Contacts of the helix formed by residues 174 - 186 (chain C) in PDB entry 3ESF
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 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B THR 5.8 0.7 - - - +
171C TYR* 2.9 27.5 + - + +
172C LYS 3.1 0.6 - - - -
173C ASN* 1.3 83.9 - - - +
175C ARG* 1.3 61.8 + - - +
176C PRO* 3.3 14.2 - - - +
177C ALA* 3.2 31.0 + - + +
178C TYR 3.3 14.2 + - - -
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Residues in contact with ARG 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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117C ALA 2.7 37.3 + - - -
118C VAL* 3.4 21.4 + - - +
120C HIS* 2.7 37.6 + - - +
122C GLY* 3.7 16.6 + - - +
162C VAL* 3.9 20.6 + - - +
164C GLU* 5.4 3.8 + - - +
167C TYR* 3.2 41.8 + - + +
173C ASN 2.9 10.8 + - - +
174C ASP* 1.3 70.0 - - - +
176C PRO* 1.4 66.8 - - + +
178C TYR* 3.1 17.3 + - + +
179C VAL* 2.8 29.9 + - + +
163D TRP* 6.0 2.4 - - - -
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Residues in contact with PRO 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 4.0 34.1 - - + -
173C ASN 4.6 2.0 - - - +
174C ASP* 3.3 14.1 - - - +
175C ARG* 1.4 93.2 - - + +
177C ALA* 1.3 55.9 + - - +
179C VAL* 3.3 3.6 + - - +
180C GLN* 3.0 33.0 + - + +
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG 6.1 0.9 - - - +
171C TYR* 3.7 18.5 - - + -
174C ASP* 3.2 31.2 + - - +
175C ARG 3.3 0.2 - - - -
176C PRO* 1.3 74.9 - - - +
178C TYR* 1.3 64.5 + - - +
180C GLN* 3.2 9.7 + - - +
181C THR* 3.0 23.7 + - - -
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Residues in contact with TYR 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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20C ILE* 4.6 15.0 - - + -
79C TYR* 2.7 35.8 + - - -
83C MET* 5.8 0.4 - - - -
160C CYS* 3.6 19.4 - - - -
161C ASP 2.7 30.0 + - - -
162C VAL* 4.3 4.3 - - + -
166C ALA* 3.8 10.6 - - + +
167C TYR* 3.4 44.6 - + + -
171C TYR* 3.7 23.9 - + + -
174C ASP 3.3 9.6 + - - +
175C ARG* 3.1 18.1 + - + +
177C ALA* 1.3 80.3 - - - +
179C VAL* 1.3 59.9 + - + +
181C THR* 3.1 6.6 + - - -
182C PHE* 2.9 28.1 + + + +
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C PHE* 5.3 3.6 - - + -
114C THR* 4.2 20.2 - - + -
117C ALA* 3.7 32.8 - - + -
118C VAL* 3.8 13.7 - - + -
160C CYS* 4.9 2.2 - - - -
162C VAL* 4.9 1.3 - - + -
175C ARG* 2.8 29.1 + - + +
176C PRO 3.7 4.9 - - - +
178C TYR* 1.3 84.1 - - + +
180C GLN* 1.3 64.0 + - - +
182C PHE* 3.1 17.8 + - + +
183C TRP* 3.1 37.8 + - + +
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Residues in contact with GLN 180 (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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110C LYS* 4.6 13.1 - - - +
114C THR* 4.3 15.1 + - - +
176C PRO 3.0 19.3 + - - +
177C ALA* 3.6 10.5 - - - +
178C TYR 3.2 0.4 - - - -
179C VAL* 1.3 73.2 - - - +
181C THR* 1.3 65.0 + - - +
183C TRP* 3.2 34.6 + - - +
184C ASN* 3.3 19.2 + - - +
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Residues in contact with THR 181 (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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61B THR 4.7 3.6 + - - -
18C LYS 3.4 21.7 + - - +
19C GLY* 3.8 2.7 - - - +
20C ILE* 3.8 27.4 - - + -
171C TYR* 2.4 36.3 + - + +
177C ALA 3.0 9.3 + - - -
178C TYR* 3.1 10.7 + - + +
180C GLN* 1.3 73.4 - - - +
182C PHE* 1.3 66.5 + - - +
184C ASN* 2.9 24.0 + - - +
185C VAL* 3.2 12.1 + - + +
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Residues in contact with PHE 182 (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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20C ILE* 6.0 0.7 - - - -
79C TYR* 4.7 1.3 - + - -
82C SER* 4.2 6.7 - - - -
83C MET* 3.9 34.5 - - + -
113C PHE* 3.9 29.6 - + - -
158C LEU* 4.8 4.7 - - + -
159C THR 3.5 28.3 - - - -
160C CYS* 3.7 30.1 - - + -
178C TYR* 2.9 20.0 + + + +
179C VAL* 3.3 12.1 - - + +
181C THR* 1.3 72.9 - - - +
183C TRP* 1.3 69.5 + + - +
185C VAL* 3.1 8.3 + - - +
186C VAL* 2.8 57.2 + - + +
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Residues in contact with TRP 183 (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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88C GLY* 3.2 19.1 - - - -
89C GLY 3.8 7.5 + - - +
106C PHE* 4.5 6.1 - + - -
109C PHE* 3.6 33.9 - + - -
110C LYS* 3.6 59.2 - - + +
113C PHE* 3.5 34.8 - + + -
114C THR* 2.9 18.5 + - - -
179C VAL* 3.1 30.4 + - + +
180C GLN* 3.5 23.1 - - - +
181C THR 3.2 0.6 - - - -
182C PHE* 1.3 81.8 - + - +
184C ASN* 1.3 60.5 + - - +
185C VAL 3.4 0.2 - - - -
186C VAL* 3.7 21.1 - - + +
188C TRP* 4.3 14.8 - + - -
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Residues in contact with ASN 184 (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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18C LYS* 3.3 31.9 + - - +
87C GLY 3.3 17.0 - - - +
88C GLY* 3.4 6.3 - - - -
89C GLY 5.8 0.2 + - - -
180C GLN* 3.3 15.3 + - - +
181C THR* 2.9 17.1 + - - +
183C TRP* 1.3 80.7 - - - +
185C VAL* 1.3 58.0 + - - +
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Residues in contact with VAL 185 (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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15C LEU* 4.2 13.5 - - + -
18C LYS* 3.5 40.6 - - + +
20C ILE* 4.6 4.5 - - + -
83C MET* 3.2 37.4 - - + -
84C SER 2.8 41.6 + - - +
87C GLY* 3.7 1.2 - - - -
88C GLY 3.7 2.5 - - - +
181C THR* 3.2 11.4 + - + +
182C PHE* 3.1 16.1 + - - +
184C ASN* 1.3 77.6 - - - +
186C VAL* 1.3 69.8 + - - +
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Residues in contact with VAL 186 (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 SER 3.5 7.0 - - - +
83C MET* 4.6 0.2 - - - +
87C GLY* 3.2 2.8 - - - -
88C GLY* 2.8 25.6 + - - +
89C GLY 4.6 0.4 - - - +
158C LEU* 3.6 36.6 - - + -
182C PHE* 2.8 32.8 + - + +
183C TRP* 3.7 28.5 - - + +
185C VAL* 1.3 74.8 - - - +
187C ASN* 1.3 61.8 + - - +
188C TRP* 3.4 42.3 + - + +
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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