Contacts of the helix formed by residues 198 - 208 (chain A) in PDB entry 4P9U
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 ASN 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A TYR* 6.3 1.1 - - + -
193A ALA 3.6 5.9 - - - +
194A PHE 4.6 3.1 - - - +
196A SER* 3.2 16.6 + - - +
197A GLY* 1.3 79.3 - - - +
199A GLN* 1.3 67.2 + - - +
200A ILE* 3.2 17.6 + - - +
201A TYR* 3.5 33.2 + - + -
100B ASP* 3.3 43.7 + - - +
103B ALA* 3.6 11.3 - - - +
104B ALA* 3.6 17.2 - - - +
107B ASN* 5.0 1.0 - - - +
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Residues in contact with GLN 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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194A PHE* 3.6 17.8 - - + -
197A GLY 4.1 2.2 - - - +
198A ASN* 1.3 74.6 + - - +
200A ILE* 1.3 54.4 + - - +
202A GLY* 2.7 26.3 + - - -
203A LEU* 2.9 25.3 + - + +
75B MET* 3.5 33.2 - - - +
83B LEU* 3.3 27.3 - - + +
86B LEU* 5.5 1.5 - - - +
97B ILE* 5.5 3.6 - - - +
100B ASP* 3.9 14.0 + - + +
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Residues in contact with ILE 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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198A ASN* 3.2 10.0 + - - +
199A GLN* 1.3 77.2 - - - +
201A TYR* 1.3 57.7 + - + +
203A LEU* 3.2 3.5 + - - +
204A ILE* 2.9 47.0 + - + +
80B LEU* 3.7 20.4 - - + -
83B LEU* 3.6 24.5 - - + -
100B ASP* 3.8 8.7 - - + +
101B LEU* 3.8 25.4 - - + +
104B ALA* 3.6 31.0 - - + -
108B ILE* 6.4 0.7 - - + -
204B ILE* 5.2 2.9 - - + -
208B LEU* 4.0 20.9 - - + -
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Residues in contact with TYR 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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108A ILE* 4.7 9.8 - - + +
111A ILE* 3.2 20.9 - - + +
112A PHE* 3.8 28.5 - + + -
115A TYR* 5.4 3.4 - + - -
193A ALA* 3.4 18.8 - - + +
196A SER* 3.8 8.5 - - - -
198A ASN* 3.7 38.8 - - + +
199A GLN 3.2 0.8 - - - -
200A ILE* 1.3 78.0 - - + +
202A GLY* 1.3 58.5 + - - +
204A ILE* 3.6 17.0 - - + +
205A PHE* 3.1 31.5 + - - -
104B ALA* 3.8 13.5 + - + -
107B ASN* 2.8 41.6 + - - +
108B ILE* 4.2 15.8 - - + +
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Residues in contact with GLY 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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190A GLN* 4.1 1.0 - - - +
193A ALA* 3.5 12.7 + - - -
194A PHE* 3.4 26.5 - - - -
199A GLN 2.7 14.8 + - - -
201A TYR* 1.3 73.4 - - - +
203A LEU* 1.3 58.3 + - - -
204A ILE 3.1 0.2 - - - -
205A PHE* 3.1 6.7 + - - +
206A ASN* 2.8 35.0 + - - -
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Residues in contact with LEU 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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80A LEU* 4.9 0.2 - - - +
194A PHE* 4.0 10.3 - - + -
199A GLN* 2.9 48.0 + - + +
200A ILE* 3.7 2.7 - - - +
202A GLY* 1.3 73.1 - - - +
204A ILE* 1.3 60.0 + - - +
206A ASN* 3.3 10.7 + - - +
207A GLY* 2.9 26.3 + - - -
75B MET* 4.5 20.9 - - - -
78B SER 3.3 24.9 - - - +
79B GLY* 3.3 25.0 - - - +
80B LEU* 3.6 27.1 + - + +
82B ILE* 4.9 7.0 - - + -
83B LEU* 5.0 8.7 - - + -
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Residues in contact with ILE 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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80A LEU* 3.8 16.2 - - + +
108A ILE* 4.4 26.5 - - + -
200A ILE* 2.9 38.3 + - + +
201A TYR* 3.6 20.6 - - + +
202A GLY 3.1 0.2 - - - -
203A LEU* 1.3 76.9 - - - +
205A PHE* 1.3 66.4 + - + +
207A GLY* 3.2 3.8 + - - -
208A LEU* 3.1 37.7 + - + +
80B LEU* 4.2 14.8 - - + -
108B ILE* 5.9 4.3 - - + -
200B ILE* 5.2 1.3 - - + -
204B ILE* 3.6 30.7 - - + -
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Residues in contact with PHE 205 (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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105A ARG* 4.1 13.9 - - + -
108A ILE* 4.8 11.4 - - + -
112A PHE* 3.7 30.7 - + - -
186A TYR* 3.1 21.7 + + - +
189A PHE* 3.4 37.9 - + + -
190A GLN* 3.7 21.5 - - + -
193A ALA* 3.6 13.2 - - + -
201A TYR 3.1 21.3 - - - -
202A GLY 3.1 7.4 + - - +
204A ILE* 1.3 79.1 - - + +
206A ASN* 1.3 66.2 + - - +
208A LEU* 3.2 7.3 + - + +
209A LYS 3.1 17.2 + - - -
212A TYR* 3.8 27.1 - + - -
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Residues in contact with ASN 206 (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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186A TYR* 3.4 8.6 + - - -
190A GLN* 3.1 14.9 + - - -
194A PHE* 3.1 28.5 - - - -
202A GLY 2.8 26.0 + - - -
203A LEU* 3.5 9.4 - - - +
205A PHE* 1.3 76.7 - - - +
207A GLY* 1.3 61.6 + - - +
209A LYS* 3.5 15.2 - - - +
75B MET 3.3 6.8 + - - -
76B GLU 2.9 25.6 - - - +
77B THR* 4.7 9.1 - - - +
78B SER 3.2 24.7 - - - +
79B GLY* 5.2 0.4 - - - -
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Residues in contact with GLY 207 (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 LEU* 3.8 25.5 - - - +
81A HIS* 4.0 13.0 - - - +
203A LEU 2.9 13.9 + - - -
204A ILE 3.2 3.8 + - - -
205A PHE 3.2 0.4 - - - -
206A ASN* 1.3 77.2 - - - +
208A LEU* 1.3 59.6 - - - +
209A LYS 3.2 2.9 + - - -
210A LYS* 4.9 4.5 + - - +
79B GLY* 4.8 9.6 - - - -
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Residues in contact with LEU 208 (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 LEU* 3.5 31.2 - - + +
83A LEU* 3.7 25.8 - - + -
101A LEU* 4.0 17.2 - - + +
104A ALA* 5.7 1.3 - - + -
204A ILE* 3.1 34.2 + - + +
205A PHE* 3.2 7.8 + - + +
207A GLY* 1.3 75.6 - - - +
209A LYS* 1.3 57.5 + - - +
210A LYS 3.4 2.5 - - - -
211A LEU* 3.3 14.0 + - + +
212A TYR* 2.8 31.2 + - + +
200B ILE* 3.9 28.0 - - + -
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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