Contacts of the helix formed by residues 170 - 188 (chain A) in PDB entry 1Z10
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.3 13.4 - - + +
169A ASP* 1.3 87.8 - - - +
171A THR* 1.3 64.4 + - - +
172A PHE 3.5 0.9 - - - -
173A PHE* 3.1 22.4 + - + +
174A LEU* 3.1 30.2 + - + +
311A ARG* 4.8 3.6 - - + -
314A PHE* 5.8 0.2 - - + -
487A TYR* 3.5 48.0 - - + +
489A MET* 3.9 16.2 - - + -
491A PHE* 4.4 13.7 - - + -
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASP* 2.6 29.4 + - - -
170A PRO* 1.3 78.1 - - - +
172A PHE* 1.3 83.3 + - + +
174A LEU* 3.5 4.8 + - - +
175A SER* 3.1 27.0 + - - +
206A LEU* 4.0 19.7 - - + -
307A SER* 4.2 2.4 + - - -
311A ARG* 3.4 39.1 + - - +
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASP* 4.6 7.3 + - - -
170A PRO 3.5 0.6 - - - -
171A THR* 1.3 87.8 - - + +
173A PHE* 1.3 66.1 + - + +
174A LEU 3.2 1.1 - - - -
175A SER* 3.5 14.8 - - - -
176A ARG* 3.0 52.2 + - + +
199A LEU* 3.7 16.6 - - + -
202A LEU* 3.8 26.5 - - + -
203A ARG* 3.8 45.5 - - + -
206A LEU* 3.7 25.8 - - + -
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.7 7.3 - - + +
159A ALA* 4.0 24.7 - - + -
160A LEU* 4.1 22.9 - - + -
163A THR* 3.8 27.8 - - + -
168A ILE* 3.5 29.4 - - + -
169A ASP 3.4 23.6 - - - -
170A PRO* 3.1 8.2 + - + +
172A PHE* 1.3 81.1 - - + +
174A LEU* 1.3 62.3 + - + +
176A ARG* 3.9 24.8 - - - +
177A THR* 3.1 25.5 + - - -
193A TYR* 5.4 1.0 - - - -
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Residues in contact with LEU 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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156A LEU* 4.2 24.5 - - + -
160A LEU* 5.9 2.2 - - + -
170A PRO* 3.1 27.5 + - + +
171A THR 3.7 6.1 - - - +
173A PHE* 1.3 78.0 - - + +
175A SER* 1.3 60.7 + - - +
177A THR* 3.2 6.0 + - - -
178A VAL* 3.0 34.4 + - - +
307A SER* 4.4 6.7 - - - +
310A LEU* 4.1 16.8 - - + -
311A ARG* 3.8 37.2 - - + +
314A PHE* 3.9 31.2 - - + -
456A VAL* 5.7 0.4 - - + -
491A PHE* 5.7 4.0 - - + -
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 3.1 11.5 + - - -
172A PHE* 3.5 23.9 - - - -
174A LEU* 1.3 77.5 - - - +
176A ARG* 1.3 60.4 + - - +
178A VAL* 4.4 0.7 - - - -
179A SER* 2.8 34.8 + - - -
202A LEU* 3.6 22.3 - - - +
303A THR* 4.2 5.0 - - - +
304A GLU* 5.1 4.7 - - - -
307A SER* 3.3 27.6 + - - -
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 3.0 51.7 + - - +
173A PHE* 3.8 34.0 - - - +
175A SER* 1.3 77.2 + - - +
177A THR* 1.3 62.8 + - - +
180A ASN* 3.2 23.4 + - - +
193A TYR* 3.4 57.1 + - + +
198A PHE* 3.4 27.2 - - + -
199A LEU* 4.4 19.2 - - - +
202A LEU* 3.4 19.7 - - + -
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Residues in contact with THR 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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152A GLU* 3.3 30.2 - - + +
156A LEU* 3.4 35.1 - - + +
173A PHE 3.1 14.0 + - - -
174A LEU 3.2 7.8 + - - -
176A ARG* 1.3 75.9 - - - +
178A VAL* 1.3 67.2 + - + +
180A ASN* 3.4 5.5 + - - +
181A VAL* 3.7 5.5 + - - +
193A TYR* 2.8 22.6 + - - -
310A LEU* 6.3 0.2 - - + -
452A PHE* 3.3 34.5 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU 3.0 20.7 + - - +
175A SER* 3.9 4.0 - - - +
177A THR* 1.3 75.8 - - - +
179A SER* 1.3 65.9 + - - +
181A VAL* 2.9 21.5 + - - +
182A ILE 3.7 2.9 + - - -
302A GLY 3.5 16.9 - - - +
303A THR* 3.4 25.4 - - - +
306A VAL* 3.7 15.5 - - + -
307A SER* 4.2 6.1 - - - +
310A LEU* 3.4 30.5 - - + -
448A GLU* 3.6 15.3 - - - +
452A PHE* 4.2 9.2 - - + -
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER 2.8 22.8 + - - -
178A VAL* 1.3 76.8 - - - +
180A ASN* 1.3 54.7 + - - +
182A ILE* 3.5 4.0 + - - +
183A SER* 2.7 38.9 + - - -
198A PHE* 3.7 12.6 - - - -
202A LEU* 3.7 17.3 - - - +
299A PHE* 3.4 20.1 - - - -
303A THR* 2.9 26.5 + - - -
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Residues in contact with ASN 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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148A ARG* 3.5 3.5 + - - -
152A GLU* 3.1 36.5 + - - +
176A ARG 3.2 13.2 + - - +
177A THR 3.7 1.3 - - - +
