Contacts of the helix formed by residues 82 - 95 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TYR* 5.0 0.2 - - - -
77A ALA 3.4 0.7 - - - +
78A ARG* 2.8 42.2 + - - +
81A PHE* 1.3 74.9 + - - -
83A PRO* 1.4 81.1 - - - +
86A GLY* 2.8 19.9 + - - -
87A TYR* 5.2 0.3 - - - -
432B HIS* 4.5 2.0 + - - +
433B LYS* 5.7 0.8 - - - +
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Residues in contact with PRO 83 (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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78A ARG* 4.9 12.6 - - - +
81A PHE* 3.1 22.2 - - + -
82A GLY* 1.4 83.2 - - - +
84A PHE* 1.3 59.7 + - - +
85A LEU 3.0 1.3 - - - -
86A GLY 2.4 31.9 + - - -
87A TYR* 3.0 32.7 + - + +
430A ARG* 3.1 28.5 - - + +
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Residues in contact with PHE 84 (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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81A PHE* 3.5 13.4 - - + -
83A PRO* 1.3 79.4 - - - +
85A LEU* 1.3 65.9 + - + +
87A TYR* 3.5 3.1 + - - +
88A GLN* 3.0 57.7 + - + +
421A THR* 2.6 51.6 - - + -
424A TYR* 4.4 20.8 + + + -
430A ARG* 3.5 24.0 - - - +
80B CYS* 3.9 14.4 - - - -
85B LEU* 3.2 30.1 - - + -
367B TYR* 4.1 15.7 - + - -
370B ALA* 6.0 0.2 - - + -
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Residues in contact with LEU 85 (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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77A ALA* 4.1 7.1 - - + +
80A CYS* 3.2 28.9 - - + +
81A PHE* 3.4 22.2 - - + -
83A PRO 2.6 4.9 + - - -
84A PHE* 1.3 93.7 - - + +
86A GLY* 1.3 57.0 + - - +
88A GLN* 3.7 10.1 + - - +
89A THR* 2.9 27.9 + - - -
367A TYR* 3.2 39.5 - - + +
81B PHE* 3.9 5.6 - - + -
84B PHE* 3.3 29.8 - - + -
85B LEU* 4.2 9.9 - - + -
367B TYR* 5.6 0.4 - - - +
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Residues in contact with GLY 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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74A TYR* 2.9 24.0 - - - -
77A ALA* 3.8 8.2 + - - -
82A GLY 2.8 16.8 + - - -
83A PRO 2.4 13.3 + - - -
85A LEU* 1.3 68.5 - - - +
87A TYR* 1.3 64.5 + - - -
88A GLN 3.1 1.6 - - - -
89A THR* 2.7 28.9 - - - +
90A ASN* 2.9 5.2 + - - +
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 2.7 31.9 - + - -
78A ARG* 3.3 24.8 + - - -
82A GLY 5.2 0.4 - - - -
83A PRO* 3.0 31.0 + - + +
84A PHE 4.2 0.7 - - - +
86A GLY* 1.3 75.5 - - - +
88A GLN* 1.3 56.1 + - - +
90A ASN* 3.8 5.0 + - - +
91A VAL* 3.1 29.3 + - + +
304A ALA* 4.8 0.2 - - + -
308A GLY* 3.5 8.9 - - - -
309A LEU* 3.4 46.4 - - + +
310A PHE* 5.9 1.8 - - - +
424A TYR* 2.7 38.9 + + + +
427A ASN* 5.3 2.0 - - - +
430A ARG* 3.2 28.0 - - - -
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Residues in contact with GLN 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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84A PHE* 3.0 52.0 + - + +
85A LEU* 3.8 4.0 - - - +
87A TYR* 1.3 75.4 - - - +
89A THR* 1.3 64.9 + - - +
90A ASN 3.1 1.8 - - - -
91A VAL* 4.5 0.2 - - - -
92A LEU* 3.1 24.0 + - + +
363A VAL* 4.3 2.3 - - + +
367A TYR* 3.2 32.8 + - + -
417A LEU* 4.1 34.2 + - + +
420A ILE* 3.9 23.0 - - + +
421A THR* 3.7 6.3 + - - -
424A TYR* 3.4 4.0 + - + +
367B TYR* 5.3 2.0 + - - -
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Residues in contact with THR 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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73A SER 3.4 17.8 + - - +
74A TYR* 3.4 17.7 - - + -
77A ALA* 3.4 15.2 - - + +
85A LEU 2.9 15.7 + - - -
