Contacts of the helix formed by residues 198 - 208 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASP* 3.3 39.9 + - - +
103A ALA* 3.7 11.5 - - - +
104A ALA* 3.5 15.4 - - - +
107A ASN* 4.7 1.0 - - - +
193B ALA 3.5 6.1 - - - +
194B PHE* 4.7 3.5 + - - -
196B SER* 3.2 15.5 + - - +
197B GLY* 1.3 78.8 - - - +
199B GLN* 1.3 67.5 + - - +
200B ILE* 3.2 17.2 + - - +
201B TYR* 3.5 38.1 + - + -
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Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET* 4.0 26.5 - - - +
83A LEU* 3.3 25.4 - - + +
86A LEU* 5.5 2.5 - - - +
97A ILE* 5.0 6.6 - - - +
100A ASP* 3.7 17.1 + - - +
194B PHE* 3.7 17.7 - - + -
197B GLY 4.1 1.5 - - - +
198B ASN* 1.3 74.9 + - - +
200B ILE* 1.3 54.5 + - - +
202B GLY* 2.7 25.8 + - - -
203B LEU* 2.9 27.0 + - + +
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Residues in contact with ILE 200 (chain B).
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* 3.6 19.7 - - + -
83A LEU* 3.5 25.4 - - + -
100A ASP* 3.8 6.7 - - + +
101A LEU* 3.6 27.1 - - + +
104A ALA* 3.6 32.1 - - + -
108A ILE* 6.3 0.9 - - + -
204A ILE* 5.2 2.2 - - + -
208A LEU* 3.9 21.5 - - + -
198B ASN* 3.2 10.0 + - - +
199B GLN* 1.3 76.4 - - - +
201B TYR* 1.3 58.9 + - + +
203B LEU* 3.2 4.4 + - - +
204B ILE* 2.9 41.3 + - + +
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.9 11.9 - - + -
107A ASN* 2.8 42.2 + - - +
108A ILE* 4.1 15.9 - - + +
108B ILE* 4.8 10.9 - - + +
111B ILE* 3.2 20.1 - - + +
112B PHE* 3.9 23.6 - + + -
115B TYR* 5.8 3.1 - + - -
193B ALA* 3.4 22.2 - - + +
196B SER* 4.0 7.2 - - - -
198B ASN* 3.5 39.6 + - + -
199B GLN 3.1 1.2 + - - -
200B ILE* 1.3 78.0 - - + +
202B GLY* 1.3 59.7 + - - +
204B ILE* 3.7 17.3 - - + +
205B PHE* 3.2 30.3 + - - -
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLN* 4.2 0.8 - - - +
193B ALA* 3.6 11.8 + - - -
194B PHE* 3.5 27.7 - - - -
199B GLN 2.7 14.6 + - - -
201B TYR* 1.3 73.4 - - - +
203B LEU* 1.3 54.1 + - - -
204B ILE 3.1 0.4 - - - -
205B PHE* 3.2 6.4 + - - +
206B ASN* 2.7 40.2 + - - -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET* 4.7 12.1 - - - -
78A SER 3.5 15.7 - - - +
79A GLY* 3.2 28.0 - - - +
80A LEU* 3.6 29.5 + - + +
82A ILE* 3.6 17.9 - - + -
83A LEU* 4.6 12.8 - - + -
80B LEU* 5.1 0.2 - - - +
194B PHE* 4.3 9.4 - - + -
199B GLN* 2.9 46.0 + - + +
200B ILE* 3.2 3.3 + - - +
202B GLY* 1.3 76.7 - - - +
204B ILE* 1.3 58.2 + - - +
206B ASN* 3.6 10.0 - - - +
207B GLY* 2.9 25.5 + - - -
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Residues in contact with ILE 204 (chain B).
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* 4.0 19.1 - - + -
108A ILE* 5.8 3.8 - - + -
200A ILE* 5.2 2.9 - - + -
204A ILE* 3.6 26.9 - - + -
80B LEU* 3.8 19.0 - - + +
108B ILE* 4.6 24.9 - - + -
200B ILE* 2.9 32.0 + - + +
201B TYR* 3.7 19.7 - - + +
202B GLY 3.1 0.2 - - - -
203B LEU* 1.3 77.6 - - - +
205B PHE* 1.3 66.2 + - + +
207B GLY* 3.2 3.5 + - - -
208B LEU* 3.1 36.2 + - + +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 6.5 0.2 - - + -
105B ARG* 4.1 15.0 - - + -
108B ILE* 4.5 14.1 - - + -
112B PHE* 3.8 28.0 - + - -
186B TYR* 3.3 19.7 + + + -
189B PHE* 3.6 41.1 - + + -
190B GLN* 3.8 21.5 - - + -
193B ALA* 3.8 8.3 - - + -
201B TYR 3.2 21.5 - - - -
202B GLY 3.2 7.6 + - - +
204B ILE* 1.3 79.7 - - + +
206B ASN* 1.3 66.5 + - - +
208B LEU* 3.1 8.8 + - + +
209B LYS 3.1 19.1 + - - -
212B TYR* 4.1 24.7 - + - -
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET 3.3 8.3 + - - -
76A GLU 2.9 29.7 - - - +
77A THR 4.6 7.7 - - - +
78A SER 3.3 21.3 - - - +
79A GLY* 5.2 0.2 - - - -
186B TYR* 3.4 8.5 + - - -
190B GLN* 2.9 17.4 + - - -
194B PHE* 3.1 29.3 - - - -
202B GLY 2.7 26.8 + - - -
203B LEU* 3.6 7.7 - - - +
204B ILE 3.3 0.2 - - - -
205B PHE* 1.3 77.1 - - - +
207B GLY* 1.3 62.0 + - - +
209B LYS* 3.5 14.5 - - - +
210B LYS* 6.0 0.5 - - - +
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 4.7 10.3 - - - -
80A LEU 5.8 0.4 - - - -
80B LEU* 4.0 22.7 - - - +
81B HIS* 4.0 13.5 - - - +
203B LEU 2.9 14.9 + - - -
204B ILE 3.6 4.3 - - - -
205B PHE 3.1 0.4 - - - -
206B ASN* 1.3 76.8 - - - +
208B LEU* 1.3 60.2 + - - +
209B LYS 3.2 3.1 + - - -
210B LYS* 4.8 6.2 + - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ILE* 4.0 16.8 - - + -
80B LEU* 3.3 36.6 - - + +
83B LEU* 3.7 24.9 - - + -
101B LEU* 3.9 23.8 - - + -
104B ALA* 5.9 0.4 - - + -
204B ILE* 3.1 33.1 + - + +
205B PHE* 3.1 9.1 + - + +
207B GLY* 1.3 75.4 - - - +
209B LYS* 1.3 64.2 + - - +
210B LYS 3.3 3.3 + - - -
211B LEU* 3.3 15.3 + - + +
212B TYR* 2.9 25.6 + - + +
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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