Contacts of the helix formed by residues 75 - 79 (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 ALA 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASP* 3.8 11.9 - - - +
69B SER* 3.2 38.1 - - - +
70B PRO* 4.3 3.7 + - + +
72B GLY* 4.1 2.4 - - - -
74B TYR* 1.3 83.9 - - - +
76B TYR* 1.3 61.8 + - + +
78B ARG* 2.7 37.3 + - - +
79B ARG* 3.2 16.0 + - - +
307B ASP* 5.3 2.2 - - - +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 4.1 8.5 - + - -
63B MET* 3.6 39.5 - - + -
64B SER* 3.6 15.6 - - - -
67B ASP* 3.0 29.8 + - + -
69B SER* 4.0 7.6 - - - -
72B GLY* 4.0 2.8 - - - -
73B SER* 2.8 37.5 - - - -
75B ALA* 1.3 79.5 - - + +
77B ALA* 1.3 53.4 + - - +
79B ARG* 2.6 25.3 + - - +
80B CYS 3.0 9.2 + - - -
211B SER* 2.2 35.0 + - - -
368B THR* 3.8 13.5 - - + -
371B ALA* 3.5 29.0 - - + +
375B LEU* 4.6 2.9 - - - -
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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
----------------------------------------------------------
73B SER 4.0 5.8 + - - +
74B TYR* 3.2 5.0 + - - +
76B TYR* 1.3 78.5 - - - +
78B ARG* 1.3 56.9 + - - +
79B ARG 3.0 3.2 + - - -
80B CYS* 3.6 11.6 + - - +
81B PHE* 3.4 14.0 + - - +
82B GLY 3.3 12.1 - - - +
85B LEU* 4.0 4.6 - - + +
86B GLY* 3.7 7.2 + - - -
89B THR* 3.4 40.2 - - + +
367B TYR* 4.1 19.3 + - + -
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Residues in contact with ARG 78 (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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432A HIS 3.6 4.7 - - - +
433A LYS* 4.2 20.2 - - - +
74B TYR* 2.8 28.8 + - + +
75B ALA* 2.7 18.1 + - - +
77B ALA* 1.3 75.5 - - - +
79B ARG* 1.3 63.8 + - + +
82B GLY* 2.9 40.0 + - - +
83B PRO* 4.9 10.4 - - + +
86B GLY* 4.8 0.2 - - - -
87B TYR* 3.3 21.2 + - - -
307B ASP* 3.3 50.4 + - - +
308B GLY* 4.0 1.0 - - - -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ARG* 5.5 2.3 - - - +
431A LEU 3.8 8.4 - - - +
432A HIS* 3.7 11.4 - - - +
433A LYS* 2.8 31.8 + - + +
434A ASN 5.0 3.8 + - - -
435A PRO* 4.1 16.3 - - - +
67B ASP* 2.4 49.8 + - - +
69B SER 5.5 1.2 + - - -
75B ALA* 3.2 14.2 + - - +
76B TYR* 2.6 13.2 + - - +
78B ARG* 1.3 82.3 - - + +
80B CYS* 1.3 53.6 + - - +
81B PHE 3.1 4.9 - - - +
371B ALA* 5.1 1.6 - - - +
374B LEU* 4.5 8.1 - - - +
375B LEU* 3.2 50.6 - - + +
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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