Contacts of the helix formed by residues 72 - 82 (chain B) in PDB entry 4M6W
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 TYR 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B VAL* 4.0 25.1 - - + -
65B ASP* 3.3 39.7 - - - +
66B LEU* 4.3 16.1 - - + +
68B ALA* 5.9 1.3 - - - -
69B GLY 3.8 14.8 - - - -
71B GLY* 1.3 78.8 - - - +
73B ARG* 1.3 107.2 + - + +
74B LYS 3.4 2.2 - - - -
75B ARG* 3.1 31.2 + - - +
76B LEU* 3.2 31.3 + - + +
104B LEU* 3.7 33.4 + - + +
107B PHE* 5.1 3.6 - + - -
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Residues in contact with ARG 73 (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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68B ALA* 3.4 32.5 + - - +
69B GLY 3.0 27.2 + - - +
70B ASN* 3.3 38.6 + - - +
71B GLY 3.9 0.2 - - - -
72B TYR* 1.3 109.3 + - + +
74B LYS* 1.3 62.7 + - + +
76B LEU* 3.3 8.8 + - - +
77B VAL* 3.2 26.5 + - - +
107B PHE* 4.3 24.4 - - + -
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Residues in contact with LYS 74 (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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70B ASN* 3.5 28.9 + - - +
72B TYR 3.4 0.4 - - - -
73B ARG* 1.3 77.8 - - + +
75B ARG* 1.3 60.5 + - - +
77B VAL* 3.4 9.4 + - + +
78B ARG* 2.9 49.7 + - + +
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Residues in contact with ARG 75 (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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24B LYS* 6.0 3.2 - - - +
47B THR* 3.5 26.8 + - + +
49B ASP* 3.2 23.7 + - - -
59B LEU* 3.4 33.7 - - + +
60B TYR 3.2 22.4 + - - -
61B VAL* 5.1 1.2 - - - +
65B ASP* 5.8 2.0 + - - -
71B GLY 3.9 17.6 + - - +
72B TYR* 3.1 25.3 + - - +
74B LYS* 1.3 77.1 - - - +
76B LEU* 1.3 60.5 + - - +
78B ARG* 3.3 23.9 + - - +
79B VAL* 3.2 27.0 + - - +
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Residues in contact with LEU 76 (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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59B LEU* 3.8 26.9 - - + -
61B VAL* 5.0 4.0 - - + -
72B TYR* 3.2 37.4 + - + +
73B ARG 3.3 4.7 + - - +
75B ARG* 1.3 77.1 - - + +
77B VAL* 1.3 62.8 + - - +
79B VAL* 3.3 2.8 + - - +
80B ARG 3.1 16.8 + - - -
89B VAL* 3.7 31.9 - - + -
104B LEU* 4.5 3.1 - - + -
107B PHE* 4.0 17.5 - - + -
108B THR* 3.9 21.3 - - + +
112B LEU* 3.7 15.0 - - + -
114B MET* 3.3 14.7 - - + +
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Residues in contact with VAL 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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73B ARG 3.2 17.1 + - - +
74B LYS* 3.7 10.5 - - + +
75B ARG 3.3 0.4 - - - -
76B LEU* 1.3 74.4 - - - +
78B ARG* 1.3 66.6 + - - +
80B ARG* 3.1 10.8 + - + +
81B ASN* 2.9 40.4 + - - +
107B PHE* 4.0 22.2 - - + -
112B LEU* 4.5 8.1 - - + -
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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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47B THR* 3.9 27.6 - - + +
74B LYS* 2.9 26.6 + - + +
75B ARG* 3.5 38.6 - - - +
76B LEU 3.3 0.2 - - - -
77B VAL* 1.3 75.9 - - - +
79B VAL* 1.3 63.0 + - + +
81B ASN* 3.0 26.7 + - - +
82B SER* 3.3 10.0 + - - -
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Residues in contact with VAL 79 (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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47B THR* 5.0 8.5 - - - +
48B PRO* 4.8 6.5 - - + -
57B CYS* 4.1 5.8 - - - -
59B LEU* 3.9 26.2 - - + -
75B ARG 3.2 13.6 + - - +
76B LEU 3.6 7.4 - - - +
78B ARG* 1.3 76.7 - - + +
80B ARG* 1.3 62.1 + - - +
82B SER* 3.3 24.3 + - - +
85B LEU* 3.9 31.8 - - + +
87B GLY* 3.9 30.5 - - - +
114B MET* 4.4 5.4 - - + -
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Residues in contact with ARG 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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76B LEU 3.1 6.8 + - - +
77B VAL* 3.1 15.5 + - + +
79B VAL* 1.3 76.9 - - - +
81B ASN* 1.3 65.9 + - - +
82B SER 3.4 5.9 + - - +
111B ASP 4.3 8.9 + - - -
112B LEU* 3.4 40.4 + - + +
114B MET* 3.7 19.5 - - + +
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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
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77B VAL* 2.9 33.0 + - - +
78B ARG* 3.0 13.8 + - - +
80B ARG* 1.3 81.2 - - - +
82B SER* 1.3 63.9 + - - +
83B ASN* 3.3 5.2 + - - +
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Residues in contact with SER 82 (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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78B ARG 3.3 9.4 + - - -
79B VAL* 3.3 15.0 + - - +
80B ARG 3.3 8.0 - - - +
81B ASN* 1.3 76.0 - - - +
83B ASN* 1.3 65.4 + - - +
84B ASN 3.3 1.6 + - - -
85B LEU* 3.7 36.5 + - - +
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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