Contacts of the helix formed by residues 187 - 204 (chain A) in PDB entry 2IAI
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 GLY 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A SER* 1.3 75.8 - - - +
188A ALA* 1.3 64.9 + - - +
189A GLY 3.3 2.9 - - - -
190A GLU* 3.2 23.4 + - - +
191A ARG* 3.0 35.5 + - - +
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Residues in contact with ALA 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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183A SER 5.2 6.3 - - - +
184A GLY 4.8 14.1 - - - +
186A SER 3.4 0.8 - - - -
187A GLY* 1.3 75.9 - - - +
189A GLY* 1.3 63.1 + - - +
191A ARG* 3.2 23.4 + - - +
192A GLU* 3.0 24.1 + - - +
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Residues in contact with GLY 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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168A TYR* 5.6 2.7 - - - -
171A GLU* 6.5 0.9 - - - -
187A GLY 3.3 0.6 - - - -
188A ALA* 1.3 79.4 - - - +
190A GLU* 1.3 67.5 + - - +
192A GLU* 3.3 14.3 + - - +
193A VAL* 3.2 28.4 + - - +
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Residues in contact with GLU 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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98A MSE 3.7 29.2 - - + +
168A TYR* 2.5 34.2 + - - +
170A PRO* 4.1 11.4 - - - +
171A GLU* 4.5 4.3 + - - +
187A GLY* 3.2 26.7 + - - +
189A GLY* 1.3 79.9 + - - +
191A ARG* 1.3 66.6 + - + +
193A VAL* 3.2 2.3 + - - -
194A VAL* 3.1 27.3 + - - +
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Residues in contact with ARG 191 (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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184A GLY* 3.9 21.8 - - - +
186A SER 3.0 30.3 + - - -
187A GLY* 3.0 20.5 + - - +
188A ALA* 3.2 21.4 - - - +
190A GLU* 1.3 76.3 - - + +
192A GLU* 1.3 64.1 + - - +
194A VAL* 3.4 6.6 + - - +
195A ASP* 2.9 36.6 + - - +
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Residues in contact with GLU 192 (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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188A ALA 3.0 17.7 + - - +
189A GLY* 3.5 13.0 - - - +
190A GLU 3.1 0.2 - - - -
191A ARG* 1.3 77.7 - - - +
193A VAL* 1.3 60.5 + - + +
195A ASP* 3.8 5.3 - - - +
196A ALA* 3.0 31.2 + - + +
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Residues in contact with VAL 193 (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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94A VAL* 3.9 17.0 - - + -
98A MSE 4.1 15.5 - - - -
164A ILE* 4.0 15.3 - - + -
167A TRP* 3.9 35.2 - - + -
168A TYR* 4.8 5.8 - - + -
189A GLY 3.3 15.0 - - - +
190A GLU 3.2 6.5 + - - +
192A GLU* 1.3 77.5 - - + +
194A VAL* 1.3 66.0 + - - +
196A ALA* 3.3 5.6 + - + +
197A VAL* 2.9 26.8 + - + +
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Residues in contact with VAL 194 (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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91A ARG* 3.7 44.8 - - + +
94A VAL* 3.6 24.7 - - + -
95A GLU* 3.7 24.5 - - + +
98A MSE 3.7 10.8 - - + -
190A GLU 3.1 18.0 + - - +
191A ARG* 3.8 6.1 - - - +
193A VAL* 1.3 76.8 - - - +
195A ASP* 1.3 59.4 + - - +
197A VAL* 3.4 2.1 + - - +
198A ALA* 2.9 28.4 + - - +
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Residues in contact with ASP 195 (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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91A ARG* 2.9 27.5 + - - +
191A ARG* 2.9 28.0 + - - +
192A GLU* 3.8 5.9 - - - +
194A VAL* 1.3 77.4 - - - +
196A ALA* 1.3 57.0 + - - +
198A ALA* 3.4 1.7 + - - +
199A ARG* 2.9 62.7 + - - +
