Contacts of the helix formed by residues 177 - 190 (chain C) in PDB entry 4IYM
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 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LEU* 3.7 19.5 - - + +
21C ILE* 3.8 10.3 - - + -
33C VAL* 3.8 18.6 - - + -
88C GLU* 3.6 11.7 - - - +
172C PRO* 5.2 0.2 - - + -
173C SER 4.0 7.0 - - - +
174C GLU* 3.6 18.8 - - - +
175C ARG 3.7 3.8 - - - +
176C ASP* 1.3 86.0 - - - +
178C SER* 1.3 66.0 + - - +
180C PRO* 3.2 17.2 - - + +
181C ILE* 3.7 13.9 + - - +
201C ASN* 3.6 23.7 - - - +
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Residues in contact with SER 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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0C TYR* 3.8 9.7 + - - -
2C LEU* 3.7 19.3 - - - +
10C ARG* 5.8 0.7 + - - -
84C MSE 3.9 27.2 - - - +
87C ARG* 5.3 1.6 + - - -
88C GLU* 2.6 34.4 + - - -
177C PRO* 1.3 79.6 - - - +
179C VAL* 1.3 64.1 + - - +
181C ILE* 3.4 3.9 + - - +
182C ARG* 3.1 21.5 + - - +
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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
----------------------------------------------------------
81C LEU* 3.7 19.3 - - + +
84C MSE 3.8 15.9 - - + -
85C LEU* 3.6 40.8 - - + -
88C GLU* 4.5 1.0 + - - +
100C ILE* 5.5 3.6 - - + -
150C PRO* 3.6 20.9 - - + +
151C GLY* 3.8 15.5 - - - -
176C ASP 4.6 1.1 + - - +
178C SER* 1.3 75.4 - - - +
180C PRO* 1.4 60.1 - - + +
182C ARG* 3.0 3.7 + - - +
183C LEU* 2.7 50.9 + - + +
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Residues in contact with PRO 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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150C PRO* 3.6 19.3 - - + +
154C PRO* 4.7 0.7 - - + -
170C LEU* 3.8 24.5 - - + +
172C PRO* 3.7 30.7 - - + -
176C ASP 3.9 7.6 - - - +
177C PRO* 3.2 18.8 - - + +
179C VAL* 1.4 92.8 - - + +
181C ILE* 1.3 62.2 + - - +
183C LEU* 3.3 14.0 + - + +
184C ALA* 3.1 22.2 + - - +
197C LEU* 5.9 0.2 - - - +
199C VAL* 3.9 8.3 - - + +
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Residues in contact with ILE 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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2C LEU* 4.1 22.7 - - + -
3C GLY 3.6 16.2 - - - +
4C HIS 4.8 2.0 - - - -
5C PHE* 4.2 14.3 - - + +
10C ARG* 3.4 45.1 - - + +
177C PRO 3.7 9.5 + - - +
178C SER* 3.4 8.1 + - - +
179C VAL 3.3 0.2 - - - -
180C PRO* 1.3 75.5 - - - +
182C ARG* 1.3 61.0 + - - +
184C ALA* 3.2 7.8 + - - +
185C GLU* 3.0 25.3 + - - +
199C VAL* 4.1 15.0 - - + -
201C ASN* 3.5 28.3 - - - +
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Residues in contact with ARG 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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10C ARG* 4.4 7.2 - - - +
77C ASN* 2.9 28.9 + - - +
80C GLU* 5.9 3.0 - - - +
81C LEU* 3.8 20.4 - - + -
84C MSE 3.9 28.0 - - + +
178C SER 3.1 12.2 + - - +
179C VAL 3.0 7.6 + - - +
181C ILE* 1.3 77.2 - - - +
183C LEU* 1.3 58.0 + - - +
185C GLU* 3.0 46.0 + - - +
186C LEU* 2.9 51.2 + - + +
189C GLU* 4.6 6.9 + - - -
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Residues in contact with LEU 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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70C PHE* 3.5 17.5 - - + -
74C LEU* 3.7 29.2 - - + -
81C LEU* 4.2 17.5 - - + -
100C ILE* 5.7 0.9 - - + -
150C PRO 4.3 3.8 - - - +
151C GLY* 4.1 10.8 - - - +
154C PRO* 4.7 4.3 - - + -
155C MSE 4.0 32.1 - - + -
158C PHE* 4.5 11.7 - - + -
170C LEU* 6.2 0.2 - - + -
179C VAL* 2.7 36.8 + - + +
