Contacts of the helix formed by residues 74 - 84 (chain B) in PDB entry 3MAX
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 SER 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR* 4.3 0.2 - - - -
72B TYR 3.8 1.2 + - - -
73B HIS* 1.3 76.3 - - - +
75B ASP* 1.3 65.0 + - - +
76B GLU* 3.6 18.7 + - - +
77B TYR* 3.2 21.3 + - - +
78B ILE* 3.2 20.4 + - - +
99B PHE* 5.1 0.7 - - - -
149B LYS* 3.2 12.0 + - - +
150B SER* 3.2 25.0 + - - -
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.9 27.4 + - + +
73B HIS 3.6 1.5 + - - +
74B SER* 1.3 74.2 - - - +
76B GLU* 1.3 66.9 + - + +
78B ILE* 3.4 1.4 + - - +
79B LYS* 2.9 31.8 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 3.6 15.5 + - - +
75B ASP* 1.3 96.5 + - + +
77B TYR* 1.3 61.5 + - - +
79B LYS* 3.7 6.8 - - - +
80B PHE* 3.0 23.7 + - - +
95B GLN* 5.5 0.2 - - - +
98B ARG* 4.5 13.8 + - - +
99B PHE* 3.9 15.3 - - + -
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.7 17.3 - + - -
74B SER* 3.2 20.6 + - - +
76B GLU* 1.3 78.7 - - - +
78B ILE* 1.3 63.5 + - + +
80B PHE* 3.3 3.5 + + - +
81B LEU* 3.0 49.2 + - + +
99B PHE* 3.5 48.1 - + + -
101B VAL* 4.7 0.7 - - + -
148B LYS 4.2 0.7 - - - -
149B LYS 3.6 15.5 - - - -
150B SER* 3.9 9.4 - - - -
151B GLU* 3.8 5.6 - - - -
152B ALA* 3.2 27.3 + - - +
157B TYR* 2.6 41.1 + - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ALA* 4.0 32.5 - - + -
69B MET* 3.9 25.1 - - + -
70B THR* 4.0 15.0 - - + -
73B HIS* 3.6 30.3 - - + -
74B SER 3.2 15.3 + - - +
75B ASP 4.0 2.7 - - - +
77B TYR* 1.3 81.2 - - + +
79B LYS* 1.3 62.1 + - - +
81B LEU* 3.1 16.6 + - + +
82B ARG* 2.9 29.0 + - + +
112B PHE* 4.2 14.3 - - + -
158B VAL* 4.2 3.6 - - + -
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Residues in contact with LYS 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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75B ASP 2.9 18.5 + - - +
76B GLU* 3.7 7.9 - - - +
78B ILE* 1.3 76.6 - - - +
80B PHE* 1.3 58.9 + - - +
82B ARG* 3.2 15.9 + - + +
83B SER* 2.7 39.3 + - - +
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Residues in contact with PHE 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 GLU 3.0 14.6 + - - +
77B TYR* 3.3 10.1 - + - +
78B ILE 3.2 0.2 - - - -
79B LYS* 1.3 76.3 - - - +
81B LEU* 1.3 72.6 + - + +
83B SER* 3.0 15.1 + - - -
84B ILE* 3.0 49.8 + - + +
92B TYR* 4.1 10.5 - + - -
95B GLN* 3.7 37.9 - - + +
96B MET* 3.9 29.8 - - + -
99B PHE* 3.3 31.2 - + + -
101B VAL* 3.8 29.8 - - + -
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Residues in contact with LEU 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 TYR* 3.0 51.6 + - + +
78B ILE* 3.1 15.9 + - + +
80B PHE* 1.3 90.1 - - + +
82B ARG* 1.3 59.4 + - - +
83B SER 3.2 1.1 + - - -
84B ILE* 3.8 15.0 + - - +
101B VAL* 4.3 2.9 - - + -
111B LEU* 4.5 12.9 - - + +
112B PHE* 3.5 28.7 + - + +
115B CYS* 4.5 5.2 - - - -
157B TYR* 4.1 24.0 - - + -
158B VAL* 3.6 31.4 - - + -
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Residues in contact with ARG 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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66B ALA* 3.3 32.5 - - - +
78B ILE* 2.9 16.4 + - - +
79B LYS* 3.5 14.3 - - - +
80B PHE 3.1 0.2 - - - -
81B LEU* 1.3 76.2 - - - +
83B SER* 1.3 58.8 + - - +
84B ILE 5.3 0.4 - - - -
85B ARG* 6.1 0.3 - - - +
112B PHE* 3.6 39.6 - - + +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS* 2.7 31.7 + - - +
80B PHE* 3.0 5.7 + - - -
82B ARG* 1.3 78.8 - - - +
84B ILE* 1.3 62.4 + - - +
85B ARG* 3.6 13.2 + - - +
88B ASN* 3.0 22.6 + - - -
92B TYR* 3.6 29.5 + - - -
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Residues in contact with ILE 84 (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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80B PHE* 3.0 43.7 + - + +
81B LEU* 3.8 16.5 - - - +
82B ARG 5.3 0.2 - - - -
83B SER* 1.3 76.5 - - - +
85B ARG* 1.3 66.0 + - - +
88B ASN* 3.8 11.4 - - - +
89B MET* 4.2 6.3 - - - -
92B TYR* 3.5 33.7 - - + -
96B MET* 3.8 17.0 - - + -
101B VAL* 4.9 0.4 - - + -
107B VAL* 3.7 24.5 - - + +
108B PHE 5.3 2.4 - - - +
111B LEU* 4.0 26.5 - - + +
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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