Contacts of the helix formed by residues 170 - 185 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 4.3 0.2 - - - -
112A LYS* 3.1 27.6 - - - +
121A ASP* 3.4 12.6 - - - +
124A MET* 5.6 3.8 - - + -
167A PRO 4.8 0.2 - - - -
168A TRP 4.7 0.2 - - - -
169A ASN* 1.3 94.3 + - - +
171A PRO* 1.3 61.7 - - - +
172A LEU 3.5 1.6 - - - -
173A LEU* 4.0 27.8 - - + -
174A MET* 2.9 46.7 + - + +
296A PHE* 3.6 35.2 - + - -
297A ASN* 3.5 20.9 - - - -
300A GLN 3.8 10.8 - - - -
301A CYS* 3.6 14.8 - - + -
302A CYS 5.4 0.4 - - - -
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Residues in contact with PRO 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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106A GLU* 3.3 30.1 - - - +
110A ASN* 4.0 8.5 - - + +
112A LYS* 4.5 1.3 - - - -
166A ILE* 3.7 9.7 - - + +
167A PRO 4.3 10.3 - - - +
168A TRP 3.4 17.9 - - - +
169A ASN 3.5 4.0 - - - +
170A PHE* 1.3 89.3 - - - +
172A LEU* 1.3 61.3 + - - +
175A GLN* 3.3 20.0 + - - +
197A THR* 3.5 33.7 - - + +
200A THR* 3.6 10.1 - - - +
201A ALA* 5.2 4.3 - - + +
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Residues in contact with LEU 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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95A ILE* 6.4 0.2 - - + -
102A LEU* 4.1 17.5 - - + +
106A GLU* 3.0 25.3 + - - +
121A ASP* 5.6 2.0 - - + +
122A LEU* 3.9 28.9 - - + -
125A VAL* 3.6 22.1 - - + +
171A PRO* 1.3 75.3 - - - +
173A LEU* 1.3 65.9 + - - +
175A GLN* 3.1 15.8 + - - +
176A ALA* 3.0 18.0 + - - +
200A THR* 3.5 34.5 - - + +
204A VAL* 3.6 30.7 - - + -
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Residues in contact with LEU 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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106A GLU* 4.7 0.6 + - - -
121A ASP* 4.7 8.8 + - - +
124A MET* 3.5 63.7 - - + +
125A VAL* 3.6 13.1 - - + +
170A PHE* 3.4 26.2 + - + -
172A LEU* 1.3 74.9 - - - +
174A MET* 1.3 63.7 + - + +
176A ALA* 3.1 3.7 + - + +
177A TRP* 2.8 70.8 + - + +
459A PHE* 6.1 0.9 - - + -
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Residues in contact with MET 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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166A ILE* 3.9 23.6 - - + -
167A PRO* 3.6 32.5 - - + +
169A ASN* 4.1 4.5 - - - +
170A PHE* 2.9 49.7 + - + +
173A LEU* 1.3 75.0 - - + +
175A GLN* 1.3 63.4 + - - +
177A TRP* 3.2 49.2 + - + +
178A LYS* 3.2 33.2 + - - +
244A THR* 4.4 14.6 - - - -
302A CYS* 5.9 3.6 - - - -
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Residues in contact with GLN 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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166A ILE* 3.7 11.9 - - + +
171A PRO 3.3 11.5 + - - +
172A LEU* 3.1 16.5 + - - +
173A LEU 3.1 0.2 - - - -
174A MET* 1.3 79.7 - - - +
176A ALA* 1.3 56.3 + - - +
178A LYS* 3.3 2.4 + - - +
179A LEU* 2.9 46.4 + - + +
191A MET* 3.8 17.7 - - - -
201A ALA* 3.2 34.9 - - + +
204A VAL* 3.4 42.4 - - - +
208A ILE* 5.0 0.2 - - - +
220A ILE* 3.5 15.8 - - - +
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Residues in contact with ALA 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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125A VAL* 4.2 26.7 - - + +
128A CYS* 3.5 20.5 - - + -
129A LEU* 4.0 20.1 - - + +
172A LEU 3.0 12.2 + - - +
173A LEU* 3.1 7.2 + - + +
175A GLN* 1.3 77.9 - - - +
177A TRP* 1.3 58.1 + - - +
179A LEU* 4.5 2.0 - - - +
180A GLY* 2.8 32.2 + - - -
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Residues in contact with TRP 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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124A MET* 5.9 1.8 - - - -
128A CYS* 3.6 23.2 - - - +
132A TYR* 5.0 3.3 + + - -
173A LEU* 2.8 46.4 + - + +
174A MET* 3.2 42.4 - - + +
175A GLN 3.4 0.2 - - - -
176A ALA* 1.3 75.9 - - - +
178A LYS* 1.3 67.8 + - + +
181A PRO* 3.1 22.7 - - - +
459A PHE* 4.4 40.2 - + + -
460A GLY 5.9 1.7 + - - -
461A ALA* 5.8 5.6 - - - +
