Contacts of the helix formed by residues 160 - 179 (chain C) in PDB entry 4A9H
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 ASP 160 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLN* 4.2 9.7 - - - +
156C ASN* 3.5 12.7 - - - +
157C LYS* 2.9 49.8 + - - +
158C PRO 4.2 0.3 - - - +
159C THR* 1.3 81.4 + - - +
161C ASP* 1.3 66.1 + - - +
162C ILE* 3.8 18.8 - - + -
163C VAL* 3.0 19.2 + - - +
164C LEU* 3.9 2.9 + - - +
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Residues in contact with ASP 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASN* 3.5 14.3 + - + +
181A PRO* 4.9 7.5 - - + +
182A GLN* 5.5 1.8 + - - +
183A GLU* 4.3 6.3 + - - +
185A GLN* 3.2 32.8 + - - +
182B GLN* 5.7 4.7 - - - +
159C THR 3.5 3.7 + - - +
160C ASP* 1.3 69.6 - - - +
162C ILE* 1.3 66.9 + - - +
163C VAL 3.2 0.5 + - - -
164C LEU* 3.2 9.5 + - - +
165C MET* 3.0 32.4 + - + +
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PRO* 3.3 39.5 - - + -
99C PHE* 4.0 5.8 - - + -
152C CYS* 3.6 17.9 - - - -
156C ASN* 3.5 37.5 - - + +
160C ASP* 3.8 10.5 - - + +
161C ASP* 1.3 77.5 - - - +
163C VAL* 1.3 59.2 + - - +
165C MET* 3.2 10.6 + - - +
166C ALA* 2.9 28.8 + - - +
1183C TVP 3.7 37.5 - - + -
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C CYS* 4.5 9.6 - - - +
153C TYR* 3.9 21.0 - - + +
156C ASN* 4.0 20.9 - - + +
157C LYS 3.4 25.8 - - - +
158C PRO* 4.0 15.9 - - + +
160C ASP 3.0 9.7 + - - +
162C ILE* 1.3 77.6 - - + +
164C LEU* 1.3 62.5 + - - +
166C ALA* 3.3 7.2 + - - +
167C GLN* 3.0 36.4 + - - +
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 5.6 7.2 - - + -
160C ASP 3.9 2.7 + - - +
161C ASP* 3.2 12.1 + - - +
163C VAL* 1.3 78.6 - - - +
165C MET* 1.3 64.1 + - + +
167C GLN* 3.2 23.0 + - + +
168C THR* 3.0 35.6 + - - +
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Residues in contact with MET 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO* 5.9 3.6 - - - -
182B GLN* 4.9 9.6 - - - +
95C PHE* 3.3 68.0 - - + +
97C TRP* 3.7 18.6 - - - +
98C PRO* 3.5 23.1 - - + -
99C PHE* 4.6 3.8 - - + -
161C ASP* 3.0 27.3 + - + +
162C ILE* 3.2 17.0 + - - +
164C LEU* 1.3 76.3 - - + +
166C ALA* 1.3 61.7 + - - +
168C THR* 3.3 3.8 + - - -
169C LEU* 3.0 29.5 + - - +
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PHE* 4.0 14.7 - - + -
149C PHE* 3.8 14.4 - - + -
152C CYS* 3.9 19.5 - - + -
153C TYR* 3.4 21.1 - - + +
162C ILE 2.9 15.9 + - - +
163C VAL 3.6 4.7 - - - +
165C MET* 1.3 71.9 - - - +
167C GLN* 1.3 56.1 + - - +
169C LEU* 3.2 2.2 + - - +
170C GLU* 2.8 36.9 + - - +
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Residues in contact with GLN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TYR* 3.3 22.6 + - + +
163C VAL* 3.0 26.0 + - - +
164C LEU* 3.2 39.0 + - + +
166C ALA* 1.3 75.9 - - - +
168C THR* 1.3 62.5 + - - +
170C GLU* 3.4 1.7 + - - +
171C LYS* 3.1 43.5 + - - +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C HIS* 4.2 16.2 - - + +
95C PHE* 3.7 28.5 - - + -
164C LEU* 3.0 22.8 + - - +
165C MET 3.5 8.1 - - - -
166C ALA 3.2 0.2 - - - -
167C GLN* 1.3 77.1 - - - +
169C LEU* 1.3 62.2 + - - +
171C LYS* 3.5 8.6 + - - +
172C ILE* 3.4 25.3 + - + +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.6 25.4 - - + +
93C HIS* 3.6 42.4 - - + +
95C PHE* 3.6 18.2 - - + +
96C ALA* 4.1 4.5 - - - +
99C PHE* 3.6 35.9 - - + -
123C MET* 4.2 8.5 - - + -
149C PHE* 3.7 19.3 - - + -
165C MET 3.0 17.4 + - - +
166C ALA 3.2 0.2 + - - -
168C THR* 1.3 75.6 - - - +
170C GLU* 1.3 58.4 + - - +
172C ILE* 3.2 6.6 + - - +
173C PHE* 2.9 25.5 + - - +
