Contacts of the helix formed by residues 88 - 97 (chain A) in PDB entry 1BLJ
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 LEU 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.5 15.3 - - + -
15A PHE* 3.8 14.8 - - + -
40A ILE* 3.4 48.2 - - + -
50A PHE* 4.0 12.6 - - + -
69A ILE* 3.8 21.1 - - + -
77A TYR* 3.1 43.0 - - + -
87A THR* 1.4 80.4 + - - +
89A GLN* 1.4 57.0 + - - +
91A LEU* 2.8 12.8 + - + +
92A VAL* 2.7 32.4 + - + +
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Residues in contact with GLN 89 (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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14A TRP* 3.4 28.8 - - + -
87A THR* 2.7 40.8 + - + +
88A LEU* 1.4 79.7 - - - +
90A ALA* 1.3 59.5 + - + +
92A VAL* 3.3 2.8 + - - +
93A GLN* 3.0 29.2 + - - +
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Residues in contact with ALA 90 (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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85A PHE* 3.1 22.9 - - + -
86A PRO* 3.8 31.2 - - + -
87A THR* 3.4 14.7 + - + +
88A LEU 3.2 0.6 - - - -
89A GLN* 1.3 80.7 - - + +
91A LEU* 1.3 58.9 + - - +
93A GLN* 3.3 38.7 - - - +
94A HIS 3.5 2.1 + - - -
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Residues in contact with LEU 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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40A ILE* 3.8 18.8 - - + -
52A LEU* 4.7 3.8 - - + -
69A ILE* 3.5 30.5 - - + -
77A TYR* 4.1 13.2 - - + +
78A TYR* 5.4 0.4 - - - -
79A ILE* 4.3 13.9 - - + -
85A PHE* 3.8 21.1 - - + -
87A THR 3.4 8.9 + - - +
88A LEU* 3.0 26.2 - - + +
90A ALA* 1.3 80.7 - - - +
92A VAL* 1.4 68.1 + - + +
93A GLN 3.2 1.8 - - - -
94A HIS* 4.3 0.2 - - - +
95A TYR* 2.9 55.7 + - + +
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Residues in contact with VAL 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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14A TRP* 3.3 65.7 - - + +
38A PHE* 5.8 1.3 - - + -
40A ILE* 4.4 3.1 - - + -
88A LEU 2.7 28.0 + - - +
89A GLN 3.6 4.9 - - - +
91A LEU* 1.4 87.9 - - + +
93A GLN* 1.4 52.8 + - - +
96A SER* 2.7 32.4 + - - +
106A LEU* 3.1 31.8 - - + +
109A PRO* 6.1 0.2 - - + -
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Residues in contact with GLN 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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85A PHE* 5.2 2.1 - - - -
89A GLN 3.0 10.5 + - - +
90A ALA* 3.3 32.9 - - - +
91A LEU 3.2 0.6 - - - -
92A VAL* 1.4 78.1 - - - +
94A HIS* 1.4 79.2 + - + +
95A TYR 3.3 0.2 - - - -
96A SER* 3.2 20.0 + - - -
97A LYS* 3.8 6.8 + - - +
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Residues in contact with HIS 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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83A ILE* 5.4 1.1 - - + -
85A PHE* 3.5 29.9 - + + -
90A ALA 3.5 14.7 + - - +
91A LEU 4.3 1.6 - - - +
93A GLN* 1.4 81.7 - - + +
95A TYR* 1.4 69.4 + - - +
97A LYS* 3.3 4.2 + - - +
98A LYS* 2.8 44.4 + - + +
100A ASP* 3.6 35.2 - - + -
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Residues in contact with TYR 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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38A PHE* 4.8 2.0 - + - -
52A LEU* 5.2 0.2 - - + -
79A ILE* 3.3 38.2 - - + +
83A ILE* 3.2 33.9 + - + +
85A PHE* 4.2 12.7 - + - -
91A LEU* 2.9 41.2 + - + +
92A VAL* 5.1 0.4 - - - -
94A HIS* 1.4 88.1 - - - +
96A SER* 1.4 66.6 + - - +
97A LYS 3.3 0.5 + - - -
98A LYS 3.3 9.2 - - - -
99A GLY* 3.2 36.7 + - - -
100A ASP* 4.5 0.2 - - + -
102A LEU* 3.3 21.1 - - + -
105A LYS* 3.3 0.7 - - - -
106A LEU* 2.9 37.8 + - + -
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Residues in contact with SER 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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92A VAL 2.7 24.1 + - - -
93A GLN* 3.2 12.4 + - - -
94A HIS 3.1 1.0 - - - -
95A TYR* 1.4 78.8 - - - +
97A LYS* 1.4 79.8 + - - +
105A LYS* 3.1 9.0 - - - +
106A LEU* 2.8 37.7 - - - +
107A THR 6.1 0.7 - - - -
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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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93A GLN 3.8 4.6 + - - +
94A HIS 3.3 5.0 + - - +
96A SER* 1.4 93.7 + - - +
98A LYS* 1.3 67.1 + - + +
105A LYS* 3.2 21.7 + - - +
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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