Contacts of the helix formed by residues 86 - 106 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU* 3.9 8.1 - - + +
84C SER* 3.1 7.2 + - - +
85C PRO* 1.3 94.5 - - + +
87C ALA* 1.3 64.5 + - - +
88C PRO* 3.4 3.1 - - - -
89C ALA* 3.5 4.0 + - - +
90C ALA* 3.2 20.4 + - - +
65D HIS* 3.7 64.7 + + + -
68D ASP* 3.6 25.1 - - + -
69D CYS* 4.0 7.2 - - - -
72D LEU* 4.0 7.0 - - + -
93D LEU* 5.5 0.7 - - - +
97D TYR* 3.3 82.0 - + + -
100D ALA* 3.9 9.8 - - + +
101D CYS* 4.5 1.8 - - + -
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 4.9 9.4 - - - +
79C LEU* 3.8 32.8 - - - +
80C MSE 4.1 18.4 - - + -
84C SER* 3.2 17.9 + - - +
86C TRP* 1.3 75.5 - - - +
88C PRO* 1.3 66.8 - - + +
90C ALA* 2.9 4.9 + - - +
91C CYS* 2.7 32.4 + - - -
129C LEU* 6.0 0.2 - - + -
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Residues in contact with PRO 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 5.9 1.6 - - - +
84C SER 4.3 1.3 - - - +
85C PRO* 3.5 17.9 - - + +
86C TRP* 3.5 1.6 - - - -
87C ALA* 1.3 93.2 - - + +
89C ALA* 1.3 63.5 + - + +
91C CYS* 3.1 8.7 + - + +
92C GLU* 2.9 23.9 + - - +
129C LEU* 3.1 34.4 - - + +
130C LEU* 5.0 0.3 - - - +
131C PRO* 4.0 19.7 - - + +
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TRP* 3.5 4.7 + - - +
87C ALA 3.2 0.4 - - - -
88C PRO* 1.3 82.9 - - + +
90C ALA* 1.3 63.0 + - - +
92C GLU* 3.3 18.4 + - - +
93C LEU* 3.4 8.1 + - - +
131C PRO* 4.7 8.2 - - + +
93D LEU* 3.6 14.6 - - + +
96D ARG* 5.5 2.0 - - - +
97D TYR* 3.2 40.8 - - + +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU 5.4 0.2 - - - +
75C LEU* 4.5 11.7 - - + +
76C ALA* 4.2 15.5 - - + -
79C LEU* 3.4 32.5 - - + -
86C TRP 3.2 2.7 + - - +
87C ALA 2.9 9.3 + - - +
89C ALA* 1.3 79.6 - - - +
91C CYS* 1.3 63.0 + - - +
93C LEU* 3.1 4.5 + - - +
94C ALA* 3.0 23.4 + - - +
72D LEU* 5.3 0.4 - - + -
93D LEU* 3.9 13.2 - - + +
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Residues in contact with CYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C CYS* 4.0 8.5 - - - -
76C ALA* 4.2 14.1 - - - -
80C MSE 3.5 44.9 - - - -
87C ALA 2.7 20.7 + - - +
88C PRO* 3.5 11.9 - - + +
90C ALA* 1.3 72.6 - - - +
92C GLU* 1.3 56.8 + - - +
94C ALA* 3.9 1.7 - - - +
95C ALA* 2.8 33.4 + - - +
126C CYS* 3.7 19.6 - - + +
129C LEU* 5.1 3.8 - - + -
130C LEU* 4.7 5.2 - - + -
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PRO 2.9 12.1 + - - +
89C ALA* 3.5 13.3 - - - +
90C ALA 3.1 0.4 - - - -
91C CYS* 1.3 78.3 - - - +
93C LEU* 1.3 58.8 + - - +
95C ALA* 3.7 2.5 - - - +
96C ARG* 3.0 29.1 + - + +
130C LEU* 4.2 24.5 - - + +
131C PRO* 4.5 20.7 - - + +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 3.5 25.1 - - + -
89C ALA 3.4 1.0 + - - +
90C ALA 3.1 7.6 + - - +
92C GLU* 1.3 79.6 + - - +
94C ALA* 1.3 66.4 + - - +
96C ARG* 3.4 7.5 + - - +
97C TYR* 3.2 60.9 + - + -
75D LEU* 5.5 1.3 - - + -
86D TRP 5.8 0.2 - - - +
89D ALA* 3.5 32.8 - - + +
90D ALA* 4.2 5.8 - - + +
93D LEU* 3.6 33.2 - - + -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C CYS* 5.2 0.3 - - - -
72C LEU* 3.7 42.0 - - + +
73C CYS* 4.4 1.7 - - - +
76C ALA* 4.2 4.7 - - + -
90C ALA 3.0 15.7 + - - +
91C CYS 3.9 0.7 - - - +
93C LEU* 1.3 76.2 - - - +
95C ALA* 1.3 53.8 + - - +
97C TYR* 3.4 1.2 + - - +
98C ALA* 2.7 37.1 + - - +
122C PHE* 3.5 25.7 - - + -
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C CYS 2.8 20.2 + - - +
92C GLU* 3.7 5.8 - - - +
94C ALA* 1.3 75.3 - - - +
96C ARG* 1.3 58.9 + - - +
98C ALA* 4.1 1.8 - - - -
99C LEU* 2.8 34.1 + - - +
122C PHE* 3.6 8.7 - - - -
123C VAL* 3.6 19.6 - - + +
126C CYS* 3.9 21.8 - - + -
130C LEU* 5.2 4.9 - - + -
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Residues in contact with ARG 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 3.0 20.1 + - + +
93C LEU* 3.6 8.1 - - - +
95C ALA* 1.3 75.8 - - - +