86A GLY* 2.7 30.7 - - - +
88A GLN* 1.3 78.7 - - - +
90A ASN* 1.3 57.9 + - - +
92A LEU* 3.9 4.1 - - - +
93A TYR* 3.2 25.6 + - - +
363A VAL* 5.1 0.4 - - - -
364A PRO* 3.6 27.8 - - - +
367A TYR* 4.0 12.6 - - - -
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Residues in contact with ASN 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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74A TYR* 4.0 13.2 - - + -
86A GLY 2.9 13.0 + - - +
87A TYR* 3.8 6.0 + - - +
88A GLN 3.1 0.6 - - - -
89A THR* 1.3 79.2 - - - +
91A VAL* 1.3 67.3 + - - +
92A LEU 3.0 1.1 - - - -
93A TYR* 2.5 27.5 + - - -
94A TRP* 2.9 14.0 + - - +
300A THR* 2.1 39.7 - - + +
301A ALA* 3.5 0.7 - - - +
304A ALA* 3.8 16.3 - - + +
309A LEU 5.3 0.6 + - - -
310A PHE* 3.2 36.1 - - - +
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Residues in contact with VAL 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 TYR* 3.1 17.4 + - + +
88A GLN 4.2 2.2 - - - +
90A ASN* 1.3 82.4 - - - +
92A LEU* 1.3 53.6 + - - +
94A TRP* 4.1 2.6 - - + +
95A LEU* 2.6 59.2 + - + +
310A PHE* 4.2 33.0 - - + +
420A ILE* 3.7 30.7 - - + -
423A MET* 5.1 13.5 - - + -
424A TYR* 4.2 10.1 - - + +
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Residues in contact with LEU 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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88A GLN 3.1 15.1 + - - +
89A THR 4.1 2.2 - - - +
90A ASN 2.9 1.0 + - - -
91A VAL* 1.3 81.4 - - - +
93A TYR* 1.3 60.6 + - - +
95A LEU* 4.1 4.9 - - - -
96A ALA* 3.5 3.3 - - - +
360A PHE* 2.9 76.9 - - + +
363A VAL* 3.4 18.2 - - + -
364A PRO* 3.4 21.1 - - + -
413A SER* 5.1 0.7 - - - +
416A THR* 4.6 0.9 - - + -
417A LEU* 3.3 33.2 - - + -
420A ILE* 3.8 12.6 - - + -
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Residues in contact with TYR 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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73A SER* 5.1 7.6 - - - -
89A THR 3.2 14.4 + - - +
90A ASN 2.5 15.0 + - - +
92A LEU* 1.3 69.6 - - - +
94A TRP* 1.3 70.7 + - - +
95A LEU 2.9 0.7 - - - -
96A ALA* 2.7 21.2 + - - +
97A CYS* 3.1 23.9 + - - -
208A GLU* 2.6 51.1 + - - +
212A VAL* 3.8 15.5 - - + +
293A TRP* 4.2 7.3 - + - -
296A LEU* 4.1 12.5 - - + +
300A THR* 3.1 44.4 - - + -
361A THR* 4.4 15.7 - - + +
364A PRO* 4.0 17.3 - - + -
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Residues in contact with TRP 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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90A ASN* 2.9 15.1 + - - +
91A VAL* 4.2 4.5 - - + -
93A TYR* 1.3 77.0 - - - +
95A LEU* 1.3 73.1 - - + +
96A ALA 2.4 15.9 + - - -
97A CYS* 2.8 20.3 + - - +
98A TRP* 3.0 51.8 + + + +
297A ALA* 2.9 32.8 + - + +
300A THR 3.8 13.2 + - - +
301A ALA* 3.5 11.0 - - + -
302A LYS* 3.1 18.0 - - - +
310A PHE* 4.1 23.8 - + + -
314A PHE* 4.3 17.3 - + - -
329A ILE* 5.9 3.8 - - + -
330A VAL* 4.1 18.3 - - + +
333A LEU* 5.2 9.4 - - + -
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Residues in contact with LEU 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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91A VAL* 2.6 40.7 + - + +
92A LEU* 4.2 6.3 - - - +
93A TYR 2.9 0.6 + - - -
94A TRP* 1.3 84.4 - - + +
96A ALA* 1.3 60.4 + - - +
98A TRP* 3.8 30.1 - - + -
99A ILE* 3.7 30.7 - - + +
360A PHE* 3.9 18.4 - - + -
416A THR* 5.7 5.4 - - + -
420A ILE* 5.7 2.2 - - + -
423A MET* 6.3 2.0 - - + -
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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