Contacts of the helix formed by residues 86 - 106 (chain B) in PDB entry 3KAV
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 TRP 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.8 25.5 - - + +
96A ARG* 3.2 42.8 - - + +
97A TYR* 3.5 26.0 - + - -
79B LEU* 4.0 8.3 - - + -
84B SER* 2.9 27.4 + - - +
85B PRO* 1.3 101.3 - - + +
87B ALA* 1.3 65.7 + - - +
88B PRO* 3.4 2.2 - - - -
89B ALA* 3.0 16.2 + - + +
90B ALA* 2.9 23.4 + - + +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.8 1.4 - - - +
79B LEU* 3.7 33.8 - - - +
80B MSE 4.0 15.9 - - + +
83B ARG* 5.4 0.7 - - - -
84B SER* 3.0 19.0 + - - +
86B TRP* 1.3 77.7 - - - +
88B PRO* 1.3 56.4 - - + +
90B ALA* 3.2 2.1 + - - +
91B CYS* 2.7 41.0 + - - +
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Residues in contact with PRO 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 4.1 1.1 - - - +
85B PRO* 3.6 19.1 - - + +
86B TRP 3.4 0.9 - - - -
87B ALA* 1.3 94.7 - - + +
89B ALA* 1.3 63.7 + - + +
91B CYS* 3.2 11.5 + - + +
92B GLU* 3.2 23.0 + - - +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PRO 5.4 0.7 - - - +
86B TRP* 3.0 25.4 + - + +
88B PRO* 1.3 83.8 - - + +
90B ALA* 1.3 63.3 + - - +
92B GLU* 3.2 13.2 + - - +
93B LEU* 3.3 11.8 + - - +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 5.2 2.0 - - + -
72B LEU* 4.9 1.5 - - - +
75B LEU* 4.5 12.1 - - + -
76B ALA* 3.9 16.9 - - - +
79B LEU* 3.5 31.6 - - + -
86B TRP* 2.9 7.6 + - + +
87B ALA 3.7 2.0 - - - +
89B ALA* 1.3 76.5 - - - +
91B CYS* 1.3 62.4 + - - +
93B LEU* 3.3 10.7 + - - +
94B ALA* 3.0 25.1 + - - +
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS* 4.3 12.8 - - - -
76B ALA* 3.9 15.0 - - - +
80B MSE 3.9 37.5 - - - -
87B ALA 2.7 22.6 + - - +
88B PRO* 3.3 11.7 - - + +
89B ALA 3.1 0.2 - - - -
90B ALA* 1.3 78.1 - - - +
92B GLU* 1.3 57.2 + - - +
94B ALA* 3.5 2.9 + - - +
95B ALA* 3.0 26.9 + - - +
122B PHE* 3.9 7.4 - - - -
126B CYS* 4.1 10.5 - - + -
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Residues in contact with GLU 92 (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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88B PRO 3.2 8.4 + - - +
89B ALA* 3.2 8.9 + - - +
90B ALA 3.2 0.2 - - - -
91B CYS* 1.3 76.0 - - - +
93B LEU* 1.3 61.2 + - - +
94B ALA 3.1 0.2 - - - -
95B ALA* 3.1 7.4 + - + +
96B ARG* 2.9 30.0 + - + +
126B CYS* 5.9 1.1 - - - -
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Residues in contact with LEU 93 (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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86A TRP* 4.4 17.3 - - + -
89A ALA* 5.9 4.9 - - + -
72B LEU* 3.6 23.2 - - + +
75B LEU* 6.2 2.9 - - + -
89B ALA 3.3 9.1 + - - +
90B ALA* 3.3 12.9 + - - +
92B GLU* 1.3 78.1 - - - +
94B ALA* 1.3 60.9 + - - +
96B ARG* 3.5 10.9 - - - +
97B TYR* 3.4 44.4 + - + -
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Residues in contact with ALA 94 (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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69B CYS* 4.5 3.1 - - - -
72B LEU* 3.8 37.8 - - + +
73B CYS* 4.1 5.2 - - - +
76B ALA* 4.3 2.7 - - + -
90B ALA 3.0 16.6 + - - +
91B CYS 3.7 4.9 - - - +
93B LEU* 1.3 76.4 - - - +
95B ALA* 1.3 53.3 + - - +
97B TYR* 3.3 3.8 + - - +
98B ALA* 2.7 34.3 + - - +
122B PHE* 3.6 18.6 - - + -
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Residues in contact with ALA 95 (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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91B CYS 3.0 17.7 + - - +
92B GLU* 3.1 10.3 + - + +
94B ALA* 1.3 73.2 - - - +
96B ARG* 1.3 66.8 + - - +
98B ALA* 3.3 4.3 - - - +
99B LEU* 3.1 26.3 + - - +
122B PHE* 3.4 10.0 - - + -
123B VAL* 3.7 19.6 - - + +
126B CYS* 4.0 20.9 - - + -
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Residues in contact with ARG 96 (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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92B GLU* 2.9 13.2 + - + +
93B LEU* 3.5 17.0 - - - +
94B ALA 3.2 0.2 - - - -
95B ALA* 1.3 76.8 - - - +
97B TYR* 1.3 78.3 + - + +
99B LEU* 3.1 32.7 - - + +
100B ALA* 3.1 13.0 + - + +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 3.3 34.3 - + - -
