Contacts of the helix formed by residues 72 - 81 (chain Z) in PDB entry 5L4K
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 ARG 72 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Z THR* 3.4 17.8 + - + +
71Z TYR* 1.3 85.7 - - + +
73Z PRO* 1.3 69.4 - - + +
74Z ALA 3.2 1.1 - - - -
75Z LEU* 3.1 19.8 + - - +
76Z GLU* 2.9 65.4 + - + +
79Z ARG* 5.2 2.0 - - - +
100Z ARG* 4.1 22.4 - - - +
102Z HIS* 3.7 28.8 + - + +
105Z LYS* 5.0 7.6 - - + -
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Residues in contact with PRO 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Z LYS* 3.6 20.0 - - + -
31Z LYS* 6.2 0.9 - - + -
59Z LEU* 5.6 0.2 - - - -
68Z THR 4.1 1.3 - - - +
69Z SER* 3.1 31.0 - - - +
72Z ARG* 1.3 94.6 - - + +
74Z ALA* 1.3 57.4 + - - +
76Z GLU 4.6 0.2 - - - +
77Z GLU* 2.9 47.9 + - + +
105Z LYS* 3.9 30.9 - - - +
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Residues in contact with ALA 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Z LYS* 4.3 4.8 - - - +
59Z LEU* 3.4 47.7 - - + +
62Z ARG* 4.2 9.0 - - + -
63Z LEU* 4.1 11.7 - - + +
70Z LEU 3.1 24.5 + - - +
71Z TYR 4.5 0.9 - - - +
72Z ARG 3.2 0.8 - - - -
73Z PRO* 1.3 79.1 - - - +
75Z LEU* 1.3 57.1 + - - +
78Z LEU* 3.3 21.5 - - - +
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Residues in contact with LEU 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Z LEU* 3.7 24.0 - - + -
71Z TYR* 3.7 19.8 + - + +
72Z ARG* 3.1 31.4 + - - +
74Z ALA* 1.3 77.0 - - - +
76Z GLU* 1.3 66.9 + - - +
77Z GLU 3.3 0.9 - - - -
78Z LEU* 3.0 19.5 + - + +
79Z ARG* 3.1 50.8 + - - +
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Residues in contact with GLU 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Z ARG* 2.9 61.5 + - + +
73Z PRO* 4.6 1.1 - - + +
75Z LEU* 1.3 74.4 - - + +
77Z GLU* 1.3 57.7 + - - +
79Z ARG* 3.0 31.1 + - - +
80Z ARG* 2.9 55.0 + - - +
99Z LEU* 2.9 24.2 - - - +
100Z ARG 3.0 19.9 + - - +
102Z HIS* 4.0 8.7 + - - +
105Z LYS* 4.8 3.8 - - + -
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Residues in contact with GLU 77 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Z LYS* 5.4 4.3 - - - +
31Z LYS* 3.1 35.9 + - - +
34Z ARG* 4.0 22.3 + - - -
39Z LYS* 5.4 7.0 - - - +
59Z LEU* 4.1 6.4 - - + +
73Z PRO* 2.9 32.8 + - + +
76Z GLU* 1.3 72.4 - - - +
78Z LEU* 1.3 59.3 + - - +
79Z ARG 3.2 0.2 - - - -
80Z ARG* 3.6 26.7 - - + +
81Z GLN* 2.9 51.4 + - + +
105Z LYS* 3.9 10.0 + - - -
109Z ILE* 5.2 2.2 - - + -
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Residues in contact with LEU 78 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Z LEU* 5.0 9.6 - - + +
55Z GLU 4.4 1.1 - - - +
56Z LEU* 3.8 40.8 - - + +
59Z LEU* 3.7 18.8 - - + +
60Z VAL* 4.1 25.6 - - + -
63Z LEU* 5.8 3.8 - - + -
74Z ALA 3.3 16.5 + - - +
75Z LEU* 3.0 16.7 + - + +
77Z GLU* 1.3 76.9 - - - +
79Z ARG* 1.3 60.8 + - + +
81Z GLN* 4.6 1.5 - - - +
82Z ILE* 3.8 19.6 + - - +
95Z PRO* 5.2 0.2 - - - +
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Residues in contact with ARG 79 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Z ARG* 5.2 1.8 - - - +
75Z LEU* 3.1 46.7 + - + +
76Z GLU* 3.0 30.8 + - - +
78Z LEU* 1.3 79.0 - - + +
80Z ARG* 1.3 58.8 + - - +
81Z GLN 3.6 0.4 - - - -
82Z ILE* 3.4 17.7 - - - +
83Z ARG* 3.8 9.0 - - - +
95Z PRO* 3.4 33.1 - - + +
98Z PHE* 3.3 42.1 + - + +
99Z LEU* 3.8 18.9 - - + +
100Z ARG* 4.2 3.0 - - - +
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Residues in contact with ARG 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z LYS* 6.2 1.3 - - - +
76Z GLU* 2.9 46.0 + - - +
77Z GLU* 3.4 17.8 + - + +
79Z ARG* 1.3 76.5 - - - +
81Z GLN* 1.3 62.6 + - + +
82Z ILE 3.4 2.0 + - - -
83Z ARG* 3.4 40.7 + - - +
84Z SER* 4.1 9.4 + - - -
99Z LEU* 3.4 18.1 - - + +
102Z HIS* 5.3 1.2 - - - -
105Z LYS* 3.1 51.1 + - - +
106Z LEU* 3.6 32.6 - - - +
109Z ILE* 3.7 30.3 - - + +
115Z PRO* 4.8 1.7 - - - +
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Residues in contact with GLN 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z LYS* 3.7 17.7 + - - +
34Z ARG* 3.5 30.6 + - - +
39Z LYS* 3.9 26.2 - - + +
52Z LEU* 3.5 13.4 - - + +
55Z GLU* 3.3 24.5 + - - +
59Z LEU* 3.8 17.0 - - - +
77Z GLU* 2.9 31.6 + - + +
78Z LEU* 4.6 2.0 - - + -
80Z ARG* 1.3 77.7 - - + +
82Z ILE* 1.3 58.4 + - - +
83Z ARG 3.3 1.6 - - - -
84Z SER* 4.2 7.6 - - - +
85Z SER* 3.1 24.9 + - - -
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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
------------------------------------------------------------
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