Contacts of the helix formed by residues 109 - 127 (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 GLU 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C CYS* 4.3 9.2 - - - -
56C THR* 5.4 3.0 + - - -
57C GLU* 2.6 44.7 + - - +
108C ASP* 1.3 78.4 - - + +
110C PRO* 1.3 70.3 - - + +
111C LEU* 3.4 9.4 - - + +
112C GLU* 2.8 29.3 + - + +
113C ARG* 3.0 22.7 + - - +
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Residues in contact with PRO 110 (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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108C ASP 3.6 1.5 - - - +
109C GLU* 1.3 86.5 - - + +
111C LEU* 1.3 59.6 + - + +
113C ARG* 3.1 29.1 + - - +
114C GLU* 2.7 53.1 + - - +
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Residues in contact with LEU 111 (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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47C ALA 5.1 1.1 - - - +
50C ARG* 3.7 40.8 - - + +
51C TYR* 3.7 10.3 - - + +
54C LEU* 3.4 46.2 - - + +
55C CYS* 3.6 17.3 - - + +
109C GLU* 3.4 7.1 - - + +
110C PRO* 1.3 82.6 - - + +
112C GLU* 1.3 61.1 + - + +
114C GLU* 3.6 14.9 + - + +
115C CYS* 3.2 22.3 + - - +
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Residues in contact with GLU 112 (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* 4.0 8.1 - - + -
55C CYS* 4.0 20.4 - - - -
57C GLU* 3.6 18.2 - - - +
62C GLN* 6.4 0.2 - - - +
105C CYS 3.5 19.5 - - - +
106C ASP* 3.8 5.7 - - - +
107C GLY* 3.3 17.8 - - - +
108C ASP 3.0 11.6 + - - -
109C GLU* 2.8 52.1 + - + +
110C PRO 3.1 0.4 - - - -
111C LEU* 1.3 75.4 - - - +
113C ARG* 1.3 65.7 + - - +
115C CYS* 3.3 3.3 + - - +
116C ALA* 3.2 18.4 + - - +
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Residues in contact with ARG 113 (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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106C ASP* 3.6 11.4 - - - +
107C GLY 3.2 20.9 - - - +
108C ASP* 3.2 19.2 + - - +
109C GLU 3.0 6.0 + - - +
110C PRO* 3.3 31.1 - - - +
112C GLU* 1.3 75.1 - - - +
114C GLU* 1.3 67.1 + - - +
115C CYS 3.3 0.2 + - - -
116C ALA* 3.4 1.9 + - - +
117C GLY* 2.8 28.6 + - - -
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Residues in contact with GLU 114 (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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47C ALA* 3.8 8.3 - - + +
50C ARG* 5.3 12.8 + - - +
110C PRO* 2.7 49.7 + - - +
111C LEU* 3.6 18.9 + - + +
113C ARG* 1.3 82.9 + - + +
115C CYS* 1.3 62.8 + - - +
117C GLY* 3.4 1.3 + - - -
118C ALA* 3.0 25.5 + - - +
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Residues in contact with CYS 115 (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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47C ALA* 4.0 10.9 - - - +
48C CYS* 3.8 35.2 - - - -
51C TYR* 4.1 23.1 - - + -
66C ALA* 4.7 0.2 - - - -
101C CYS* 4.2 17.5 - - - -
105C CYS* 4.3 10.3 - - + -
111C LEU 3.2 16.6 + - - +
112C GLU* 3.6 4.9 - - - +
113C ARG 3.2 0.6 - - - -
114C GLU* 1.3 81.5 - - - +
116C ALA* 1.3 66.9 + - - +
118C ALA* 3.1 2.6 + - - +
119C CYS* 3.0 24.4 + - - -
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Residues in contact with ALA 116 (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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102C ALA* 3.7 25.6 - - + +
105C CYS* 5.4 0.2 - - - +
106C ASP* 3.4 46.8 - - + +
112C GLU 3.2 5.5 + - - +
113C ARG 3.9 1.1 - - - +
115C CYS* 1.3 79.3 - - - +
117C GLY* 1.3 57.7 + - - +
119C CYS* 3.3 1.4 + - - +
120C ARG* 2.9 40.3 + - - +
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Residues in contact with GLY 117 (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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113C ARG 2.8 22.0 + - - -
114C GLU* 3.8 2.0 - - - -
115C CYS 3.1 0.2 - - - -
116C ALA* 1.3 74.8 - - - +
118C ALA* 1.3 55.5 + - - +
120C ARG* 3.5 5.4 + - - +
121C ARG* 3.0 30.7 + - - +