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Residues in contact with GLU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASN* 3.9 19.6 - - - +
149C PHE* 3.3 40.0 - - + +
150C THR* 5.5 0.9 + - - -
153C TYR* 3.2 32.2 + - - +
166C ALA 2.8 20.9 + - - +
167C GLN 3.9 2.5 - - - +
169C LEU* 1.3 73.6 - - - +
171C LYS* 1.3 56.9 + - + +
173C PHE* 3.3 10.0 + - + +
174C LEU* 2.9 41.2 + - + +
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Residues in contact with LYS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLN* 3.1 34.7 + - - +
168C THR* 3.9 7.4 - - - +
169C LEU 3.3 0.2 - - - -
170C GLU* 1.3 75.7 - - + +
172C ILE* 1.3 58.1 + - + +
174C LEU* 3.4 9.7 + - + +
175C GLN* 3.0 32.3 + - - +
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ALA* 5.0 6.5 - - + -
90C LEU* 3.8 15.7 - - + -
93C HIS* 3.6 35.9 - - + +
168C THR* 3.4 21.5 + - + +
169C LEU* 3.2 9.7 + - - +
171C LYS* 1.3 73.9 - - + +
173C PHE* 1.3 66.8 + - - +
175C GLN* 3.2 7.4 + - + +
176C LYS* 2.9 49.0 + - + +
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Residues in contact with PHE 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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82C LEU* 4.8 1.6 - - + -
86C VAL* 4.0 16.4 - - + -
90C LEU* 3.9 15.4 - - + +
142C MET* 3.9 27.1 - - + -
145C PHE* 3.3 48.2 - + + -
146C ASN* 5.0 5.2 - - + -
149C PHE* 4.2 13.9 - + + -
169C LEU 2.9 13.8 + - - +
170C GLU* 3.3 20.9 - - + +
172C ILE* 1.3 77.0 - - - +
174C LEU* 1.3 77.9 + - + +
176C LYS* 3.3 2.3 + - - +
177C VAL* 2.9 54.2 + - + +
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Residues in contact with LEU 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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142C MET* 6.4 0.9 - - + -
170C GLU* 2.9 34.2 + - + +
171C LYS* 3.8 7.9 - - + +
173C PHE* 1.3 89.0 - - + +
175C GLN* 1.3 66.9 + - - +
177C VAL* 3.3 11.9 + - + +
178C ALA* 3.0 23.9 + - - +
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Residues in contact with GLN 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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171C LYS 3.0 19.8 + - - +
172C ILE* 3.4 8.7 - - + +
174C LEU* 1.3 74.2 - - - +
176C LYS* 1.3 66.9 + - + +
178C ALA* 3.1 21.6 + - - +
179C SER* 3.6 9.2 + - - -
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Residues in contact with LYS 176 (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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81C TYR* 2.8 29.2 + - - +
85C VAL* 4.3 21.6 - - + +
86C VAL* 3.6 28.9 - - + +
89C ALA* 4.1 24.2 - - + +
172C ILE* 2.9 35.1 + - + +
173C PHE 3.6 3.6 - - - +
175C GLN* 1.3 77.7 - - + +
177C VAL* 1.3 64.0 + - - +
179C SER* 3.1 9.7 + - - -
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TYR* 4.9 1.1 - - - -
82C LEU* 4.3 16.4 - - + -
86C VAL* 5.0 1.6 - - + -
142C MET* 3.7 27.8 - - + -
173C PHE* 2.9 50.8 + - + +
174C LEU* 3.3 14.6 + - + +
176C LYS* 1.3 77.0 - - - +
178C ALA* 1.3 63.1 + - - +
180C MET* 3.1 32.1 + - + +
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Residues in contact with ALA 178 (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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174C LEU 3.0 12.7 + - - +
175C GLN* 3.1 14.5 + - - +
177C VAL* 1.3 77.1 - - - +
179C SER* 1.3 59.8 + - - +
180C MET 3.3 4.3 + - - +
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TYR* 3.8 20.1 + - - -
175C GLN 3.6 8.5 + - - -
176C LYS* 3.1 6.8 + - - -
178C ALA* 1.3 75.9 - - - +
180C MET* 1.3 64.9 + - - +
181C PRO* 3.7 2.9 - - - +
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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