 15.8 + - - +
176J ALA* 3.0 23.9 + - - +
200J THR* 3.6 32.5 - - + +
204J VAL* 3.4 32.3 - - + -
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Residues in contact with LEU 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J GLU* 4.7 0.4 + - - -
121J ASP* 4.4 8.8 + - - +
124J MET* 3.3 63.9 - - + +
125J VAL* 3.7 11.6 - - + +
170J PHE* 3.3 24.9 + - + -
172J LEU* 1.3 76.0 - - - +
174J MET* 1.3 66.6 + - + +
176J ALA* 3.2 2.2 + - + +
177J TRP* 2.8 68.5 + - + +
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Residues in contact with MET 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J ILE* 3.9 22.0 - - + -
167J PRO* 3.8 27.4 - - + +
169J ASN* 4.1 5.4 - - - +
170J PHE* 2.8 50.5 + - + +
171J PRO 4.1 2.2 - - - +
173J LEU* 1.3 75.0 - - + +
175J GLN* 1.3 64.9 + - - +
177J TRP* 3.3 46.7 + - + +
178J LYS* 3.1 32.4 + - + +
244J THR* 4.5 16.6 - - - -
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Residues in contact with GLN 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J ILE* 3.8 14.3 - - + +
171J PRO 3.3 12.1 + - - +
172J LEU* 3.5 15.0 + - - +
173J LEU 3.2 0.6 - - - -
174J MET* 1.3 78.5 - - - +
176J ALA* 1.3 57.1 + - - +
178J LYS* 3.2 3.5 + - - +
179J LEU* 2.9 42.2 + - + +
191J MET* 3.7 16.2 - - - +
201J ALA* 3.3 34.5 - - + +
204J VAL* 3.4 39.5 - - - +
208J ILE* 5.3 0.3 - - - +
220J ILE* 3.3 19.4 - - - +
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Residues in contact with ALA 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J VAL* 4.0 31.0 - - + +
128J CYS* 3.4 23.9 - - + -
129J LEU* 4.3 15.7 - - + +
172J LEU 3.0 13.8 + - - +
173J LEU* 3.2 7.4 + - + +
175J GLN* 1.3 79.4 - - - +
177J TRP* 1.3 56.2 + - - +
179J LEU* 4.5 2.7 - - - +
180J GLY* 2.9 25.8 + - - -
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Residues in contact with TRP 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J MET* 5.5 0.6 + - - -
128J CYS* 3.7 16.3 - - - +
132J TYR* 5.2 0.9 - - - -
173J LEU* 2.8 51.3 + - + +
174J MET* 3.3 39.0 + - + +
176J ALA* 1.3 73.3 - - - +
178J LYS* 1.3 61.2 + - + +
181J PRO* 3.1 22.7 - - - +
302J CYS* 6.2 1.6 - - - -
459J PHE* 4.0 36.1 - + + -
461J ALA* 5.8 0.8 - - - +
465J PHE* 4.3 20.9 - + + -
476J GLU* 4.3 26.9 - - + +
477J LEU* 3.5 49.1 + - + +
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Residues in contact with LYS 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J GLN* 3.1 39.5 + - + +
165J ILE 4.9 0.2 - - - -
166J ILE* 3.7 17.9 - - + +
174J MET* 3.1 21.9 + - - +
175J GLN 3.7 3.1 - - - +
177J TRP* 1.3 80.6 - - - +
179J LEU* 1.3 64.1 + - - +
181J PRO* 3.5 5.5 - - - +
182J ALA* 3.3 13.3 + - - +
191J MET* 4.2 5.6 - - + -
242J ALA* 4.0 22.4 - - + -
244J THR* 2.9 30.2 + - - +
268J GLU* 3.5 9.5 + - - -
476J GLU* 3.1 29.4 + - - +
485J TYR* 3.8 16.4 - - - +
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Residues in contact with LEU 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J LEU* 5.3 0.2 - - - -
91J LEU* 5.0 7.2 - - + -
129J LEU* 4.9 7.4 - - + -
164J GLN* 3.9 6.7 - - - +