65B HIS* 4.7 11.0 - + - +
68B ASP* 3.7 28.3 - - + -
69B CYS* 3.8 13.7 - - - +
72B LEU* 3.5 20.2 - - + -
93B LEU* 3.4 27.6 + - + -
94B ALA 3.3 4.1 + - - +
96B ARG* 1.3 95.9 + - + +
98B ALA* 1.3 60.5 + - - +
99B LEU 3.3 0.2 - - - -
100B ALA* 3.7 12.0 - - + +
101B CYS* 2.9 30.5 + - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B CYS* 3.4 18.4 - - - -
94B ALA 2.7 17.0 + - - +
95B ALA* 3.1 8.0 + - - +
97B TYR* 1.3 80.1 - - - +
99B LEU* 1.3 60.2 + - - +
102B ALA 3.3 5.0 + - - -
119B CYS* 2.8 36.1 - - + +
122B PHE* 3.5 27.6 - - + -
123B VAL* 3.6 8.3 - - + -
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Residues in contact with LEU 99 (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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95B ALA 3.1 16.0 + - - +
96B ARG* 3.1 21.1 - - + +
98B ALA* 1.3 72.8 - - - +
100B ALA* 1.3 75.4 + - + +
101B CYS 3.0 1.8 - - - -
102B ALA* 3.0 8.7 + - - +
103B GLU* 2.9 60.0 + - + +
119B CYS* 5.1 0.9 - - - -
120B ARG* 6.3 1.6 - - - +
123B VAL* 4.3 19.5 - - + +
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Residues in contact with ALA 100 (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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65B HIS* 3.5 26.5 - - + +
96B ARG* 3.1 16.0 + - + +
97B TYR* 3.9 13.5 - - + +
99B LEU* 1.3 87.7 - - + +
101B CYS* 1.3 60.3 + - - +
103B GLU* 3.6 13.3 + - - +
104B ARG* 3.3 22.1 + - - +
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Residues in contact with CYS 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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48B CYS* 4.1 3.8 - - - -
65B HIS* 3.9 19.3 - - - +
66B ALA* 3.7 24.2 - - - -
69B CYS* 4.1 2.5 - - + -
97B TYR 2.9 19.9 + - - +
98B ALA 3.6 6.3 - - - +
100B ALA* 1.3 75.6 - - - +
102B ALA* 1.3 55.1 + - - +
104B ARG 4.6 0.2 - - - +
105B CYS* 2.7 46.6 + - - +
115B CYS* 3.7 21.1 - - - -
119B CYS* 3.6 18.6 - - - -
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Residues in contact with ALA 102 (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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98B ALA 3.3 10.1 + - - +
99B LEU* 3.0 11.3 + - - +
101B CYS* 1.3 78.2 - - - +
103B GLU* 1.3 64.1 + - + +
106B ASP* 3.1 30.0 + - - +
116B ALA* 3.8 37.5 - - + +
119B CYS* 4.1 2.4 - - + -
120B ARG* 4.2 23.7 + - + +
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Residues in contact with GLU 103 (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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99B LEU* 2.9 52.0 + - + +
100B ALA* 3.8 11.6 - - - +
102B ALA* 1.3 76.5 - - + +
104B ARG* 1.3 61.6 + - + +
106B ASP* 4.9 1.3 + - - +
120B ARG* 5.7 2.9 - - - +
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Residues in contact with ARG 104 (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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61B GLU* 2.7 31.0 + - + +
62B GLN* 2.7 36.7 + - + +
65B HIS* 2.8 53.8 + - + +
100B ALA* 3.3 15.0 + - - +
101B CYS 4.0 1.6 - - - +
102B ALA 3.1 0.4 - - - -
103B GLU* 1.3 83.3 - - - +
105B CYS* 1.3 57.4 + - - +
106B ASP 3.6 3.6 + - - +
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Residues in contact with CYS 105 (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 TYR* 3.6 30.3 - - + -
62B GLN* 3.2 42.8 - - - +
65B HIS* 4.3 4.7 - - - -
66B ALA 4.4 0.2 - - - -
101B CYS* 2.7 34.2 + - - +
102B ALA* 4.1 0.4 - - - -
104B ARG* 1.3 73.2 - - - +
106B ASP* 1.3 62.1 + - - +
112B GLU* 3.5 26.9 - - - +
115B CYS* 4.3 13.9 - - - +
116B ALA* 4.8 1.6 - - - -
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Residues in contact with ASP 106 (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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62B GLN* 5.5 1.2 + - - -
102B ALA 3.1 21.0 + - - +
103B GLU 4.9 1.7 - - - +
104B ARG 3.6 4.3 - - - +
105B CYS* 1.3 78.5 - - - +
107B GLY* 1.3 69.8 + - - +
112B GLU* 3.4 9.7 - - - +
113B ARG* 3.5 13.2 - - - +
116B ALA* 3.3 22.1 - - + +
120B ARG* 4.1 14.8 + - - +
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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