Contacts of the helix formed by residues 177 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.5 15.1 - - + +
21A ILE* 3.8 16.4 - - + -
33A VAL* 3.7 24.2 - - + -
88A GLU* 3.6 5.2 - - - +
172A PRO* 5.1 0.2 - - + -
173A SER 4.0 6.3 - - - +
174A GLU* 3.6 17.5 - - - +
175A ARG 3.8 3.8 - - - +
176A ASP* 1.3 85.8 - - - +
178A SER* 1.3 64.7 + - - +
179A VAL 3.4 2.2 - - - -
180A PRO* 3.6 15.9 - - + +
181A ILE* 3.6 16.3 + - - +
201A ASN* 3.5 25.1 - - - +
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Residues in contact with SER 178 (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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0A TYR* 3.8 9.2 + - - -
2A LEU* 3.5 19.3 - - - +
10A ARG* 5.4 1.4 + - - -
84A MSE 3.6 26.4 - - - +
87A ARG* 5.2 1.4 + - - -
88A GLU* 2.6 34.5 + - - -
177A PRO* 1.3 75.1 - - - +
179A VAL* 1.3 67.3 + - - +
181A ILE* 3.6 3.5 + - - +
182A ARG* 3.1 23.2 + - - +
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Residues in contact with VAL 179 (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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81A LEU* 3.6 9.6 - - + +
84A MSE 3.5 28.9 - - + -
85A LEU* 3.6 32.1 - - + -
88A GLU* 4.6 0.6 + - - +
100A ILE* 4.1 11.4 - - + -
150A PRO* 3.8 19.3 - - + +
151A GLY* 4.0 12.1 - - - +
176A ASP 4.6 1.4 + - - +
178A SER* 1.3 77.4 - - - +
180A PRO* 1.4 66.4 - - + +
182A ARG* 3.0 3.7 + - - +
183A LEU* 2.8 47.5 + - + +
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Residues in contact with PRO 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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150A PRO* 3.4 22.2 - - + +
154A PRO* 4.6 3.4 - - + -
170A LEU* 3.8 22.7 - - + +
172A PRO* 3.7 32.1 - - + -
176A ASP 3.9 8.3 - - - +
177A PRO 3.6 13.9 - - - +
179A VAL* 1.4 93.7 - - + +
181A ILE* 1.3 63.0 + - - +
183A LEU* 3.3 13.5 + - + +
184A ALA 3.2 16.6 + - - -
197A LEU* 5.7 0.3 - - - +
199A VAL* 3.7 13.4 - - + +
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Residues in contact with ILE 181 (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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2A LEU* 3.9 25.8 - - + -
3A GLY 3.8 15.5 - - - +
4A HIS* 5.0 1.3 - - - +
5A PHE* 4.1 14.3 - - + +
10A ARG* 3.4 45.5 - - + +
177A PRO 3.6 10.0 + - - +
178A SER* 3.6 6.8 + - - +
179A VAL 3.3 0.6 - - - -
180A PRO* 1.3 76.2 - - - +
182A ARG* 1.3 58.4 + - - +
184A ALA* 3.1 5.3 + - - +
185A GLU* 3.0 26.2 + - - +
199A VAL* 4.3 16.6 - - + -
201A ASN* 3.6 26.9 - - - +
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Residues in contact with ARG 182 (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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10A ARG* 4.3 8.7 - - - +
77A ASN* 3.2 24.7 + - - -
80A GLU* 3.1 22.5 + - - -
81A LEU* 3.8 21.3 - - + -
84A MSE 3.9 20.6 - - + -
178A SER 3.1 17.2 + - - +
179A VAL 3.0 4.8 + - - +
181A ILE* 1.3 76.5 - - - +
183A LEU* 1.3 56.5 + - - +
185A GLU* 2.9 41.5 + - - +
186A LEU* 2.9 54.7 + - + +
189A GLU* 4.7 8.3 + - - -
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Residues in contact with LEU 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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70A PHE* 3.4 17.2 - - + -
74A LEU* 3.8 28.7 - - + -
81A LEU* 4.1 18.8 - - + -
100A ILE* 5.1 1.1 - - + -
150A PRO 4.4 4.5 - - - +
151A GLY* 4.0 12.3 - - - +
154A PRO* 4.7 2.7 - - + -
155A MSE 4.0 31.0 - - + -
