Contacts of the helix formed by residues 170 - 185 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I GLU* 4.4 0.2 - - - -
112I LYS* 3.4 25.8 - - - +
121I ASP* 3.4 14.6 - - - +
124I MET* 5.3 3.4 - - + -
167I PRO 4.7 0.7 - - - -
169I ASN* 1.3 95.4 + - - +
171I PRO* 1.3 60.0 - - - +
172I LEU 3.4 2.0 - - - -
173I LEU* 3.3 29.5 + - + -
174I MET* 2.8 48.3 + - + +
296I PHE* 3.7 37.5 - + - -
297I ASN* 3.6 21.5 - - + -
300I GLN 3.8 9.4 - - - -
301I CYS* 4.3 16.2 - - + -
302I CYS* 6.3 0.9 - - - -
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Residues in contact with PRO 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I GLU* 3.3 29.6 - - - +
110I ASN* 4.0 8.1 - - + +
112I LYS* 4.6 1.8 - - - -
166I ILE* 3.7 9.4 - - + +
167I PRO 4.2 10.3 - - - +
168I TRP 3.3 19.0 - - - +
169I ASN 3.6 2.9 - - - +
170I PHE* 1.3 89.4 - - - +
172I LEU* 1.3 61.4 + - - +
175I GLN* 3.2 20.4 + - - +
197I THR* 3.4 36.3 - - + +
200I THR* 3.7 9.6 - - - +
201I ALA* 5.3 4.5 - - + +
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Residues in contact with LEU 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I ILE* 6.3 0.4 - - + -
102I LEU* 4.2 17.3 - - + +
106I GLU* 3.0 28.1 + - - +
121I ASP* 5.6 2.2 - - + -
122I LEU* 3.7 34.8 - - + -
125I VAL* 3.6 22.4 - - + +
171I PRO* 1.3 71.9 - - - +
173I LEU* 1.3 60.7 + - - +
175I GLN* 3.3 14.4 + - - +
176I ALA* 3.0 23.4 + - - +
200I THR* 3.4 31.9 - - - +
204I VAL* 3.7 29.6 - - + -
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Residues in contact with LEU 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I GLU* 4.6 0.8 + - - -
121I ASP* 4.8 8.4 + - - +
124I MET* 3.4 65.7 - - + +
125I VAL* 3.7 12.0 - - + +
128I CYS* 4.9 0.9 - - + -
170I PHE* 3.3 28.9 + - + -
172I LEU* 1.3 75.1 - - - +
174I MET* 1.3 62.8 + - + +
176I ALA* 3.2 2.0 + - + +
177I TRP* 2.8 72.0 + - + +
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Residues in contact with MET 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I ILE* 4.0 20.6 - - + -
167I PRO* 3.7 28.7 - - + +
169I ASN* 4.2 4.3 - - - +
170I PHE* 2.8 48.2 + - + +
171I PRO 4.1 2.0 - - - +
173I LEU* 1.3 73.4 - - + +
175I GLN* 1.3 65.4 + - - +
177I TRP* 3.2 49.8 + - + +
178I LYS* 3.2 32.0 + - - +
244I THR* 4.2 16.8 - - - -
302I CYS* 6.5 2.2 - - - -
476I GLU* 5.3 1.8 - - - +
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Residues in contact with GLN 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I ILE* 3.7 13.6 - - + +
171I PRO 3.2 12.0 + - - +
172I LEU* 3.4 16.1 + - - +
173I LEU 3.2 0.4 - - - -
174I MET* 1.3 78.4 - - - +
176I ALA* 1.3 55.9 + - - +
178I LYS* 3.2 3.5 + - - +
179I LEU* 2.9 39.7 + - + +
191I MET* 3.7 19.9 - - + +
201I ALA* 3.3 38.3 - - + +
204I VAL* 3.4 39.7 - - - +
208I ILE* 4.9 0.2 - - - +
220I ILE* 3.6 14.2 - - - +
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Residues in contact with ALA 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I VAL* 4.0 31.6 - - + +
128I CYS* 3.4 23.5 - - + -
129I LEU* 4.3 14.7 - - + +
172I LEU 3.0 14.4 + - - +
173I LEU* 3.2 8.3 + - - +
175I GLN* 1.3 75.2 - - - +
177I TRP* 1.3 59.8 + - - +
179I LEU* 4.5 2.7 - - - +
180I GLY* 3.0 24.8 + - - -
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Residues in contact with TRP 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I MET* 6.2 0.7 - - - -
128I CYS* 3.7 17.4 - - - +
173I LEU* 2.8 49.5 + - + +
174I MET* 3.2 37.2 - - + +
175I GLN 3.3 0.2 - - - -
176I ALA* 1.3 77.4 - - - +
178I LYS* 1.3 59.4 + - + +
181I PRO* 3.1 23.4 - - - +
268I GLU* 5.7 0.2 - - - -
302I CYS* 6.0 2.5 - - - -
459I PHE* 4.1 36.6 - + + -
461I ALA* 5.9 0.6 - - - +
465I PHE* 4.2 19.1 - + + -
476I GLU* 3.5 37.3 - - + +
477I LEU* 3.5 48.2 + - + +
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Residues in contact with LYS 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I GLN* 3.1 37.3 + - + +