178A VAL 3.1 1.2 + - - -
179A SER* 1.3 75.1 - - - +
181A VAL* 1.3 61.9 + - - +
183A SER* 3.8 3.0 - - - -
184A SER* 3.0 28.2 + - - -
190A ARG* 3.5 11.5 - - + +
191A PHE* 2.7 59.6 + - - +
193A TYR* 3.3 15.8 - - - -
198A PHE* 3.7 3.5 - - - -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 4.4 11.4 - - + -
148A ARG* 4.5 8.0 - - + +
149A ILE* 3.8 27.4 - - + +
152A GLU* 4.5 9.9 - - + -
177A THR 3.7 11.0 - - - +
178A VAL 2.9 14.4 + - - +
180A ASN* 1.3 75.2 - - - +
182A ILE* 1.3 67.6 + - - +
184A SER* 3.1 19.3 + - - -
185A ILE* 3.5 7.3 + - - +
444A LEU* 4.0 14.1 - - + -
448A GLU* 3.3 22.2 - - - +
452A PHE* 3.8 22.0 - - + -
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.4 13.7 - - + -
178A VAL 3.7 1.2 + - - -
179A SER 3.5 9.9 - - - +
181A VAL* 1.3 79.7 - - - +
183A SER* 1.3 66.2 + - - +
185A ILE* 3.1 16.9 + - + +
186A VAL* 3.0 32.7 + - + +
298A LEU* 3.5 26.9 - - + +
299A PHE* 4.1 9.9 - - + +
302A GLY* 3.9 20.4 - - - +
303A THR* 3.9 19.3 - - - +
444A LEU* 4.1 13.2 - - + -
448A GLU* 4.7 0.6 + - - +
500A HEM 3.9 25.8 - - + -
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Residues in contact with SER 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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179A SER* 2.7 25.0 + - - -
180A ASN* 3.9 9.9 - - - -
181A VAL 3.1 0.2 - - - -
182A ILE* 1.3 78.7 - - - +
184A SER* 1.3 56.7 + - - +
186A VAL* 4.0 2.9 - - - -
187A PHE* 2.8 45.1 + - - +
188A GLY 3.5 0.7 + - - -
189A ASP 3.6 6.1 - - - +
191A PHE* 3.2 34.3 - - - -
299A PHE* 3.3 16.9 - - - -
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Residues in contact with SER 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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138A PHE* 6.0 0.3 - - - -
145A ILE* 5.7 0.4 - - - -
148A ARG* 3.1 38.7 + - - -
180A ASN 3.0 17.1 + - - -
181A VAL 3.1 11.6 + - - -
183A SER* 1.3 76.5 - - - +
185A ILE* 1.3 60.5 + - - +
188A GLY* 3.1 27.9 + - - +
189A ASP* 3.9 13.5 + - - +
190A ARG 3.9 10.7 + - - -
265A ARG 5.2 0.3 - - - +
266A ASP* 4.7 0.2 - - - +
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Residues in contact with ILE 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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135A LEU* 3.7 24.2 - - + -
138A PHE* 4.1 30.7 - - + +
140A VAL* 3.7 20.9 - - + -
145A ILE* 3.5 34.8 - - + -
181A VAL 3.5 10.5 + - - +
182A ILE* 3.1 22.9 + - + +
184A SER* 1.3 79.3 - - - +
186A VAL* 1.3 63.6 + - + +
266A ASP* 3.2 11.1 - - - +
267A PHE* 2.9 27.2 + - + -
444A LEU* 4.4 5.6 - - + -
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Residues in contact with VAL 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 ILE* 3.0 32.5 + - + +
183A SER* 4.0 2.0 - - - -
185A ILE* 1.3 81.9 - - + +
187A PHE* 1.3 92.3 + - + +
266A ASP* 3.4 15.5 - - - +
267A PHE* 3.6 20.4 - - + -
268A ILE* 3.4 19.1 + - - +
295A THR* 4.2 16.6 - - + -
298A LEU* 4.1 26.2 - - + -
299A PHE* 5.1 7.2 - - + -
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Residues in contact with PHE 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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183A SER* 2.8 34.1 + - - +
186A VAL* 1.3 92.0 - - + +
188A GLY* 1.3 59.4 + - - +
189A ASP* 3.5 17.2 + - - +
191A PHE* 4.0 11.7 - + - -
247A PHE* 3.8 14.8 - + - -
248A ILE* 3.7 32.8 - - + -
251A LYS* 4.2 33.3 + - + +
255A ASN* 5.1 3.6 - - - +
266A ASP* 3.2 14.8 - - - +
268A ILE* 3.9 20.6 - - + -
295A THR* 4.1 3.1 - - + -
299A PHE* 3.8 29.8 - + + -
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Residues in contact with GLY 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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184A SER* 3.1 19.4 + - - +
187A PHE* 1.3 76.7 - - - +
189A ASP* 1.3 64.7 + - - +
265A ARG* 3.9 13.0 - - - +
266A ASP* 3.3 19.0 - - - +
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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
------------------------------------------------------------
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