97C TYR* 1.3 91.5 + - + +
99C LEU* 3.6 13.6 - - + +
100C ALA* 3.2 22.0 + - - +
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Residues in contact with TYR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C CYS* 4.5 2.0 - - - -
72C LEU* 3.5 24.5 - - + -
93C LEU* 3.2 49.3 + - + +
94C ALA 4.2 0.2 - - - +
96C ARG* 1.3 104.0 + - - +
98C ALA* 1.3 61.8 + - - +
99C LEU 3.1 1.6 - - - -
100C ALA* 3.6 8.6 - - + +
101C CYS* 2.9 28.1 + - - +
86D TRP* 3.3 61.4 - + + -
89D ALA* 3.1 28.8 - - + +
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C CYS* 3.6 23.3 - - - -
94C ALA 2.7 23.4 + - - +
95C ALA 3.6 3.8 - - - +
97C TYR* 1.3 73.8 - - - +
99C LEU* 1.3 58.4 + - - +
101C CYS* 3.3 1.2 + - - +
102C ALA 2.9 24.1 + - - -
119C CYS* 3.3 20.0 - - + +
122C PHE* 3.6 25.1 - - + -
123C VAL* 3.8 7.9 - - + -
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA 2.8 16.9 + - - +
96C ARG* 3.6 12.1 - - + +
98C ALA* 1.3 75.5 - - - +
100C ALA* 1.3 58.7 + - - +
102C ALA* 3.4 5.1 + - + +
103C GLU* 3.0 60.2 + - + +
120C ARG* 4.6 15.7 - - + +
123C VAL* 3.8 20.6 - - + +
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Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 4.5 1.1 - - - -
96C ARG 3.2 13.8 + - - +
97C TYR* 3.7 14.8 - - + +
98C ALA 3.3 0.2 - - - -
99C LEU* 1.3 80.6 - - - +
101C CYS* 1.3 61.5 + - - +
103C GLU* 3.5 12.8 + - - +
104C ARG* 3.2 51.0 + - - +
86D TRP* 4.2 11.0 - - + -
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Residues in contact with CYS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C CYS* 4.4 0.4 - - - -
65C HIS* 4.1 15.0 - - + +
66C ALA* 3.8 31.0 - - - -
69C CYS* 4.1 11.4 - - + -
97C TYR 2.9 17.4 + - - +
98C ALA 3.4 6.3 - - - +
100C ALA* 1.3 75.3 - - - +
102C ALA* 1.3 57.3 + - - +
103C GLU 3.0 1.6 - - - -
104C ARG 3.0 2.1 + - - -
105C CYS* 2.7 51.1 + - - +
115C CYS* 4.2 7.9 - - - -
119C CYS* 3.9 16.2 - - - -
86D TRP* 4.7 0.4 - - + -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ALA 2.9 17.5 + - - +
99C LEU* 3.8 6.7 - - - +
101C CYS* 1.3 76.2 - - - +
103C GLU* 1.3 60.3 + - - +
105C CYS* 5.1 0.4 - - - -
106C ASP* 3.3 27.8 + - - +
116C ALA* 3.7 25.4 - - - +
119C CYS* 3.6 18.6 - - + -
120C ARG* 3.6 25.5 + - + +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 3.0 48.2 + - + +
100C ALA* 3.7 14.4 - - - +
101C CYS 3.0 0.4 - - - -
102C ALA* 1.3 80.1 - - - +
104C ARG* 1.3 73.4 + - - +
106C ASP* 4.4 5.7 + - - +
120C ARG* 3.9 19.3 + - - +
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Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 6.5 0.7 - - + -
62C GLN* 2.7 37.9 + - + +
65C HIS* 2.7 48.4 + - + +
100C ALA* 3.2 33.0 + - - +
101C CYS 3.0 3.1 + - - +
103C GLU* 1.3 94.8 + - - +
105C CYS* 1.3 51.9 + - - +
106C ASP 3.7 1.8 - - - +
86D TRP* 4.2 10.7 - - - +
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Residues in contact with CYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.8 21.3 + - + -
62C GLN* 3.4 47.2 + - - +
65C HIS* 4.6 3.8 - - - -
66C ALA* 4.4 1.1 - - - -
101C CYS* 2.7 36.1 + - - +
102C ALA* 5.1 1.3 - - - +
104C ARG* 1.3 74.3 - - - +
106C ASP* 1.3 65.5 + - - +
112C GLU* 3.5 25.0 - - - +
115C CYS* 4.3 16.2 - - - -
116C ALA* 5.0 0.9 - - - +
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Residues in contact with ASP 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN* 5.1 2.6 + - - -
102C ALA 3.3 19.9 + - - +
103C GLU 4.4 5.6 + - - +
104C ARG 3.7 2.8 - - - +
105C CYS* 1.3 79.6 - - - +
107C GLY* 1.3 70.2 + - - +
112C GLU 3.9 5.8 - - - -
113C ARG* 3.6 17.7 - - - +
116C ALA* 3.4 20.7 - - + +
120C ARG* 4.0 10.7 + - - +
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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
------------------------------------------------------------
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