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Residues in contact with ALA 196 (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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192A GLU* 3.0 20.9 + - + +
193A VAL* 3.6 7.2 - - - +
195A ASP* 1.3 73.1 - - - +
197A VAL* 1.3 67.8 + - + +
199A ARG* 3.3 8.6 + - - +
200A LEU* 2.9 35.7 + - + +
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Residues in contact with VAL 197 (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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90A VAL* 3.9 10.5 - - + -
94A VAL* 3.7 29.6 - - + -
160A MSE 4.7 13.9 - - + -
161A ILE* 4.0 10.1 - - + -
164A ILE* 4.0 18.8 - - + -
167A TRP* 6.2 0.7 - - + -
193A VAL* 2.9 23.8 + - + +
194A VAL 3.8 3.1 - - - +
196A ALA* 1.3 76.2 - - + +
198A ALA* 1.3 59.2 + - - +
200A LEU* 4.6 3.6 - - - +
201A VAL* 2.8 52.3 + - + +
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Residues in contact with ALA 198 (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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87A GLU* 4.0 11.2 - - + +
90A VAL* 4.7 5.1 - - + +
91A ARG* 3.4 49.6 - - + +
194A VAL 2.9 13.5 + - - +
195A ASP 3.8 1.3 - - - +
197A VAL* 1.3 78.4 - - - +
199A ARG* 1.3 61.4 + - - +
201A VAL* 4.7 0.9 - - - -
202A PHE* 3.1 35.3 + - - +
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Residues in contact with ARG 199 (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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91A ARG* 5.7 5.1 - - - +
195A ASP* 2.9 49.8 + - - +
196A ALA* 3.7 7.5 - - - +
198A ALA* 1.3 77.9 - - + +
200A LEU* 1.3 62.6 + - + +
202A PHE* 5.4 0.4 - - - -
203A GLY* 2.8 29.7 + - - +
204A GLY 3.3 4.9 + - - +
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Residues in contact with LEU 200 (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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160A MSE 4.3 30.6 - - + +
196A ALA* 2.9 23.5 + - + +
197A VAL* 4.1 2.0 - - - +
199A ARG* 1.3 77.9 - - + +
201A VAL* 1.4 64.0 + - - +
204A GLY* 2.8 44.6 + - - +
205A LEU* 3.9 26.9 - - + -
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Residues in contact with VAL 201 (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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86A LEU* 6.3 0.4 - - + -
90A VAL* 4.3 7.4 - - + -
157A VAL* 4.0 44.2 - - + +
160A MSE 3.9 16.6 - - + -
161A ILE* 5.3 0.2 - - + -
197A VAL* 2.8 42.2 + - + +
200A LEU* 1.4 74.7 - - - +
202A PHE* 1.3 86.3 + - + +
204A GLY 4.8 0.2 + - - -
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Residues in contact with PHE 202 (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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83A ALA* 4.3 11.9 - - + -
86A LEU* 4.0 25.6 - - + -
87A GLU* 3.5 57.2 - - + +
90A VAL* 4.4 10.5 - - + -
144A VAL* 4.9 12.6 - - + -
198A ALA 3.1 21.3 + - - +
199A ARG* 4.6 0.4 - - - +
201A VAL* 1.3 97.4 - - + +
203A GLY* 1.3 59.9 - - - +
204A GLY 3.8 0.2 - - - -
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Residues in contact with GLY 203 (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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199A ARG 2.8 16.9 + - - -
202A PHE* 1.3 76.7 - - - +
204A GLY* 1.3 63.8 + - - +
206A ARG* 4.3 13.7 + - - +
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Residues in contact with GLY 204 (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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199A ARG 3.3 4.2 + - - +
200A LEU* 2.8 44.1 + - - +
201A VAL 4.8 0.2 + - - -
202A PHE 3.8 0.4 - - - -
203A GLY* 1.3 77.9 - - - +
205A LEU* 1.3 62.2 + - - -
206A ARG 4.4 1.8 - - - +
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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