180C PRO* 3.5 11.2 - - + +
181C ILE 3.3 0.2 - - - -
182C ARG* 1.3 73.4 - - - +
184C ALA* 1.3 55.8 + - - +
186C LEU* 3.2 5.1 + - + -
187C MSE 2.9 27.3 + - - +
197C LEU* 4.8 0.7 - - - -
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Residues in contact with ALA 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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5C PHE* 3.7 21.7 - - + -
180C PRO 3.1 6.0 + - - +
181C ILE 3.2 8.3 + - - +
183C LEU* 1.3 73.5 - - - +
185C GLU* 1.3 65.3 + - - +
187C MSE 3.3 4.0 + - - +
188C ILE* 3.2 26.2 + - - +
197C LEU* 3.9 24.5 - - + +
199C VAL* 3.7 29.8 - - + -
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Residues in contact with GLU 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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5C PHE* 3.9 19.0 - - + -
10C ARG* 2.7 50.4 + - - +
181C ILE 3.0 11.0 + - - +
182C ARG* 3.0 37.1 + - - +
184C ALA* 1.3 74.5 - - - +
186C LEU* 1.3 62.8 + - - +
188C ILE* 3.3 6.8 + - - +
189C GLU* 3.1 19.3 + - - +
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Residues in contact with LEU 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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70C PHE* 3.7 14.1 - - + -
73C LEU* 3.6 17.3 - - + +
74C LEU* 4.5 10.5 - - + -
77C ASN* 3.9 24.9 - - + +
81C LEU* 4.3 22.7 - - + -
182C ARG* 2.9 53.5 + - + +
183C LEU* 3.2 8.2 + - - +
185C GLU* 1.3 74.3 - - - +
187C MSE 1.3 58.3 + - - +
189C GLU* 3.2 26.9 + - - +
190C ALA* 2.8 29.6 + - - +
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Residues in contact with MSE 187 (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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66C VAL* 4.4 9.4 - - + -
67C PHE* 3.7 33.2 - - + -
70C PHE* 3.4 45.8 - - + -
158C PHE* 4.0 12.3 - - + -
162C ILE* 4.2 5.6 - - + -
183C LEU 2.9 16.0 + - - +
184C ALA 3.6 8.7 - - - +
185C GLU 3.3 0.4 - - - -
186C LEU* 1.3 74.4 - - - +
188C ILE* 1.3 62.7 + - - +
190C ALA* 3.0 13.4 + - - +
191C GLY 3.2 0.5 + - - -
192C LEU* 3.1 63.1 + - + +
197C LEU* 3.6 17.5 - - + -
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Residues in contact with ILE 188 (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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5C PHE* 3.8 20.2 - - + -
8C GLY* 3.7 27.4 - - - +
184C ALA 3.2 15.3 + - - +
185C GLU* 3.6 7.0 - - - +
186C LEU 3.3 0.2 - - - -
187C MSE 1.3 76.5 - - - +
189C GLU* 1.3 56.5 + - - +
191C GLY* 3.0 19.6 + - - -
192C LEU* 3.6 24.9 + - + +
193C PRO 4.0 3.4 - - - +
194C ALA* 3.8 17.5 - - + +
195C GLY 5.0 0.9 - - - +
197C LEU 5.7 3.4 - - - +
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Residues in contact with GLU 189 (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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73C LEU* 3.7 30.3 - - + +
77C ASN* 5.4 0.7 + - - -
182C ARG* 4.6 7.8 + - - -
185C GLU 3.1 12.9 + - - +
186C LEU* 3.2 27.5 + - - +
188C ILE* 1.3 76.2 - - - +
190C ALA* 1.3 59.1 + - - +
191C GLY 3.2 1.2 + - - -
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Residues in contact with ALA 190 (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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66C VAL* 3.6 37.7 - - + +
69C LYS* 3.8 16.6 - - + +
70C PHE* 3.6 24.7 - - + +
73C LEU* 3.8 7.9 - - + -
186C LEU 2.8 16.0 + - - +
187C MSE 3.0 7.8 + - - +
189C GLU* 1.3 75.6 - - - +
191C GLY* 1.3 57.7 + - - +
192C LEU 3.7 0.4 - - - -
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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