Contacts of the helix formed by residues 76 - 86 (chain B) in PDB entry 3LB2
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 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL 5.3 0.2 + - - -
69B ARG* 3.9 49.1 - - + +
70B ALA* 4.9 1.6 - - - +
71B THR 6.2 0.2 - - - +
74B VAL 5.5 1.1 - - - +
75B PRO* 1.3 77.4 - - - +
77B ALA* 1.3 65.1 + - - +
78B SER* 3.7 20.2 - - - +
79B ASP* 3.1 25.9 + - - +
80B ALA* 3.1 13.0 + - - +
130B ALA* 5.8 0.2 - - - -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PRO 3.6 2.6 + - - -
76B LEU* 1.3 72.4 - - - +
78B SER* 1.3 58.0 + - - +
80B ALA* 3.3 8.9 + - - +
81B ASN 2.9 24.3 + - - -
130B ALA* 5.6 3.4 - - - -
134B ALA* 5.1 2.4 - - - +
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.7 20.1 - - - +
77B ALA* 1.3 79.8 - - - +
79B ASP* 1.3 61.2 + - - +
81B ASN 3.4 1.3 + - - +
82B THR* 3.0 31.5 + - - -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 5.1 1.7 - - - +
66B VAL* 3.8 37.5 - - + +
69B ARG* 2.9 49.8 + - - +
75B PRO* 5.2 0.2 - - + -
76B LEU* 3.1 22.5 + - + +
78B SER* 1.3 82.9 + - - +
80B ALA* 1.3 63.0 - - - +
82B THR* 3.3 9.1 + - - -
83B LEU* 3.1 28.4 + - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PRO* 5.7 0.2 - - + -
76B LEU 3.1 8.7 + - - +
77B ALA* 3.3 9.4 + - - +
79B ASP* 1.3 77.6 - - - +
81B ASN 1.3 59.2 + - - +
83B LEU* 3.1 8.0 + - - +
84B VAL* 3.0 30.6 + - - +
127B LEU* 4.8 5.9 - - + +
130B ALA* 3.6 44.6 - - + +
131B LEU* 3.7 11.2 - - + +
134B ALA* 4.3 2.5 - - + -
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Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA 2.9 16.6 + - - -
78B SER* 3.4 2.1 + - - +
79B ASP 3.3 0.4 - - - -
80B ALA* 1.3 72.5 + - - +
82B THR* 1.3 62.1 - - - +
84B VAL* 3.2 4.1 - - - -
85B GLN* 2.9 33.0 - - - -
134B ALA* 4.2 8.0 - - - +
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 5.2 11.0 - - + -
78B SER 3.0 15.6 + - - -
79B ASP* 3.6 13.3 + - - -
80B ALA 3.3 0.2 - - - -
81B ASN 1.3 73.7 - - - +
83B LEU* 1.3 64.4 + - + +
85B GLN* 3.3 3.3 + - - -
86B MET* 3.0 44.3 + - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.1 10.8 - - + -
66B VAL* 4.8 12.1 - - + -
79B ASP 3.1 17.8 + - - +
80B ALA 3.1 5.8 + - - +
82B THR* 1.3 76.2 - - + +
84B VAL* 1.3 62.3 + - - +
86B MET* 3.9 13.3 + - - -
89B HIS* 2.8 42.9 + - + +
97B PHE* 4.9 4.9 - - + -
127B LEU* 4.1 26.7 - - + -
131B LEU* 3.8 12.1 - - + -
136B MET* 4.3 3.4 - - - +
139B HEM 3.8 46.9 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA 3.0 18.5 + - - +
81B ASN 3.7 6.7 - - - -
83B LEU* 1.3 77.4 - - - +
85B GLN* 1.3 81.4 + - + +
86B MET 3.6 5.0 + - - +
89B HIS* 4.7 7.8 - - - +
90B SER* 5.5 1.6 - - - -
131B LEU* 3.7 34.8 - - + +
134B ALA* 3.8 22.0 - - + +
135B GLY 4.4 2.7 - - - -
136B MET* 4.0 29.8 - - + +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASN 2.9 20.0 - - - -
82B THR* 3.8 3.6 - - - +
84B VAL* 1.3 94.9 - - + +
86B MET* 1.3 68.3 + - - +
87B LYS* 3.3 3.6 + - - -
134B ALA 4.9 4.6 + - - -
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Residues in contact with MET 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 4.6 5.8 - - - -
82B THR* 3.0 37.0 + - + +
83B LEU* 4.0 19.1 - - - +
84B VAL 3.4 2.7 - - - +
85B GLN* 1.3 76.9 - - - +
87B LYS* 1.3 66.7 + - - +
88B GLN* 4.2 14.6 - - + +
89B HIS* 2.9 42.4 + - + +
90B SER* 3.6 4.3 + - - -
139B HEM 3.6 46.4 - - + +
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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