Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 2LBP
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ALA 4.3 9.0 - - - +
59A VAL* 4.5 1.3 - - - +
62A ALA* 4.3 8.5 - - - -
76A HIS* 3.6 32.5 - - + +
81A SER 3.4 12.7 + - - +
82A THR 2.9 8.0 + - - +
84A PRO* 1.3 77.3 - - - +
86A SER* 1.3 53.6 + - - +
88A ILE* 2.7 30.0 + - - +
89A TYR* 2.9 26.0 + - + -
96A MET* 5.2 0.2 - - - -
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Residues in contact with SER 86 (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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82A THR 2.7 14.3 + - - -
83A GLN 2.8 10.2 + - - -
85A ALA* 1.3 71.6 - - - +
87A ASP* 1.3 61.8 + - - +
89A TYR* 3.8 12.9 - - - -
90A GLU* 3.1 25.6 + - - +
96A MET* 4.0 5.6 - - - -
106A LEU* 3.8 10.1 - - - +
109A ARG* 2.3 34.9 + - - -
111A TYR* 3.7 2.1 - - - -
114A ILE* 3.7 22.3 - - - +
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Residues in contact with ASP 87 (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 GLN* 3.3 9.1 + - - +
84A PRO* 3.2 14.5 + - - +
85A ALA 2.9 1.8 + - - -
86A SER* 1.3 80.3 + - - +
88A ILE* 1.3 61.6 - - + +
90A GLU* 3.9 2.1 - - - +
91A ASP* 2.9 29.8 + - - +
109A ARG* 2.6 33.2 + - - -
111A TYR* 2.9 17.6 + - - +
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Residues in contact with ILE 88 (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 VAL* 3.5 33.2 - - + +
62A ALA* 3.8 28.3 - - + +
63A ASN* 3.3 33.0 - - - +
66A VAL* 4.2 10.8 - - + -
84A PRO 3.6 9.8 + - - +
85A ALA 2.7 7.0 + - - +
87A ASP* 1.3 78.8 - - + +
89A TYR* 1.3 57.0 + - - +
91A ASP* 2.7 28.7 - - + +
92A GLU* 3.3 13.9 + - + +
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Residues in contact with TYR 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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8A VAL* 4.5 1.0 - - - +
62A ALA* 3.3 40.4 + - + +
65A ILE* 3.9 14.3 - - + +
66A VAL* 4.8 3.8 - - + -
73A VAL* 3.9 29.8 - - + +
76A HIS* 3.0 33.5 + + - -
85A ALA* 2.9 26.9 + - + +
86A SER* 4.1 4.7 - - - +
88A ILE* 1.3 78.5 - - - +
90A GLU* 1.3 61.3 + - - +
92A GLU* 3.5 1.6 + - - -
93A GLY 3.2 4.0 + - - -
94A ILE* 3.0 58.0 + - + +
96A MET* 3.6 31.4 - - + -
114A ILE* 4.4 1.8 - - + -
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Residues in contact with GLU 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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86A SER 3.1 17.3 + - - +
87A ASP 3.9 2.9 - - - +
89A TYR* 1.3 78.4 - - - +
91A ASP* 1.3 63.0 + - - +
93A GLY* 3.2 13.3 + - - -
110A GLY 4.0 2.9 - - - +
111A TYR* 3.0 44.9 - - + -
112A GLN* 2.8 30.4 + - - +
113A HIS* 4.1 21.0 + - - +
114A ILE* 4.1 9.3 - - + +
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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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87A ASP* 2.9 15.8 + - - +
88A ILE* 2.7 28.1 - - - +
90A GLU* 1.3 75.9 + - - +
92A GLU* 1.3 72.3 + - - +
93A GLY 3.6 0.5 + - - -
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Residues in contact with GLU 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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66A VAL* 4.1 37.9 - - + +
71A LYS* 5.6 2.3 - - - -
88A ILE* 3.3 15.7 + - + +
89A TYR 4.3 1.3 - - - +
91A ASP* 1.3 95.1 - - - +
93A GLY* 1.3 59.9 + - - +
94A ILE* 3.5 9.8 + - + +
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Residues in contact with GLY 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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71A LYS* 4.3 5.2 - - - +
89A TYR 3.2 3.9 + - - -
90A GLU 3.2 7.4 + - - -
91A ASP 3.5 1.8 + - - -
92A GLU* 1.3 76.4 - - - +
94A ILE* 1.3 61.5 + - - +
113A HIS* 3.3 27.8 + - - -
299A PRO* 3.3 21.3 - - - +
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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