175J GLN* 2.9 43.0 + - + +
176J ALA* 4.4 4.0 - - - +
178J LYS* 1.3 71.1 - - - +
180J GLY* 1.3 67.7 + - - +
182J ALA* 4.5 2.2 - - - -
183J LEU* 2.9 39.2 + - + +
189J VAL* 4.2 12.1 - - + -
191J MET* 3.6 22.7 - - + -
204J VAL* 5.0 3.8 - - + -
208J ILE* 3.8 26.7 - - + -
218J VAL* 4.2 23.3 - - + -
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Residues in contact with GLY 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J LEU* 4.1 5.8 - - - +
129J LEU* 4.3 13.3 - - - +
132J TYR* 3.5 23.9 - - - +
176J ALA 2.9 16.9 + - - -
179J LEU* 1.3 80.0 - - - +
181J PRO* 1.3 61.5 - - - +
184J ALA* 3.0 27.4 + - - +
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Residues in contact with PRO 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J TYR* 3.6 38.1 - - + +
177J TRP 3.1 29.2 - - - +
178J LYS 3.5 6.3 - - - +
180J GLY* 1.3 84.5 - - - +
182J ALA* 1.3 62.3 + - - +
184J ALA* 3.8 0.3 - - - +
185J THR* 2.8 33.7 + - - +
476J GLU* 5.9 1.1 - - - +
477J LEU 6.1 0.9 - - - +
481J GLY* 3.9 13.9 - - - +
482J LEU* 4.3 4.3 - - + -
485J TYR* 3.7 26.9 - - + -
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Residues in contact with ALA 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J CYS* 5.2 0.2 - - - -
164J GLN* 3.6 15.9 - - - +
178J LYS 3.3 16.6 - - - +
179J LEU 3.9 1.8 - - - +
180J GLY 3.4 0.4 - - - -
181J PRO* 1.3 81.2 - - - +
183J LEU* 1.3 58.9 + - - +
185J THR* 3.1 5.3 + - - -
187J ASN* 3.0 36.3 + - + +
189J VAL* 3.9 18.4 - - + -
485J TYR* 3.8 22.4 - - + -
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Residues in contact with LEU 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J TRP* 3.5 12.9 - - + -
84J ARG* 3.4 17.9 + - - +
88J LEU* 4.2 17.9 - - + -
91J LEU* 5.6 1.6 - - + -
179J LEU* 2.9 39.5 + - + +
182J ALA* 1.3 71.4 - - + +
184J ALA* 1.3 66.5 + - - +
185J THR 3.1 2.2 - - - -
186J GLY 3.1 8.8 + - - -
187J ASN 3.7 11.7 - - - +
189J VAL* 4.4 7.9 - - + -
208J ILE* 5.6 1.3 - - + -
213J PHE* 3.8 26.0 - - + -
217J VAL* 3.6 31.2 - - + +
218J VAL* 3.9 21.8 - - + -
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Residues in contact with ALA 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J ARG* 3.0 22.2 + - - +
88J LEU* 4.1 9.1 - - + +
132J TYR* 3.4 30.3 - - + +
135J TRP* 4.8 0.4 - - + -
136J ALA* 3.4 24.4 - - - +
180J GLY 3.0 20.6 + - - +
181J PRO* 3.8 6.1 - - + +
183J LEU* 1.3 77.7 - - - +
185J THR* 1.3 58.0 + - - +
482J LEU* 4.6 7.4 - - + -
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Residues in contact with THR 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J ARG* 3.9 9.6 + - - +
139J TYR* 4.4 11.0 - - + -
156J HIS 5.5 0.9 - - - +
157J GLU 4.9 0.7 - - - -
158J PRO* 3.1 23.9 - - - +
181J PRO 2.8 11.4 + - - +
182J ALA 3.1 0.3 + - - -
184J ALA* 1.3 79.0 - - - +
186J GLY* 1.3 55.8 + - - +
187J ASN* 2.7 25.9 + - - -
482J LEU* 3.6 38.6 - - + +
485J TYR* 3.5 4.8 - - + +
486J THR* 3.8 22.4 - - - +
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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