Contacts of the helix formed by residues 86 - 104 (chain B) in PDB entry 6W4E
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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 5.3 1.6 - - - +
14B VAL* 5.6 1.1 - - + -
83B ALA* 3.0 21.2 + - + +
84B ILE 3.4 1.0 - - - -
85B ASN* 1.3 83.5 + - - +
87B THR* 1.3 62.3 + - - +
88B LYS* 3.3 13.0 + - - +
89B SER* 2.7 64.0 + - - +
90B PHE* 3.5 3.6 + - - +
124B THR* 3.5 0.6 + - - -
125B VAL* 4.6 0.9 - - - -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN* 1.3 73.3 - - - +
88B LYS* 1.3 62.4 + - - +
90B PHE* 3.1 10.9 + - + +
91B GLU* 3.1 34.2 + - + +
124B THR* 4.0 24.0 + - + +
125B VAL* 4.2 20.0 - - + -
129B GLN* 5.7 3.8 - - - +
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN* 3.2 13.5 + - - +
87B THR* 1.3 78.0 + - - +
89B SER* 1.3 58.4 + - - +
91B GLU* 3.0 20.3 + - + +
92B ASP* 2.6 68.1 + - - +
95B HIS* 5.3 6.7 + - - -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.8 19.9 + - - +
14B VAL* 3.6 26.9 - - - -
81B VAL 5.2 0.2 - - - -
82B PHE* 3.5 5.9 - - - +
83B ALA 3.0 22.2 + - - -
86B ASN* 2.7 37.6 + - - +
88B LYS* 1.3 72.9 - - - +
90B PHE* 1.3 57.0 + - - +
92B ASP* 3.6 4.4 + - - +
93B ILE* 3.1 30.3 + - - +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 3.7 25.4 - + + -
86B ASN 3.5 0.4 + - - +
87B THR* 3.1 16.1 + - + +
88B LYS 3.0 0.4 - - - -
89B SER* 1.3 80.7 + - - +
91B GLU* 1.3 69.4 - - + +
93B ILE* 3.6 17.4 - - + +
94B HIS 4.3 1.6 + - - -
113B LEU* 5.1 3.6 - - + -
125B VAL* 3.7 38.6 - - + -
129B GLN* 3.9 36.8 - - + -
130B ALA* 3.8 22.7 - - + -
133B LEU* 3.9 34.4 - - + +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR* 3.1 24.1 + - + +
88B LYS* 3.0 23.3 + - - +
90B PHE* 1.3 81.3 - - + +
92B ASP* 1.3 67.0 + - - +
93B ILE 3.1 2.2 - - - -
94B HIS* 3.0 25.4 + - - +
95B HIS* 3.4 13.8 + - + +
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 5.0 12.2 - - + +
62B GLU* 5.0 10.9 - - - +
88B LYS* 2.6 54.3 + - - +
89B SER* 3.7 11.8 - - - +
91B GLU* 1.3 77.4 - - - +
93B ILE* 1.3 56.9 + - + +
95B HIS* 3.2 14.8 + - - +
96B TYR* 2.9 52.9 + - + -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL 5.3 0.4 - - - -
10B GLY* 4.6 12.1 - - - -
80B CYS* 3.6 43.1 - - + -
81B VAL 4.1 17.5 - - - +
82B PHE* 4.1 16.2 - - + -
89B SER 3.1 20.4 - - - +
90B PHE* 3.6 12.1 - - + +
91B GLU 3.1 0.2 - - - -
92B ASP* 1.3 78.1 - - - +
94B HIS* 1.3 57.1 + - - +
96B TYR* 3.2 8.0 + - + +
97B ARG* 2.9 30.3 + - + +
113B LEU* 3.8 13.0 - - + -
133B LEU* 5.8 3.4 - - + -
137B TYR* 5.5 10.5 - - + -
139B ILE* 6.0 0.9 - - + -
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Residues in contact with HIS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE 4.3 1.2 + - - -
91B GLU* 3.0 14.5 + - - +
93B ILE* 1.3 80.1 - - - +
95B HIS* 1.3 87.4 + + - +
97B ARG* 3.3 6.4 + - - +
98B GLU* 3.1 43.3 + - + +
133B LEU* 5.3 8.9 - - + +
137B TYR* 3.5 27.9 + - - +
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Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 5.3 6.8 + - - -
91B GLU* 3.4 25.0 + - + +
92B ASP* 3.2 13.3 + - - +
94B HIS* 1.3 93.5 - + - +
96B TYR* 1.3 65.7 + - + +
98B GLU* 3.3 8.4 + - - +
99B GLN* 3.0 23.8 + - - +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.6 35.4 - - + -