165I ILE 4.7 0.4 - - - -
166I ILE* 3.7 19.7 - - + +
174I MET* 3.2 20.6 + - - +
175I GLN 3.7 3.4 - - - +
177I TRP* 1.3 78.8 - - - +
179I LEU* 1.3 65.5 + - - +
181I PRO* 3.5 5.9 - - - +
182I ALA* 3.4 13.7 + - - +
191I MET* 3.9 5.2 - - + -
242I ALA* 4.0 28.0 - - - -
244I THR* 2.7 31.9 + - - +
268I GLU* 5.6 0.6 - - - +
476I GLU* 2.7 32.5 + - - +
485I TYR* 4.0 15.6 + - + +
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Residues in contact with LEU 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I LEU* 5.2 5.6 - - + -
129I LEU* 5.0 7.2 - - + -
164I GLN* 3.7 17.0 - - - +
175I GLN* 2.9 36.5 + - + +
176I ALA* 4.5 3.4 - - - +
178I LYS* 1.3 73.0 - - - +
180I GLY* 1.3 67.6 + - - +
182I ALA* 4.6 0.9 - - - -
183I LEU* 2.9 40.3 + - + +
189I VAL* 4.1 18.8 - - + -
191I MET* 3.7 11.9 - - + -
204I VAL* 5.1 2.5 - - + -
208I ILE* 3.7 29.4 - - + -
218I VAL* 4.2 19.7 - - + -
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Residues in contact with GLY 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I LEU* 4.0 6.0 - - - +
129I LEU* 4.4 13.1 - - - +
132I TYR* 3.5 22.5 - - - +
176I ALA 3.0 17.6 + - - -
179I LEU* 1.3 80.6 - - - +
181I PRO* 1.3 61.0 - - - +
184I ALA* 3.1 26.7 + - - +
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Residues in contact with PRO 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I TYR* 3.6 40.3 - - + +
177I TRP 3.1 28.3 - - - +
178I LYS 3.5 6.5 - - - +
180I GLY* 1.3 85.2 - - - +
182I ALA* 1.3 62.2 + - - +
184I ALA* 3.5 0.5 + - - +
185I THR* 2.8 32.6 + - - +
476I GLU* 6.6 0.2 - - + -
477I LEU 5.9 1.8 - - - +
481I GLY* 4.0 11.2 - - - +
482I LEU* 4.1 4.5 - - + -
485I TYR* 3.9 25.7 - - + +
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Residues in contact with ALA 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I GLN* 3.6 15.5 - - - +
178I LYS 3.4 16.6 + - - +
179I LEU 4.1 1.3 - - - +
180I GLY 3.4 0.6 - - - -
181I PRO* 1.3 81.6 - - - +
183I LEU* 1.3 60.0 + - - +
185I THR* 3.2 3.8 + - - -
187I ASN* 3.0 36.9 + - + +
189I VAL* 4.0 18.4 - - + -
485I TYR* 3.6 25.1 - - + -
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Residues in contact with LEU 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I TRP* 3.6 13.4 - - + -
84I ARG* 3.5 15.6 - - - +
88I LEU* 4.1 18.4 - - + -
91I LEU* 5.5 3.1 - - + -
179I LEU* 2.9 36.2 + - + +
182I ALA* 1.3 73.3 - - + +
184I ALA* 1.3 67.2 + - - +
185I THR 3.1 1.8 - - - -
186I GLY 3.1 9.4 + - - -
187I ASN 3.8 9.9 - - - +
189I VAL* 4.7 7.4 - - + -
208I ILE* 5.8 0.7 - - + -
213I PHE* 3.7 26.2 - - + -
217I VAL* 3.6 31.6 - - + +
218I VAL* 4.0 22.9 - - + -
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Residues in contact with ALA 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ARG* 2.9 24.2 + - - +
88I LEU* 3.9 9.8 - - + +
132I TYR* 3.3 32.3 - - + +
135I TRP* 4.7 4.3 - - + -
136I ALA* 3.4 23.2 - - - +
180I GLY 3.1 18.8 + - - +
181I PRO* 3.9 5.8 - - + +
182I ALA 3.4 0.2 - - - -
183I LEU* 1.3 77.9 - - - +
185I THR* 1.3 58.5 + - + +
482I LEU* 4.8 2.7 - - + -
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Residues in contact with THR 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ARG* 3.9 9.6 + - - +
139I TYR* 4.6 9.2 - - + -
156I HIS 5.5 0.9 - - - +
157I GLU 4.9 0.5 - - - -
158I PRO* 3.1 23.7 - - - +
181I PRO 2.8 21.5 + - - +
182I ALA 3.2 0.3 + - - -
183I LEU 3.1 0.4 - - - -
184I ALA* 1.3 78.0 - - - +
186I GLY* 1.3 58.3 + - - +
187I ASN* 2.8 23.8 + - - -
482I LEU* 3.9 30.7 - - + +
485I TYR* 3.4 4.9 - - - +
486I THR* 3.8 27.2 - - + +
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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
------------------------------------------------------------
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