Contacts of the helix formed by residues 197 - 205 (chain C) in PDB entry 1B06
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 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C LYS 5.8 0.6 + - - -
97C GLY* 5.6 0.2 - - - -
98C GLY 3.3 25.2 + - - -
99C GLY 3.2 19.6 + - - -
100C LYS 3.8 10.1 - - - +
101C PRO* 3.5 35.8 - - + +
102C GLY 5.1 2.4 + - - +
105C LEU* 3.7 25.0 - - + +
109C ILE* 4.8 3.4 - - + -
116C PHE* 3.6 31.6 - + - -
119C PHE* 4.4 6.1 - + - -
138C LEU* 6.1 0.9 - - + -
167C LEU* 3.9 34.3 - - + -
192C TRP* 4.0 13.2 + + - -
195C VAL* 3.3 26.2 + - + +
196C ASN* 1.3 73.5 + - - +
198C ASP* 1.3 56.8 + - - +
200C ALA* 3.7 6.6 - - + +
201C GLU* 3.0 29.6 + - - +
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Residues in contact with ASP 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LYS* 3.0 32.5 + - - +
196C ASN* 3.1 10.6 + - - +
197C TRP* 1.3 74.9 - - - +
199C ASP* 1.3 67.3 + - - +
201C GLU* 3.4 5.9 + - - +
202C LYS* 3.0 43.7 + - - +
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Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASN* 3.2 33.3 - - - +
90C ASN* 2.8 21.5 - - - +
196C ASN* 3.1 19.4 + - + +
198C ASP* 1.3 79.7 - - - +
200C ALA* 1.3 61.1 + - - +
202C LYS* 3.2 12.2 + - - +
203C ARG* 2.6 62.3 + - - +
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Residues in contact with ALA 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASN* 4.4 3.1 - - - +
105C LEU* 3.7 20.2 - - + -
166C ILE* 3.5 34.5 - - + +
167C LEU* 4.9 4.0 - - + -
196C ASN 3.1 9.4 + - - +
197C TRP* 3.7 20.2 - - + +
198C ASP 3.3 0.2 - - - -
199C ASP* 1.3 82.3 + - - +
201C GLU* 1.3 62.0 + - - +
203C ARG* 3.3 5.4 + - - +
204C LEU* 3.1 18.2 + - - +
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLY 3.4 10.5 - - - +
103C GLY* 3.8 5.7 - - - -
104C ALA* 3.0 18.4 + - - -
105C LEU* 2.9 35.8 + - + +
197C TRP 3.0 17.2 + - - +
198C ASP* 3.8 7.2 - - - +
199C ASP 3.3 0.2 - - - -
200C ALA* 1.3 76.5 - - - +
202C LYS* 1.3 58.1 + - - +
204C LEU* 3.3 5.6 + - - +
205C GLN* 2.9 60.3 + - + +
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Residues in contact with LYS 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ASP* 3.0 32.3 + - - +
199C ASP* 3.4 13.6 - - - +
201C GLU* 1.3 78.8 - - - +
203C ARG* 1.3 61.9 + - + +
205C GLN* 3.5 8.6 + - - +
206C LYS* 3.3 30.9 + - - +
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Residues in contact with ARG 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ILE* 3.7 41.9 + - - +
89C ASN* 4.0 15.4 - - - +
90C ASN* 4.6 0.9 - - - -
165C VAL 3.3 20.9 + - - +
166C ILE* 3.8 24.5 - - + -
199C ASP* 2.6 61.0 + - - +
200C ALA 3.6 5.8 - - - +
201C GLU 3.3 0.2 - - - -
202C LYS* 1.3 77.4 - - + +
204C LEU* 1.3 60.8 + - - +
206C LYS* 3.3 25.6 - - - +
207C TYR* 2.9 34.0 - - + -
162E GLU* 5.3 2.8 + - - -
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA* 3.8 16.6 - - + +
105C LEU* 3.5 42.0 - - + +
108C LEU* 4.2 12.1 - - + -
140C TYR* 3.7 41.5 - - + -
147C LEU* 4.7 4.5 - - + -
166C ILE* 3.6 14.3 - - + +
200C ALA 3.1 12.5 + - - +
201C GLU* 3.3 8.9 + - - +
203C ARG* 1.3 75.1 - - - +
205C GLN* 1.3 66.6 + - - +
207C TYR* 2.9 15.8 + - - +
208C LEU* 3.2 23.1 + - + +
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Residues in contact with GLN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA* 3.6 19.2 - - - +
201C GLU* 2.9 46.9 + - + +
202C LYS* 3.7 8.7 - - - +
203C ARG 3.4 0.2 - - - -
204C LEU* 1.3 76.4 - - - +
206C LYS* 1.3 61.2 + - - +
207C TYR 3.3 1.0 + - - -
208C LEU* 3.6 25.0 + - - +
210C LYS* 4.7 4.2 - - - +
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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