Contacts of the helix formed by residues 187 - 197 (chain B) in PDB entry 3ESF
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B GLU* 3.0 32.8 + - - +
82B SER* 2.8 17.1 + - - +
83B MET 3.7 16.0 + - - -
84B SER* 3.8 16.4 + - - -
87B GLY* 4.6 2.1 - - - -
158B LEU* 5.4 1.0 - - - +
185B VAL 4.0 0.2 - - - -
186B VAL* 1.3 72.1 - - - +
188B TRP* 1.3 58.1 + - - +
189B ASP* 3.2 27.0 + - - +
190B HIS* 3.5 14.6 - - - +
191B ALA* 3.1 24.5 + - - +
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Residues in contact with TRP 188 (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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87B GLY* 5.4 1.3 - - - -
88B GLY 3.2 19.8 + - - -
89B GLY 3.0 19.0 + - - -
90B GLU 3.7 12.3 - - - +
91B PRO* 3.6 29.8 - - + -
95B LEU* 3.8 15.5 - - + -
99B ILE* 4.3 7.2 - - + -
106B PHE* 3.6 35.4 - + - -
109B PHE* 3.9 15.3 - + - -
128B LEU* 5.2 0.7 - - + -
158B LEU* 3.7 25.4 - - + -
183B TRP* 4.5 2.5 - + - -
186B VAL* 3.5 28.3 + - + +
187B ASN* 1.3 69.4 + - - +
189B ASP* 1.3 60.6 + - - +
191B ALA* 3.7 5.3 - - + +
192B GLU* 2.8 51.0 + - - +
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Residues in contact with ASP 189 (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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86B ASN* 6.0 1.7 - - - +
187B ASN* 3.2 12.7 + - - +
188B TRP* 1.3 80.2 - - - +
190B HIS* 1.3 60.4 + - - +
192B GLU* 3.8 14.9 - - - +
193B ASN* 3.1 33.9 + - - +
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Residues in contact with HIS 190 (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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78B PHE* 3.3 33.2 - + - -
81B GLU* 3.2 56.1 + - + +
82B SER* 3.8 13.8 + - - -
157B ILE 3.6 13.7 - - - -
158B LEU* 5.2 0.7 - - + -
187B ASN* 3.3 14.6 + - - +
189B ASP* 1.3 75.3 - - - +
191B ALA* 1.3 66.3 + - - +
193B ASN* 3.3 7.5 + - - +
194B GLN* 2.9 56.0 + - + +
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Residues in contact with ALA 191 (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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95B LEU* 3.4 21.5 - - + -
157B ILE* 3.5 29.8 - - + +
158B LEU* 4.1 10.8 - - + -
187B ASN 3.1 16.1 + - - +
188B TRP* 3.7 15.7 - - + +
189B ASP 3.4 0.2 - - - -
190B HIS* 1.3 76.5 - - - +
192B GLU* 1.3 56.0 + - - +
194B GLN* 3.3 1.9 + - - +
195B PHE* 2.9 28.8 + - - +
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Residues in contact with GLU 192 (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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91B PRO* 4.1 0.5 - - - +
92B SER* 3.4 37.0 + - - +
95B LEU* 3.8 27.4 - - + +
188B TRP* 2.8 38.8 + - - +
189B ASP* 3.8 17.3 - - - +
190B HIS 3.4 0.2 - - - -
191B ALA* 1.3 70.9 - - - +
193B ASN* 1.3 60.3 + - - +
195B PHE* 3.3 5.7 + - - +
196B THR* 3.0 36.0 + - + +
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Residues in contact with ASN 193 (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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189B ASP* 3.1 21.4 + - - +
190B HIS* 3.3 6.8 + - - +
192B GLU* 1.3 78.4 - - - +
194B GLN* 1.3 71.9 + - - +
196B THR* 3.6 7.9 + - - -
197B ARG 3.2 24.8 + - - -
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Residues in contact with GLN 194 (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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78B PHE* 3.8 18.1 - - + -
155B LYS* 3.3 24.8 + - - +
156B PRO 3.6 16.3 - - - +
157B ILE* 3.9 9.2 - - - +
190B HIS* 2.9 56.6 + - - +
191B ALA 3.6 5.4 - - - +
193B ASN* 1.3 85.2 + - - +
195B PHE* 1.3 62.1 + - - +
197B ARG* 3.6 12.4 + - - +
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Residues in contact with PHE 195 (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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94B LYS* 3.8 28.5 - - + -
95B LEU* 4.2 26.9 - - + -
98B ALA* 3.4 28.5 - - + -
130B GLN* 3.6 32.6 - - - +
135B LYS 4.9 1.1 - - - -
137B LEU* 4.1 17.3 - - + -
155B LYS* 2.9 19.6 + - - -
157B ILE* 3.6 12.5 - - + +
191B ALA 2.9 13.9 + - - +
192B GLU* 3.4 8.7 - - - +
194B GLN* 1.3 75.7 - - - +
196B THR* 1.3 72.2 + - + +
197B ARG* 4.9 0.2 - - - +
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Residues in contact with THR 196 (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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94B LYS* 4.2 26.2 - - + +
192B GLU* 3.0 21.4 + - + +
193B ASN* 3.6 11.4 + - - -
195B PHE* 1.3 90.2 - - + +
197B ARG* 1.3 72.7 + - - +
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Residues in contact with ARG 197 (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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132B THR* 5.6 8.5 - - - +
135B LYS* 5.8 3.8 - - - +
155B LYS* 4.2 22.3 - - + +
193B ASN 3.2 19.9 + - - -
194B GLN* 3.6 18.8 - - - +
195B PHE 4.2 0.4 - - - -
196B THR* 1.3 84.0 + - - +
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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