Contacts of the helix formed by residues 82 - 95 (chain B) in PDB entry 3LRB
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 GLY 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A HIS* 4.5 2.2 + - - +
433A LYS* 5.7 0.8 - - - +
74B TYR* 5.1 0.3 - - - -
77B ALA 3.3 0.9 - - - +
78B ARG* 2.9 41.4 + - - +
81B PHE* 1.3 74.8 + - - -
83B PRO* 1.4 81.0 - - - +
86B GLY* 2.8 19.9 + - - -
87B TYR* 5.2 0.2 - - - -
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.8 13.5 - - + +
81B PHE* 3.1 21.9 - - + -
82B GLY* 1.4 97.9 - - - +
84B PHE* 1.3 71.5 + - - +
85B LEU 3.1 0.9 - - - -
86B GLY 2.5 6.8 + - - -
87B TYR* 3.0 33.7 + - + +
430B ARG* 3.0 28.7 - - + +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A CYS* 4.1 14.8 - - - -
85A LEU* 3.3 30.5 - - + -
367A TYR* 4.1 17.3 - + - -
81B PHE* 3.5 15.4 - - + -
83B PRO* 1.3 78.3 - - - +
85B LEU* 1.3 65.6 + - + +
87B TYR* 3.9 2.9 - - - +
88B GLN* 2.9 58.0 + - + +
421B THR* 2.7 51.6 - - + -
424B TYR* 4.4 20.3 + + + -
430B ARG* 3.5 22.6 - - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.9 5.4 - - + -
84A PHE* 3.2 30.1 - - + -
85A LEU* 4.2 9.2 - - + -
367A TYR* 5.6 0.4 - - - +
77B ALA* 4.0 7.4 - - + +
80B CYS* 3.2 29.6 - - + +
81B PHE* 3.4 21.6 - - + -
83B PRO 2.7 3.8 + - - -
84B PHE* 1.3 95.0 - - + +
86B GLY* 1.3 56.3 + - - +
88B GLN* 3.8 8.5 + - - +
89B THR* 2.9 28.1 + - - -
367B TYR* 3.3 39.2 - - + +
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 2.9 26.1 - - - -
77B ALA* 3.7 7.7 + - - -
82B GLY 2.8 16.6 + - - -
83B PRO 2.5 12.7 + - - -
85B LEU* 1.3 69.7 - - - +
87B TYR* 1.3 63.0 + - - -
88B GLN 3.1 1.6 - - - -
89B THR* 2.8 27.4 - - - +
90B ASN* 2.9 4.9 + - - +
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 2.7 31.9 - + - -
78B ARG* 3.3 24.8 + - - -
82B GLY 5.2 0.4 - - - -
83B PRO* 3.0 32.9 + - + +
84B PHE 4.1 0.2 - - - +
86B GLY* 1.3 74.7 - - - +
88B GLN* 1.3 56.6 + - - +
90B ASN* 3.8 4.8 + - - +
91B VAL* 3.1 28.8 + - + +
304B ALA* 4.8 0.2 - - + -
308B GLY* 3.5 9.3 - - - -
309B LEU* 3.4 45.5 - - + +
310B PHE* 5.9 1.8 - - - +
424B TYR* 2.7 38.2 + + + +
427B ASN* 5.3 2.7 - - - +
430B ARG* 3.2 28.0 - - - -
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Residues in contact with GLN 88 (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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367A TYR* 5.4 1.4 + - - -
84B PHE* 2.9 52.6 + - + +
85B LEU* 3.8 3.6 - - - +
87B TYR* 1.3 73.7 - - - +
89B THR* 1.3 65.3 + - - +
90B ASN 3.1 1.6 - - - -
92B LEU* 3.1 24.0 + - + +
363B VAL* 4.2 2.7 - - + +
367B TYR* 3.2 33.8 + - - -
417B LEU* 4.1 34.9 + - + +
420B ILE* 3.9 25.7 - - + +
421B THR* 3.8 5.9 + - - -
424B TYR* 3.4 1.5 + - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER 3.4 18.7 + - - +
74B TYR* 3.4 12.1 - - + -
77B ALA* 3.4 27.2 - - + +
85B LEU 2.9 15.7 + - - -
86B GLY* 2.8 24.8 + - - +
88B GLN* 1.3 78.1 - - - +
90B ASN* 1.3 56.9 + - - +
92B LEU* 3.9 6.1 - - - +
93B TYR* 3.1 25.6 + - - +
363B VAL* 5.1 0.4 - - - -
364B PRO* 3.5 26.0 - - - +
367B TYR* 4.0 12.4 - - - +