158A PHE* 4.4 15.0 - - + -
170A LEU* 6.2 0.2 - - + -
179A VAL* 2.8 35.0 + - + +
180A PRO* 3.5 10.3 - - + +
181A ILE 3.2 0.2 - - - -
182A ARG* 1.3 73.9 - - - +
184A ALA* 1.3 57.4 + - - +
186A LEU* 3.2 4.6 + - + +
187A MSE 2.9 26.6 + - - +
197A LEU* 4.7 0.9 - - + -
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Residues in contact with ALA 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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5A PHE* 3.6 25.7 - - + -
180A PRO 3.2 4.0 + - - -
181A ILE 3.1 7.8 + - - +
183A LEU* 1.3 73.0 - - - +
185A GLU* 1.3 64.8 + - - +
187A MSE 3.2 3.3 + - - +
188A ILE* 3.2 26.2 + - - +
197A LEU* 3.7 26.6 - - + +
199A VAL* 3.7 25.1 - - + -
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.7 21.3 - - + -
10A ARG* 3.0 46.8 + - - +
181A ILE 3.0 11.3 + - - +
182A ARG* 2.9 36.7 + - - +
184A ALA* 1.3 77.6 - - - +
186A LEU* 1.3 59.6 + - - +
188A ILE* 3.3 7.5 + - + +
189A GLU* 3.2 19.4 + - - +
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Residues in contact with LEU 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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70A PHE* 3.7 11.4 - - + -
73A LEU* 3.4 20.5 - - + +
74A LEU* 4.4 12.6 - - + -
77A ASN* 3.5 31.6 - - + +
81A LEU* 4.2 31.9 - - + -
182A ARG* 2.9 47.4 + - + +
183A LEU* 3.2 6.7 + - - +
185A GLU* 1.3 73.7 - - - +
187A MSE 1.3 60.9 + - - +
189A GLU* 3.2 17.6 + - - +
190A ALA* 2.8 26.3 + - - +
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Residues in contact with MSE 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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66A VAL* 4.2 11.2 - - + -
67A PHE* 3.7 32.3 - - + -
70A PHE* 3.4 46.9 - - + -
158A PHE* 4.3 5.8 - - + -
162A ILE* 4.2 11.2 - - + -
183A LEU 2.9 18.1 + - - +
184A ALA 3.6 9.0 - - - +
185A GLU 3.2 0.6 - - - -
186A LEU* 1.3 76.8 - - - +
188A ILE* 1.3 62.6 + - - +
190A ALA* 3.1 11.2 + - - +
191A GLY 3.2 0.7 + - - -
192A LEU* 3.1 60.9 + - + +
197A LEU* 3.8 16.4 - - + -
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Residues in contact with ILE 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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5A PHE* 3.8 20.6 - - + -
8A GLY* 4.1 16.6 - - - +
184A ALA 3.2 13.6 + - - +
185A GLU* 3.4 9.6 - - + +
186A LEU 3.3 0.2 - - - -
187A MSE 1.3 76.9 - - - +
189A GLU* 1.3 58.3 + - - +
191A GLY* 2.9 20.6 + - - -
192A LEU* 3.3 26.3 + - + +
193A PRO 4.0 3.1 - - - +
194A ALA* 4.0 23.6 - - + +
195A GLY 5.3 0.2 - - - +
197A LEU 5.9 1.8 - - - +
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Residues in contact with GLU 189 (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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69A LYS* 3.8 15.7 + - - +
73A LEU* 3.7 28.7 - - + +
77A ASN* 5.5 1.0 + - - -
182A ARG* 4.7 8.7 + - - -
185A GLU 3.2 9.6 + - - +
186A LEU* 3.2 24.9 + - - +
188A ILE* 1.3 80.6 - - - +
190A ALA* 1.3 58.4 + - - +
191A GLY 3.2 1.3 + - - -
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Residues in contact with ALA 190 (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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66A VAL* 3.6 21.9 - - + +
69A LYS* 3.7 25.1 - - - +
70A PHE* 3.6 37.0 - - + +
73A LEU* 3.5 3.1 - - + +
186A LEU 2.8 13.8 + - - +
187A MSE 3.1 11.4 + - - +
189A GLU* 1.3 75.7 - - - +
191A GLY* 1.3 56.2 + - - +
192A LEU 3.6 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