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Residues in contact with LYS 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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164A GLN* 3.0 41.7 + - + +
165A ILE 5.2 0.2 - - - -
166A ILE* 3.8 17.3 - - + +
174A MET* 3.2 21.9 + - - +
176A ALA 3.1 0.4 - - - -
177A TRP* 1.3 87.6 + - - +
179A LEU* 1.3 64.9 + - - +
180A GLY 3.3 0.4 + - - -
181A PRO* 3.7 4.2 - - - +
182A ALA* 3.2 14.2 + - - +
191A MET* 3.8 8.3 - - + -
242A ALA* 4.0 22.9 - - + -
244A THR* 3.2 20.3 + - - +
268A GLU* 3.1 25.3 + - - -
485A TYR* 3.7 17.3 - - - +
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Residues in contact with LEU 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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88A LEU* 5.0 1.1 - - + -
91A LEU* 5.1 4.5 - - + -
129A LEU* 5.0 6.5 - - + -
164A GLN* 3.8 7.4 - - - +
175A GLN* 2.9 38.8 + - + +
176A ALA* 4.2 3.4 - - - +
178A LYS* 1.3 75.8 - - - +
180A GLY* 1.3 65.3 + - - +
182A ALA* 4.6 0.9 - - - -
183A LEU* 2.9 41.2 + - + +
189A VAL* 3.9 21.1 - - + -
191A MET* 3.6 20.4 - - + -
204A VAL* 5.1 2.2 - - + -
208A ILE* 3.6 30.7 - - + -
218A VAL* 4.2 15.7 - - + -
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Residues in contact with GLY 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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88A LEU* 4.1 5.7 - - - +
129A LEU* 4.4 11.6 - - - +
132A TYR* 3.6 23.6 - - - +
176A ALA 2.8 19.9 + - - -
179A LEU* 1.3 72.8 - - - +
181A PRO* 1.3 62.5 - - - +
184A ALA* 3.0 31.5 + - - +
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Residues in contact with PRO 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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132A TYR* 3.7 39.2 - - + +
177A TRP 3.1 28.5 - - - +
178A LYS* 3.7 5.6 - - - +
180A GLY* 1.3 84.8 - - - +
182A ALA* 1.3 61.7 + - - +
184A ALA* 3.8 0.8 - - + +
185A THR* 2.8 33.0 + - - +
481A GLY* 4.1 7.6 - - - +
482A LEU* 4.1 11.0 - - + -
485A TYR* 4.0 25.3 - - + +
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Residues in contact with ALA 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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164A GLN* 3.6 7.0 - - - +
178A LYS 3.2 17.7 - - - +
179A LEU 4.1 1.1 - - - +
180A GLY 3.4 0.8 - - - -
181A PRO* 1.3 80.1 - - - +
183A LEU* 1.3 60.4 + - - +
185A THR* 3.2 9.6 + - - -
187A ASN* 3.0 31.5 + - + -
189A VAL* 3.9 19.5 - - + -
485A TYR* 3.5 31.3 - - + -
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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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76A TRP* 3.5 11.7 - - + -
84A ARG* 3.4 15.2 + - - +
88A LEU* 4.3 17.5 - - + -
91A LEU* 5.5 1.3 - - + -
179A LEU* 2.9 38.5 + - + +
180A GLY 4.3 0.7 - - - +
182A ALA* 1.3 72.6 - - + +
184A ALA* 1.3 65.5 + - - +
185A THR 3.1 1.8 - - - -
186A GLY 2.9 11.6 + - - -
187A ASN 3.7 12.1 - - - +
189A VAL* 4.5 7.2 - - + -
208A ILE* 5.4 2.0 - - + -
213A PHE* 3.8 24.2 - - + -
217A VAL* 3.6 30.7 - - + +
218A VAL* 3.8 24.5 - - + -
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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
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84A ARG* 2.8 24.1 + - - -
88A LEU* 3.9 9.8 - - + +
132A TYR* 3.5 28.9 - - + +
135A TRP* 4.8 3.8 - - + -
136A ALA* 3.4 23.7 - - - +
180A GLY 3.0 20.6 + - - +
181A PRO* 3.8 6.5 - - + +
182A ALA 3.4 0.2 - - - -
183A LEU* 1.3 76.4 - - - +
185A THR* 1.3 60.5 + - + +
482A LEU* 5.0 1.1 - - + -
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Residues in contact with THR 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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84A ARG* 3.8 9.1 + - - +
139A TYR* 4.8 8.1 - - + -
156A HIS 5.5 1.2 - - - +
157A GLU 5.0 0.3 - - - -
158A PRO* 3.3 23.9 - - - +
181A PRO 2.8 20.0 + - - +
182A ALA 3.2 0.3 + - - -
183A LEU 3.1 0.2 - - - -
184A ALA* 1.3 79.4 - - - +
186A GLY* 1.3 56.3 + - - +
187A ASN* 2.8 26.8 + - - -
482A LEU* 3.9 29.6 - - + +
485A TYR* 3.4 4.4 - - + +
486A THR* 3.8 27.7 - - + +
500D SER* 5.3 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