Contacts of the helix formed by residues 75 - 87 (chain B) in PDB entry 4WAA
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 ASN 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B HIS 3.3 3.2 + - - +
74B VAL* 1.3 78.6 - - - +
76B MET* 1.3 59.3 + - - +
77B SER* 3.0 6.4 + - - -
78B GLU* 2.8 50.3 + - - +
79B LEU* 2.9 25.7 + - - +
107B VAL 3.1 17.0 + - - +
108B SER* 3.7 20.8 + - - +
109B THR 3.4 19.7 - - - +
110B PRO 4.6 0.4 - - - -
111B ILE* 4.6 1.3 - - - +
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 1.3 77.2 - - - +
77B SER* 1.3 59.0 + - - +
79B LEU* 3.6 10.2 - - - +
80B ILE* 2.8 39.0 + - + +
97B LEU* 4.0 33.2 - - + +
99B VAL* 4.1 15.3 - - + -
104B MET* 4.1 21.1 - - + +
106B SER 4.1 12.1 - - - +
107B VAL* 3.5 21.5 + - + -
109B THR 4.2 1.7 + - - +
111B ILE* 4.7 11.4 - - + -
114B VAL* 4.5 15.3 - - + -
127B MET* 3.8 26.5 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.0 4.4 + - - -
76B MET* 1.3 76.6 - - - +
78B GLU* 1.3 64.2 + - - +
80B ILE* 3.5 10.7 + - - +
81B LYS* 3.2 22.2 + - - +
107B VAL* 3.2 35.4 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 4.1 9.7 + - - +
74B VAL* 3.4 19.6 - - + +
75B ASN* 2.8 50.5 + - - +
77B SER* 1.3 71.9 - - - +
79B LEU* 1.3 60.7 + - - +
81B LYS* 3.2 12.1 + - + +
82B ILE* 2.9 37.0 + - + +
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Residues in contact with LEU 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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49B VAL* 5.0 0.7 - - + -
51B ILE* 4.7 8.1 - - + -
70B VAL* 4.6 22.2 - - + -
74B VAL* 3.9 8.1 - - + +
75B ASN 2.9 16.9 + - - +
76B MET* 3.6 9.4 - - - +
78B GLU* 1.3 76.9 - - - +
80B ILE* 1.3 64.3 + - - +
82B ILE* 3.2 15.8 + - + -
83B ILE* 3.0 39.7 + - + +
97B LEU* 4.2 9.9 - - + -
111B ILE* 4.1 16.6 - - + -
127B MET* 3.9 36.3 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 2.8 36.2 + - + +
77B SER* 3.7 10.1 - - - +
78B GLU 3.3 0.2 - - - -
79B LEU* 1.3 72.8 - - - +
81B LYS* 1.3 58.7 + - - +
83B ILE* 3.4 2.0 + - - +
84B ARG* 2.9 46.1 + - - +
95B PHE* 4.0 23.9 - - + +
96B PHE* 6.3 0.4 - - - -
97B LEU* 4.0 35.7 - - + +
107B VAL* 5.1 9.4 - - + -
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Residues in contact with LYS 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 SER 3.2 11.0 + - - +
78B GLU* 3.5 13.9 - - + +
80B ILE* 1.3 77.8 - - - +
82B ILE* 1.3 69.1 + - + +
84B ARG* 3.5 9.7 + - - +
85B ARG* 3.1 53.1 + - - +
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Residues in contact with ILE 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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74B VAL* 4.8 14.6 - - + -
78B GLU* 2.9 25.0 + - + +
79B LEU* 3.2 18.8 + - + +
81B LYS* 1.3 79.6 - - + +
83B ILE* 1.3 66.7 + - + +
85B ARG* 3.2 7.7 + - - +
86B ARG* 3.0 39.0 + - + +
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Residues in contact with ILE 83 (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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51B ILE* 4.0 27.4 - - + -
63B LEU* 4.4 18.8 - - + -
68B PHE* 4.9 5.6 - - + -
79B LEU* 3.0 34.7 + - + +
80B ILE* 3.9 3.4 - - - +
82B ILE* 1.3 75.9 - - + +
84B ARG* 1.3 67.0 + - - +
86B ARG* 3.4 21.2 + - - +
87B LEU* 3.0 37.8 + - + +
95B PHE* 3.7 24.5 - - + -
97B LEU* 4.9 5.2 - - + -
129B TYR* 4.8 6.1 - - + -
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Residues in contact with ARG 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 ILE* 2.9 40.8 + - - +
81B LYS* 3.7 8.7 - - - +
83B ILE* 1.3 76.3 - - - +
85B ARG* 1.3 57.1 + - - +
87B LEU* 3.5 1.2 + - - -
88B GLN 3.1 20.4 + - - -
89B LEU* 3.1 37.9 + - + +
90B ASN 3.0 27.5 + - - -
91B ALA* 3.7 15.4 + - - +
93B GLN 2.9 25.9 + - - -
94B ALA* 4.8 0.2 - - - +
95B PHE* 3.3 37.8 + - + +
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Residues in contact with ARG 85 (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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81B LYS* 3.1 60.7 + - - +
82B ILE* 3.6 6.5 - - - +
83B ILE 3.1 0.2 - - - -
84B ARG* 1.3 75.2 - - - +
86B ARG* 1.3 59.6 - - - +
88B GLN* 2.8 29.9 + - + +
89B LEU 5.2 0.2 - - - +
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Residues in contact with ARG 86 (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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63B LEU* 4.1 18.3 - - + +
64B ASP* 3.2 46.1 + - - +
65B LYS* 4.1 18.0 - - - +
68B PHE* 4.0 20.9 - - - -
82B ILE* 3.0 25.6 + - + +
83B ILE* 3.6 20.9 - - - +
85B ARG* 1.3 76.1 - - - +
87B LEU* 1.3 59.2 + - - +
88B GLN* 3.5 5.5 + - - +
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Residues in contact with LEU 87 (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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60B LEU* 5.3 0.9 - - + -
61B PRO* 3.3 52.6 - - + +
62B VAL 4.1 2.7 - - - +
63B LEU* 3.8 23.3 - - + +
83B ILE* 3.0 37.2 + - + +
84B ARG 3.8 4.3 - - - +
86B ARG* 1.3 74.3 - - - +
88B GLN* 1.3 68.5 + - - +
89B LEU* 3.4 16.8 + - + +
95B PHE* 3.7 21.8 - - + -
129B TYR* 3.5 19.7 - - + +
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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