Contacts of the helix formed by residues 197 - 205 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D LYS 5.8 0.4 + - - -
98D GLY 3.4 26.3 + - - +
99D GLY 3.3 19.8 + - - -
100D LYS 3.8 11.0 - - - +
101D PRO* 3.6 34.2 - - + +
102D GLY 5.2 1.6 + - - +
105D LEU* 3.7 24.7 - - + +
109D ILE* 4.9 3.4 - - + -
116D PHE* 3.5 30.7 - + - -
119D PHE* 4.3 7.0 - + - -
138D LEU* 6.1 1.3 - - + -
167D LEU* 4.0 32.5 - - + -
192D TRP* 3.9 17.3 + + - -
195D VAL* 3.4 21.9 + - + +
196D ASN* 1.3 69.3 + - - +
198D ASP* 1.3 61.2 + - - +
200D ALA* 3.5 7.6 - - + +
201D GLU* 2.9 30.8 + - - +
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Residues in contact with ASP 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LYS* 3.3 31.9 + - - +
196D ASN* 3.2 10.6 + - - +
197D TRP* 1.3 78.2 - - - +
199D ASP* 1.3 63.5 + - - +
201D GLU* 3.4 6.0 + - - +
202D LYS* 3.0 45.5 + - - +
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Residues in contact with ASP 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASN* 3.2 31.0 - - - +
90D ASN* 2.8 23.9 - - - +
196D ASN* 3.1 19.6 + - + +
198D ASP* 1.3 80.7 - - - +
200D ALA* 1.3 58.1 + - - +
202D LYS* 3.2 11.0 + - - +
203D ARG* 2.7 65.3 + - - +
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Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ASN* 4.4 2.7 - - - +
105D LEU* 3.8 18.6 - - + -
166D ILE* 3.6 34.4 - - + +
167D LEU* 5.1 3.8 - - + -
196D ASN 3.1 9.4 + - - +
197D TRP* 3.5 21.5 - - + +
198D ASP 3.3 0.2 - - - -
199D ASP* 1.3 80.6 + - - +
201D GLU* 1.3 62.0 + - - +
203D ARG* 3.3 5.5 + - - +
204D LEU* 3.2 18.4 + - - +
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Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLY 3.4 13.3 - - - +
103D GLY* 3.9 5.0 - - - -
104D ALA* 3.1 17.0 + - - -
105D LEU* 2.9 38.6 + - + +
197D TRP 2.9 17.2 + - - +
198D ASP* 3.9 6.1 - - - +
200D ALA* 1.3 73.8 - - - +
202D LYS* 1.3 60.5 + - - +
204D LEU* 3.3 5.8 + - - +
205D GLN* 2.8 59.2 + - + +
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Residues in contact with LYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LYS* 6.0 0.6 - - - +
198D ASP* 3.0 33.9 + - - +
199D ASP* 3.4 12.8 - - - +
201D GLU* 1.3 76.2 - - + +
203D ARG* 1.3 66.4 + - + +
205D GLN* 3.4 10.4 + - + +
206D LYS* 3.3 27.8 + - - +
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Residues in contact with ARG 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA 5.5 0.2 - - - -
86D ILE* 3.6 41.2 + - - +
89D ASN* 4.1 14.5 - - - +
90D ASN* 4.6 1.3 - - - -
165D VAL 3.4 26.7 + - - +
166D ILE* 4.0 15.9 - - + -
199D ASP* 2.7 60.3 + - - +
200D ALA 3.6 6.1 - - - +
201D GLU 3.3 0.2 - - - -
202D LYS* 1.3 78.1 - - + +
204D LEU* 1.3 59.2 + - - +
206D LYS* 3.2 25.0 - - - +
207D TYR* 2.9 34.1 - - + -
162F GLU* 5.2 4.4 + - - -
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ALA* 3.9 15.5 - - + -
105D LEU* 3.6 40.6 - - + +
108D LEU* 4.2 11.9 - - + -
140D TYR* 3.8 42.0 - - + -
147D LEU* 4.6 4.7 - - + -
166D ILE* 3.7 13.9 - - + +
200D ALA 3.2 9.7 + - - +
201D GLU* 3.6 10.5 - - - +
202D LYS 3.3 0.2 - - - -
203D ARG* 1.3 76.8 - - - +
205D GLN* 1.3 65.5 + - - +
207D TYR* 2.9 15.6 + - - +
208D LEU* 3.2 23.5 + - + +
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Residues in contact with GLN 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ALA* 3.7 18.0 - - - +
201D GLU* 2.8 47.9 + - + +
202D LYS* 3.6 10.3 - - + +
204D LEU* 1.3 74.8 - - - +
206D LYS* 1.3 61.2 + - - +
207D TYR 3.2 0.9 + - - -
208D LEU* 3.5 24.7 + - - +
210D 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