Contacts of the helix formed by residues 160 - 175 (chain C) in PDB entry 3P05
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 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C LYS 3.4 6.8 - - - +
159C GLU* 1.3 93.4 - - + +
161C PHE* 1.3 65.9 + - - +
162C ARG* 3.2 4.0 - - + +
163C ASP* 3.2 40.9 + - - +
164C TYR* 3.3 10.0 + - - +
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Residues in contact with PHE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLN* 3.6 25.2 - - - +
159C GLU 3.6 1.2 + - - -
160C PRO* 1.3 71.6 - - - +
162C ARG* 1.3 58.4 + - - +
164C TYR* 3.2 26.4 + + - +
165C VAL* 2.9 51.5 + - + +
190C LEU* 4.9 4.7 - - + -
194C ALA* 4.3 4.5 - - + -
198C CYS* 4.3 7.3 - - - -
202C LEU* 3.7 29.8 - - + -
211C LEU* 5.0 0.9 - - + -
214C MET* 3.7 46.0 - - + -
215C MET* 4.0 15.3 - - + +
218C CYS* 3.6 30.5 + - + +
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Residues in contact with ARG 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C PRO* 3.2 4.2 - - + +
161C PHE* 1.3 80.5 - - - +
163C ASP* 1.3 72.2 + - - +
165C VAL* 3.3 3.2 + - - +
166C ASP* 2.9 31.7 + - - +
215C MET* 3.4 31.6 - - + +
219C GLN* 5.8 1.0 + - - -
64D ALA* 4.3 6.7 - - + -
144D MET* 4.1 10.3 + - - +
145D TYR* 3.5 72.4 + - + +
147D PRO* 5.9 2.0 - - - +
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Residues in contact with ASP 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C GLU* 3.7 16.1 - - + +
160C PRO* 3.2 36.6 + - - +
162C ARG* 1.3 88.0 + - - +
164C TYR* 1.3 58.0 + - - +
166C ASP* 3.3 11.1 + - - +
167C ARG* 3.1 30.1 + - - +
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Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ILE* 3.9 18.6 - - + -
154C ARG 3.7 7.4 - - - -
155C GLN* 3.4 44.2 - - + -
159C GLU* 3.6 21.5 + - - +
160C PRO 3.3 3.6 + - - +
161C PHE* 3.2 29.3 + + - +
162C ARG 3.2 0.4 - - - -
163C ASP* 1.3 76.7 - - - +
165C VAL* 1.3 58.1 + - + +
167C ARG* 3.1 9.2 + - - +
168C PHE* 2.8 37.9 + + - +
189C LEU 3.7 2.8 + - - -
190C LEU* 2.9 46.1 + - + +
193C ASN* 3.4 22.9 - - - +
194C ALA* 4.2 3.1 - - - -
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PHE* 2.9 56.2 + - + +
162C ARG* 3.8 5.2 - - - +
164C TYR* 1.3 78.5 - - + +
166C ASP* 1.3 57.8 + - - +
168C PHE* 3.5 5.3 - - - +
169C TYR* 3.0 53.7 + - + -
190C LEU* 4.7 6.1 - - + -
211C LEU* 4.0 17.3 - - + -
215C MET* 4.6 2.0 - - + -
64D ALA* 3.4 23.3 - - + -
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Residues in contact with ASP 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ARG* 2.9 28.4 + - - +
163C ASP* 3.3 15.6 - - - +
164C TYR 3.2 0.2 - - - -
165C VAL* 1.3 78.0 - - - +
167C ARG* 1.3 63.2 + - + +
169C TYR 3.5 0.2 + - - -
170C LYS* 3.0 26.7 + - - +
61D GLY* 6.4 0.2 - - - -
62D HIS* 3.6 14.3 + - - +
63D GLN* 3.2 14.7 + - - +
64D ALA* 2.7 41.6 + - - +
145D TYR* 4.4 4.3 + - - -
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASP 5.5 0.2 + - - -
153C ILE* 3.5 41.6 - - + +
154C ARG 3.0 23.4 + - - +
156C GLY 4.1 0.8 - - - +
159C GLU* 2.6 42.4 + - - +
163C ASP 3.1 11.8 + - - +
164C TYR* 3.1 8.6 + - - +
166C ASP* 1.3 73.2 - - + +
168C PHE* 1.3 67.3 + - - +
170C LYS* 3.8 5.3 - - - +
171C THR* 2.8 32.5 + - - +
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Residues in contact with PHE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ILE* 3.5 33.2 - - + +
