Contacts of the helix formed by residues 188 - 198 (chain A) in PDB entry 1AR5
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 TRP 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ALA* 4.4 1.0 - - - +
89A PRO* 3.1 33.4 + - + +
90A GLU* 3.4 16.4 + - - -
91A ARG 3.5 21.5 - - - +
92A PRO* 3.5 28.9 - - + -
96A LEU* 4.0 8.3 - - + +
100A ILE* 4.5 4.5 - - + -
107A PHE* 3.6 21.5 - + - -
110A MET* 3.8 27.1 - - + -
129A LEU* 5.1 0.9 - - + -
158A LEU* 3.8 24.2 - - + -
183A TRP* 3.9 15.7 + + - -
186A VAL* 3.3 24.8 + - + +
187A ASN* 1.3 72.0 - - - +
189A ASP* 1.3 58.3 + - - +
191A VAL* 3.9 25.6 - - + +
192A ALA* 3.0 27.5 + - - +
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Residues in contact with ASP 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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87A SER 5.0 2.1 - - - +
88A ALA* 4.5 3.8 - - - +
89A PRO* 3.6 31.6 - - - +
187A ASN* 3.0 13.2 + - - +
188A TRP* 1.3 77.1 - - - +
190A ASP* 1.3 65.8 + - - +
192A ALA* 3.4 7.2 + - - +
193A LEU* 3.1 23.0 + - - +
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Residues in contact with ASP 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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80A LYS* 3.2 42.4 - - - +
81A ASN* 2.8 27.3 - - - +
187A ASN* 3.1 17.6 + - - +
189A ASP* 1.3 77.6 - - - +
191A VAL* 1.3 64.2 + - - +
193A LEU* 3.3 13.5 + - - +
194A ARG* 2.9 44.1 + - - +
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Residues in contact with VAL 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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81A ASN* 4.2 5.4 - - - +
96A LEU* 3.7 22.4 - - + -
129A LEU* 4.9 4.3 - - + -
157A LEU* 3.7 39.2 - - + +
158A LEU* 4.0 25.4 - - + -
186A VAL* 4.5 1.1 - - + -
187A ASN 3.5 14.4 - - - +
188A TRP* 3.9 26.2 - - + +
189A ASP 3.3 0.4 - - - -
190A ASP* 1.3 77.3 - - - +
192A ALA* 1.3 55.7 + - - +
194A ARG* 3.4 3.2 + - - +
195A PHE* 3.0 27.5 + - - +
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Residues in contact with ALA 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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93A THR 5.6 2.5 - - - +
96A LEU* 3.6 22.8 - - + +
188A TRP 3.0 19.7 + - - +
189A ASP* 3.7 9.0 - - - +
191A VAL* 1.3 77.8 - - - +
193A LEU* 1.3 56.0 - - - +
195A PHE* 3.4 6.8 + - - +
196A SER* 2.9 31.6 + - - -
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Residues in contact with LEU 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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189A ASP 3.1 13.9 + - - +
190A ASP* 3.5 16.4 - - - +
191A VAL 3.2 0.2 - - - -
192A ALA* 1.3 74.8 - - - +
194A ARG* 1.3 66.4 + - + +
196A SER* 3.2 11.4 + - - -
197A GLU* 3.1 47.7 + - + +
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Residues in contact with ARG 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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76A SER 5.0 0.2 - - - -
77A VAL* 4.0 31.4 - - - +
80A LYS* 3.2 42.4 - - - +
81A ASN* 3.7 3.4 + - - -
155A ILE* 5.2 1.5 - - + +
156A PRO* 4.0 12.8 + - - +
157A LEU* 3.5 34.1 - - + -
190A ASP* 2.9 33.8 + - - +
191A VAL 3.7 4.7 - - - +
193A LEU* 1.3 78.1 - - + +
195A PHE* 1.3 58.8 + - - +
197A GLU* 3.5 9.3 + - - +
198A ALA* 2.8 31.7 + - - +
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Residues in contact with PHE 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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95A GLU* 4.1 20.9 - - + -
96A LEU* 4.1 26.0 - - + -
99A ALA* 3.7 17.3 - - + -
131A TRP* 3.6 37.0 - + - -
138A ILE* 4.0 18.6 - - + -
157A LEU* 3.8 16.4 - - + +
191A VAL 3.0 17.5 + - - +
192A ALA 3.6 6.5 - - - +
193A LEU 3.2 0.2 - - - -
194A ARG* 1.3 75.4 - - - +
196A SER* 1.3 67.2 + - - +
199A ARG* 3.1 68.1 + - + +
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Residues in contact with SER 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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95A GLU* 6.0 1.7 - - - +
192A ALA 2.9 17.0 + - - -
193A LEU* 3.2 15.3 + - - -
195A PHE* 1.3 81.3 - - - +
197A GLU* 1.3 62.5 + - - +
199A ARG* 3.8 17.4 - - - +
200A VAL* 4.0 9.5 - - - +
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Residues in contact with GLU 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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193A LEU* 3.1 44.5 + - + +
194A ARG* 4.1 6.3 - - - +
196A SER* 1.3 79.1 - - - +
198A ALA* 1.3 61.5 + - - +
200A VAL* 4.1 15.5 - - - +
201A ALA 5.0 2.6 - - - +
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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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131A TRP* 3.2 24.4 - - + -
155A ILE* 3.6 40.5 - - + +
157A LEU* 3.9 12.6 - - + -
194A ARG 2.8 19.5 + - - +
195A PHE* 3.2 2.6 + - - +
197A GLU* 1.3 75.0 - - - +
199A ARG* 1.3 52.3 + - - +
200A VAL 2.7 17.7 + - - -
201A ALA 3.3 8.4 + - - +
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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