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Residues in contact with ASN 90 (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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74B TYR* 3.9 15.3 - - + -
86B GLY 2.9 17.1 + - - +
87B TYR* 3.8 5.8 + - - +
88B GLN 3.1 0.6 - - - -
89B THR* 1.3 75.0 - - - +
91B VAL* 1.3 68.2 + - - +
92B LEU 3.0 0.9 - - - -
93B TYR* 2.5 28.0 + - - -
94B TRP* 2.9 13.3 + - - +
300B THR* 2.1 39.7 - - + +
301B ALA* 3.5 1.2 - - - +
304B ALA* 3.9 13.6 - - + +
309B LEU 5.4 0.6 + - - -
310B PHE* 3.1 36.7 - - - +
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Residues in contact with VAL 91 (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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87B TYR 3.1 17.2 + - - +
88B GLN 4.1 2.5 - - - +
90B ASN* 1.3 84.2 - - - +
92B LEU* 1.3 53.2 + - - +
94B TRP* 4.1 3.1 - - + +
95B LEU* 2.6 58.9 + - + +
310B PHE* 4.2 31.6 - - + +
420B ILE* 3.6 30.5 - - + -
423B MET* 5.2 13.0 - - + -
424B TYR* 4.2 11.0 - - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 6.4 0.2 - - + -
88B GLN 3.1 14.6 + - - +
89B THR 4.1 2.7 - - - +
90B ASN 3.0 1.0 - - - -
91B VAL* 1.3 81.1 - - - +
93B TYR* 1.3 59.7 + - - +
95B LEU* 4.1 4.7 - - - -
96B ALA* 3.5 3.3 - - - +
360B PHE* 3.0 76.6 - - + +
363B VAL* 3.4 17.9 - - + -
364B PRO* 3.4 21.3 - - + -
413B SER 5.1 0.4 - - - +
416B THR* 4.6 0.9 - - + -
417B LEU* 3.3 33.2 - - + -
420B ILE* 3.7 11.9 - - + -
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Residues in contact with TYR 93 (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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73B SER* 5.1 7.4 - - - -
89B THR 3.1 14.6 + - - +
90B ASN 2.5 14.6 + - - +
92B LEU* 1.3 69.0 - - - +
94B TRP* 1.3 70.4 + - - +
95B LEU 2.9 0.7 - - - -
96B ALA* 2.7 21.7 + - - +
97B CYS* 3.1 23.8 + - - -
208B GLU* 2.5 53.4 + - - +
212B VAL* 3.7 15.1 - - + +
293B TRP* 4.3 5.4 - + - -
296B LEU* 4.1 12.2 - - + +
300B THR* 3.1 43.7 - - + -
361B THR* 4.4 16.2 - - + +
364B PRO* 4.0 18.6 - - + -
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Residues in contact with TRP 94 (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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90B ASN* 2.9 14.7 + - - +
91B VAL* 4.2 3.8 - - + -
93B TYR* 1.3 77.8 - - - +
95B LEU* 1.3 74.0 - - + +
96B ALA 2.5 15.1 + - - -
97B CYS* 2.9 20.3 + - - +
98B TRP* 2.9 52.7 + + + +
297B ALA* 2.9 33.1 + - + +
300B THR 3.9 13.4 + - - +
301B ALA* 3.5 11.2 - - + -
302B LYS* 3.1 18.2 - - - +
310B PHE* 4.0 24.2 - + + -
314B PHE* 4.4 17.5 - + - -
329B ILE* 5.9 4.7 - - + -
330B VAL* 4.1 17.4 - - + +
333B LEU* 5.2 9.4 - - + -
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Residues in contact with LEU 95 (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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91B VAL* 2.6 40.6 + - + +
92B LEU* 4.1 7.0 - - - +
93B TYR 2.8 1.0 + - - -
94B TRP* 1.3 85.5 - - + +
96B ALA* 1.3 58.7 + - - +
98B TRP* 3.8 26.0 - - + -
99B ILE* 3.6 33.3 - - + +
360B PHE* 3.9 18.9 - - + -
416B THR* 5.7 5.4 - - + -
420B ILE* 5.5 3.1 - - + -
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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