10B GLY* 2.7 41.4 + - - -
11B ALA* 5.3 0.4 - - - -
59B ALA 4.4 2.4 + - - -
60B GLY* 4.1 7.8 - - - -
68B ARG* 3.3 50.9 + - - +
72B MET* 3.9 15.7 - - + +
80B CYS* 5.8 2.2 - - - -
92B ASP* 2.9 43.3 + - + +
93B ILE* 3.2 16.1 + - + +
95B HIS* 1.3 78.0 - - + +
97B ARG* 1.3 62.4 + - - +
99B GLN* 3.2 8.7 + - - +
100B ILE* 3.0 29.5 + - + +
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Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS* 6.1 2.4 - - - -
93B ILE* 2.9 14.1 + - + +
94B HIS* 3.6 10.4 + - - +
95B HIS 3.3 0.2 - - - -
96B TYR* 1.3 76.9 - - - +
98B GLU* 1.3 79.6 + - - +
100B ILE* 3.1 13.8 + - - +
101B LYS* 3.0 50.6 + - + +
107B GLU* 4.5 17.8 + - - +
111B MET* 3.9 30.4 - - + +
136B SER 4.9 3.2 + - - -
137B TYR* 3.3 60.4 + - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 3.1 36.8 + - + +
95B HIS* 3.3 11.2 + - - +
97B ARG* 1.3 91.8 + - - +
99B GLN* 1.3 62.1 + - - +
101B LYS* 3.4 34.3 + - - +
102B ARG* 3.2 21.2 + - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 4.3 7.1 + - - +
68B ARG* 2.8 51.8 + - - +
69B ASP* 2.6 29.2 + - - +
72B MET* 3.5 19.2 - - - +
95B HIS 3.0 12.1 + - - +
96B TYR* 3.5 12.0 - - - +
97B ARG 3.2 0.2 - - - -
98B GLU* 1.3 75.8 - - - +
100B ILE* 1.3 57.2 + - - +
102B ARG* 3.0 29.1 + - - +
103B VAL* 2.9 34.2 + - + +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.2 4.7 - - + -
72B MET* 3.7 24.2 - - + -
78B PHE* 3.8 49.6 - - + -
80B CYS* 5.2 5.2 - - - -
96B TYR* 3.0 21.4 + - + +
97B ARG* 3.1 16.8 + - - +
99B GLN* 1.3 75.9 - - - +
101B LYS* 1.3 64.0 + - + +
103B VAL* 4.6 1.6 - - - +
104B LYS* 3.1 29.3 + - + +
106B SER 4.5 0.2 - - - +
109B VAL* 3.9 25.4 - - + -
111B MET* 4.0 14.8 - - + -
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Residues in contact with LYS 101 (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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97B ARG* 3.0 39.4 + - + +
98B GLU* 3.5 38.3 + - - +
99B GLN 3.3 0.2 - - - -
100B ILE* 1.3 78.5 - - + +
102B ARG* 1.3 57.4 + - - +
105B ASP* 3.0 26.8 - - - +
106B SER 3.4 19.1 + - - +
107B GLU* 2.6 49.4 + - + +
109B VAL* 5.8 0.9 - - + -
111B MET* 6.1 2.0 - - + -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER 5.5 0.2 + - - -
69B ASP* 3.1 36.3 + - - -
98B GLU 3.2 10.8 + - - +
99B GLN* 3.0 34.1 + - - +
101B LYS* 1.3 77.9 - - - +
103B VAL* 1.3 67.8 + - - +
105B ASP* 3.2 16.1 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 3.2 63.3 - - + +
72B MET* 3.8 18.2 - - + +
73B ARG* 3.7 41.8 + - + +
99B GLN* 2.9 21.0 + - + +
100B ILE 4.1 2.5 - - - +
102B ARG* 1.3 80.0 - - - +
104B LYS* 1.3 59.8 + - + +
105B ASP* 4.5 1.7 - - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET 3.4 20.4 - - - +
73B ARG* 3.0 27.6 + - - +
74B THR 4.6 0.6 + - - -
75B GLY 2.7 26.9 + - - +
76B GLU* 4.6 6.2 - - - +
78B PHE* 3.9 13.7 - - + -
100B ILE* 3.1 13.1 + - + +
103B VAL* 1.3 77.2 - - + +
105B ASP* 1.3 64.3 + - - +
106B SER* 2.8 29.0 + - - +
109B VAL* 4.1 22.9 - - + -
110B PRO* 6.1 0.4 - - - -
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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
------------------------------------------------------------
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