Contacts of the helix formed by residues 90 - 101 (chain A) in PDB entry 1B5X
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 ALA 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.3 28.3 - - + +
88A ASN* 3.0 20.2 + - - +
89A ILE* 1.3 75.9 - - - +
91A ASP* 1.3 61.5 + - - +
93A VAL* 3.3 4.6 + - - +
94A ALA* 3.0 27.2 + - - +
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Residues in contact with ASP 91 (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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79A LEU* 3.8 25.2 - - + +
83A ALA* 4.0 17.9 - - + +
86A GLN* 3.0 30.8 + - - +
88A ASN* 4.7 2.2 + - - +
89A ILE 3.3 0.6 - - - -
90A ALA* 1.3 77.4 - - - +
92A ALA* 1.3 66.7 + - - +
94A ALA* 3.2 7.3 + - - +
95A CYS* 3.0 23.6 + - - +
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Residues in contact with ALA 92 (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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55A GLY* 6.3 0.2 - - - -
56A ILE* 4.5 9.2 - - + +
57A PHE* 4.0 17.6 - - + +
59A ILE* 4.1 3.6 - - + +
83A ALA 4.7 2.5 + - - +
84A LEU* 3.7 31.7 - - + +
88A ASN 5.4 0.2 + - - -
89A ILE* 3.2 21.5 + - + +
91A ASP* 1.3 77.2 - - - +
93A VAL* 1.3 58.3 + - - +
95A CYS* 3.3 2.4 + - - +
96A ALA* 2.8 29.1 + - - +
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Residues in contact with VAL 93 (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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12A LEU* 3.8 27.8 - - + -
15A LEU* 4.0 31.6 - - + +
17A MET* 3.6 28.8 - - + +
57A PHE* 4.2 6.5 - - + -
89A ILE* 2.9 23.1 + - + +
90A ALA 3.6 5.8 - - - +
92A ALA* 1.3 74.3 - - - +
94A ALA* 1.3 65.6 + - - +
96A ALA* 3.3 2.0 + - - +
97A LYS* 3.0 37.6 + - - +
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Residues in contact with ALA 94 (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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79A LEU* 5.8 1.8 - - + -
90A ALA 3.0 13.4 + - - +
91A ASP* 3.2 11.9 + - - +
93A VAL* 1.3 77.5 - - - +
95A CYS* 1.3 59.4 + - - +
97A LYS* 3.4 13.6 + - - +
98A ARG* 3.1 25.3 + - - +
101A ARG* 4.6 2.1 + - - -
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Residues in contact with CYS 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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59A ILE* 3.9 21.1 - - + -
64A TRP* 4.0 15.0 - - - -
65A CYS* 5.7 0.2 - - - -
77A CYS* 2.0 52.9 - - + -
79A LEU* 4.0 9.4 - - + +
84A LEU* 4.3 6.5 - - + -
91A ASP 3.0 16.2 + - - +
92A ALA 3.7 4.7 - - - +
94A ALA* 1.3 76.0 - - - +
96A ALA* 1.3 59.8 + - - +
98A ARG* 3.1 3.5 + - - +
99A VAL* 2.9 32.7 + - - +
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Residues in contact with ALA 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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17A MET* 3.9 19.3 - - + -
28A TRP* 4.0 12.3 - - + -
57A PHE* 3.9 17.3 - - + -
59A ILE* 4.0 4.4 - - + +
92A ALA 2.8 17.6 + - - +
93A VAL 3.3 4.9 + - - +
95A CYS* 1.3 76.3 - - - +
97A LYS* 1.3 64.0 + - - +
99A VAL* 3.2 10.9 + - - +
100A VAL* 3.1 26.5 + - - +
109A TRP* 4.3 7.1 - - + -
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Residues in contact with LYS 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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15A LEU 2.6 29.8 + - - -
16A GLY* 3.9 15.2 + - - -
17A MET* 3.8 15.7 - - - -
20A TYR* 3.6 37.7 - - + -
28A TRP* 4.9 0.9 - - - -
93A VAL* 3.0 31.9 + - + +
94A ALA* 3.5 13.7 - - - +
95A CYS 3.2 0.2 - - - -
96A ALA* 1.3 75.5 - - - +
98A ARG* 1.3 61.9 + - - +
100A VAL* 3.3 9.9 + - - +
101A ARG* 3.3 35.0 + - - +
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Residues in contact with ARG 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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64A TRP* 3.8 13.8 - - + -
76A ALA* 3.9 31.9 + - - +
77A CYS* 3.9 20.4 - - - -
94A ALA 3.1 14.0 + - - +
95A CYS 3.4 8.1 - - - +
97A LYS* 1.3 76.3 - - - +
99A VAL* 1.3 63.1 + - - +
101A ARG* 3.1 45.1 + - - +
102A ASP* 3.1 28.9 + - - -
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Residues in contact with VAL 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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59A ILE* 4.5 9.4 - - + -
64A TRP* 3.7 50.2 - - + +
95A CYS* 2.9 23.6 + - - +
96A ALA* 3.2 10.7 + - - +
98A ARG* 1.3 76.4 - - - +
100A VAL* 1.3 58.2 + - - +
101A ARG 3.2 3.8 + - - -
102A ASP* 3.3 19.6 + - - +
105A GLY 4.7 2.1 + - - +
108A ALA* 3.8 23.9 - - + +
109A TRP* 3.6 27.1 - - + -
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Residues in contact with VAL 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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20A TYR* 3.9 21.5 - - + -
21A ARG* 4.3 15.9 + - + +
23A ILE* 3.8 22.2 - - + -
28A TRP* 3.6 23.6 - - + -
96A ALA 3.1 5.5 + - - +
97A LYS 3.4 12.6 - - - +
99A VAL* 1.3 71.3 - - - +
101A ARG* 1.3 57.5 + - - +
102A ASP 3.1 13.9 - - - +
105A GLY* 3.6 35.7 - - - +
106A ILE* 3.8 1.3 - - - +
109A TRP* 3.7 20.6 - - + -
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Residues in contact with ARG 101 (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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20A TYR* 2.7 30.3 + - - +
21A ARG* 4.1 29.2 + - - +
94A ALA 4.6 2.2 + - - -
97A LYS* 3.3 24.3 + - - +
98A ARG* 3.1 56.4 + - - +
100A VAL* 1.3 76.9 - - - +
102A ASP* 1.3 63.4 + - - +
103A PRO* 4.8 0.2 - - - +
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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