Contacts of the helix formed by residues 94 - 100 (chain A) in PDB entry 1BQ2
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 TYR 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.6 40.2 - + + -
80A TRP* 3.8 25.1 - + - -
93A VAL* 1.3 79.5 - - + +
95A GLY* 1.3 59.0 + - - +
97A GLN* 3.1 6.3 + - - +
98A TRP* 2.8 52.9 + + - +
132A ALA* 4.0 15.9 - - + +
143A LEU* 5.6 4.3 - - + -
145A PRO* 3.9 14.8 - - + +
146A CYS* 2.9 30.7 + - - +
147A HIS* 3.0 50.4 + + + -
181A TYR* 4.7 2.2 - - - -
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Residues in contact with GLY 95 (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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62A PHE* 3.4 31.0 - - - -
65A GLY* 3.2 17.5 - - - -
66A ASP 3.7 17.2 + - - -
67A THR* 4.7 0.6 + - - -
93A VAL* 3.3 2.8 + - - +
94A TYR* 1.3 75.5 - - - +
96A LYS* 1.3 61.2 + - - +
98A TRP* 3.9 2.3 - - - +
99A ARG* 3.2 18.9 + - - +
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Residues in contact with LYS 96 (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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65A GLY* 3.9 11.1 + - - +
67A THR* 3.9 15.2 + - + +
92A PRO* 3.5 29.6 - - + +
93A VAL 3.2 9.6 + - - +
95A GLY* 1.3 73.6 - - - +
97A GLN* 1.3 60.7 + - - +
100A ALA* 2.8 66.7 + - + +
102A PRO* 4.0 8.7 - - - -
108A HIS* 4.6 10.1 - - - -
137A GLU* 3.1 30.5 + - - +
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Residues in contact with GLN 97 (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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92A PRO* 3.0 22.3 + - - +
93A VAL 3.2 13.8 + - - +
94A TYR 3.1 6.5 + - - +
96A LYS* 1.3 77.8 - - - +
98A TRP* 1.3 53.9 + - - +
101A TRP* 3.9 28.5 + - - +
102A PRO* 4.1 2.6 - - - +
111A GLN* 2.6 28.8 + - - -
131A SER 4.1 2.0 - - - +
132A ALA* 3.8 35.2 - - + +
134A ASN* 3.7 21.6 - - - +
137A GLU* 3.1 26.2 + - - +
141A MET* 3.6 12.2 - - + +
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Residues in contact with TRP 98 (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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59A LEU* 4.1 13.9 - - + -
62A PHE* 3.7 47.8 - + + -
63A LEU* 4.1 15.9 - - + -
94A TYR* 2.8 41.0 + + + +
95A GLY* 3.9 4.0 - - - +
97A GLN* 1.3 74.8 - - - +
99A ARG* 1.3 63.3 + - + +
111A GLN* 2.9 34.8 + - - +
112A ILE* 3.4 31.2 + - + -
130A VAL* 3.9 11.0 - - + -
131A SER 4.8 0.9 - - - -
132A ALA* 4.4 14.6 - - + +
147A HIS 5.7 0.4 + - - -
150A PHE* 3.5 18.2 - + - -
181A TYR* 3.2 27.8 + + - -
184A LEU* 4.1 20.9 - - + -
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Residues in contact with ARG 99 (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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62A PHE 4.1 2.2 - - - +
63A LEU* 3.0 34.9 + - - +
64A GLN* 4.2 12.1 + - - +
65A GLY* 3.6 21.1 - - - +
95A GLY 3.2 10.6 + - - +
98A TRP* 1.3 79.4 - - + +
100A ALA* 1.3 61.2 + - + +
108A HIS 5.2 0.7 - - - -
109A ILE 3.6 5.8 - - - -
110A ASP* 3.0 51.9 + - - +
112A ILE* 4.0 12.8 - - - -
240A PHE* 3.3 39.2 - - - +
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Residues in contact with ALA 100 (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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96A LYS* 2.8 35.0 + - + +
98A TRP 3.7 0.2 - - - -
99A ARG* 1.3 78.0 - - + +
101A TRP* 1.4 66.8 + - - +
102A PRO* 3.0 11.3 - - - +
108A HIS* 3.3 28.9 - - + -
109A ILE 3.3 9.1 + - - +
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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