153C ILE* 3.9 16.5 - - + +
164C TYR* 2.8 34.6 + + + +
165C VAL 3.2 4.9 + - - +
167C ARG* 1.3 74.6 - - - +
169C TYR* 1.3 79.8 + + - +
172C LEU* 3.0 41.6 + - + +
185C ALA* 3.4 33.2 - - + -
186C THR* 4.5 0.9 - - - -
189C LEU* 3.7 22.4 - - + -
190C LEU* 3.6 37.0 - - + -
193C ASN* 5.2 0.2 - - - -
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Residues in contact with TYR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 3.0 42.3 + - + +
168C PHE* 1.3 87.7 - + - +
170C LYS* 1.3 60.4 + - - +
172C LEU* 3.4 23.5 + - + +
173C ARG* 3.0 29.5 + - - +
182C LYS* 6.0 1.8 - - + -
186C THR* 2.9 40.0 + - - +
190C LEU* 4.3 10.0 - - + +
211C LEU* 4.2 6.6 - - + +
63D GLN* 3.6 26.4 - - + +
67D GLN* 3.5 48.9 + - + +
71D GLU* 5.6 1.2 + - - -
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 3.5 23.8 - - - +
34C PRO* 4.3 7.6 - - + +
146C SER* 6.1 3.8 - - - +
166C ASP 3.0 20.1 + - - +
167C ARG* 3.8 6.3 - - - +
169C TYR* 1.3 76.1 - - - +
171C THR* 1.3 65.2 + - - +
173C ARG* 3.1 6.7 + - - +
174C ALA* 3.0 24.8 + - + +
232C IOD 3.4 22.9 - - + -
61D GLY* 5.5 3.6 - - - +
63D GLN* 3.9 12.5 - - + +
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Residues in contact with THR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C SER* 4.7 6.9 + - - +
148C THR* 3.4 28.0 - - - +
150C ILE* 4.0 13.7 - - - +
153C ILE* 3.6 25.9 - - + +
167C ARG* 2.8 19.0 + - - +
168C PHE 3.6 3.8 - - - -
170C LYS* 1.3 75.6 - - - +
172C LEU* 1.3 66.1 + - - +
174C ALA* 3.2 15.4 + - - +
175C GLU* 3.2 23.9 + - + +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ILE* 3.6 36.1 - - + -
168C PHE* 3.0 30.4 + - + +
169C TYR* 3.7 22.7 - - + +
171C THR* 1.3 76.9 - - - +
173C ARG* 1.3 64.4 + - - +
175C GLU* 3.3 15.6 + - - +
177C ALA* 3.5 38.1 + - + +
181C VAL* 5.2 4.3 - - + +
182C LYS* 4.0 31.0 - - + +
185C ALA* 4.1 12.1 - - + -
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Residues in contact with ARG 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO* 3.9 21.2 + - + +
35C GLU* 3.8 10.4 - - - +
38C PRO* 3.8 12.7 - - - +
169C TYR 3.0 18.1 + - - +
170C LYS* 3.1 6.3 + - - +
172C LEU* 1.3 76.4 - - - +
174C ALA* 1.3 56.8 + - - +
176C GLN* 3.0 27.5 + - - +
232C IOD 3.7 19.8 - - - +
56D LEU 5.4 0.8 + - - -
57D ASN* 2.6 47.2 + - - +
59D VAL 3.7 16.2 + - - -
63D GLN* 3.8 20.2 + - - +
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Residues in contact with ALA 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO* 3.4 21.9 - - + +
142C VAL* 3.5 11.0 - - + +
143C ARG* 3.8 11.5 - - - -
146C SER* 3.1 38.1 - - - +
170C LYS* 3.0 14.4 + - + +
171C THR 3.2 6.7 + - - +
173C ARG* 1.3 77.7 - - - +
175C GLU* 1.3 57.3 + - - +
176C GLN* 3.2 17.3 + - - -
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Residues in contact with GLU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG* 5.3 12.3 - - + +
146C SER 4.8 9.2 - - - +
147C PRO 5.0 1.2 - - - +
148C THR 3.1 24.1 - - - +
149C SER* 3.4 6.3 + - - -
150C ILE* 3.3 31.4 + - - +
171C THR* 3.2 19.2 + - + +
172C LEU* 3.9 10.9 - - - +
173C ARG 3.1 1.6 - - - -
174C ALA* 1.3 76.3 - - - +
176C GLN* 1.3 72.8 + - - +
177C ALA* 3.2 6.0 + - + +
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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
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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