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Residues in contact with ALA 118 (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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40C ALA 4.5 1.9 - - - +
43C ALA* 3.9 9.0 - - + +
44C CYS* 3.6 21.6 - - - +
47C ALA* 3.5 32.1 - - + -
114C GLU 3.0 8.9 + - - +
115C CYS 3.7 0.9 - - - +
117C GLY* 1.3 71.9 - - - +
119C CYS* 1.3 61.5 + - - +
121C ARG* 3.3 8.4 + - - +
122C PHE* 2.9 29.8 + - - +
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Residues in contact with CYS 119 (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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44C CYS* 3.7 24.5 - - - -
48C CYS* 3.7 17.7 - - - -
69C CYS* 3.9 7.2 - - - -
98C ALA* 3.3 27.8 - - - +
101C CYS* 3.9 12.1 - - - -
102C ALA* 3.6 7.9 - - + -
115C CYS* 3.0 18.6 + - - -
116C ALA 3.5 7.4 - - - +
118C ALA* 1.3 77.6 - - - +
120C ARG* 1.3 57.5 + - - +
122C PHE* 3.1 4.7 + - - +
123C VAL* 2.9 33.0 + - - +
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.6 13.3 - - + +
102C ALA* 3.6 32.1 + - + +
103C GLU* 3.9 25.1 + - - +
106C ASP* 4.0 15.8 + - - +
116C ALA* 2.9 23.3 + - - +
117C GLY* 3.9 5.4 - - - +
119C CYS* 1.3 71.5 - - - +
121C ARG* 1.3 60.1 + - - +
123C VAL* 3.3 9.4 + - + +
124C GLU* 2.9 47.2 + - - +
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Residues in contact with ARG 121 (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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40C ALA* 4.3 15.9 - - + +
43C ALA* 6.1 5.2 - - - +
117C GLY 3.0 19.3 + - - +
118C ALA* 3.4 10.2 - - - +
120C ARG* 1.3 76.5 - - - +
122C PHE* 1.3 63.9 + - - +
124C GLU* 3.4 12.7 + - - +
125C ALA* 3.0 24.6 + - - +
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Residues in contact with PHE 122 (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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37C CYS* 3.9 14.1 - - - -
40C ALA* 3.8 17.4 - - + +
41C ALA* 3.7 33.4 - - + -
44C CYS* 4.1 5.2 - - + -
73C CYS* 3.7 15.7 - - - -
76C ALA* 4.4 10.5 - - + -
80C MSE 5.6 0.2 - - - -
91C CYS* 4.4 1.1 - - - -
94C ALA* 3.5 45.1 - - + -
95C ALA* 3.6 2.9 - - - -
98C ALA* 3.6 20.2 - - + -
118C ALA 2.9 13.4 + - - +
119C CYS 3.4 6.7 - - - +
121C ARG* 1.3 77.2 - - - +
123C VAL* 1.3 62.3 + - - +
125C ALA* 3.0 4.3 + - - +
126C CYS* 3.0 48.0 + - - -
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Residues in contact with VAL 123 (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* 3.6 40.8 - - + +
98C ALA* 3.8 11.4 - - + -
99C LEU* 3.8 23.3 - - + +
119C CYS 2.9 23.6 + - - +
120C ARG* 3.6 10.1 - - - +
122C PHE* 1.3 74.0 - - - +
124C GLU* 1.3 65.6 + - + +
126C CYS* 3.0 18.2 + - - +
127C ARG* 3.5 5.2 + - - +
130C LEU* 6.1 0.2 - - - +
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Residues in contact with GLU 124 (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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120C ARG* 2.9 35.3 + - - +
121C ARG* 3.6 10.9 + - - +
123C VAL* 1.3 77.6 - - + +
125C ALA* 1.3 62.6 + - - +
127C ARG* 3.3 23.1 + - - +
128C PRO* 3.7 3.3 - - - +
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Residues in contact with ALA 125 (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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33C PRO 4.4 1.6 - - - +
36C ARG* 4.6 4.9 - - + +
37C CYS* 3.7 30.9 - - - +
40C ALA* 3.8 10.8 - - + -
121C ARG* 3.0 13.4 + - - +
122C PHE 3.0 9.9 + - - +
124C GLU* 1.3 78.6 - - - +
126C CYS* 1.3 57.1 + - - +
127C ARG 3.3 0.2 - - - -
128C PRO* 3.2 22.4 - - - +
129C LEU* 3.5 9.0 - - - +
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Residues in contact with CYS 126 (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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37C CYS* 3.7 12.8 - - - -
91C CYS* 3.7 18.2 - - + +
95C ALA* 3.9 9.0 - - + -
122C PHE* 3.0 60.0 + - - -
123C VAL 3.0 10.3 + - - +
125C ALA* 1.3 76.3 - - - +
127C ARG* 1.3 64.5 + - - +
128C PRO* 3.4 0.7 - - - -
129C LEU* 3.0 16.5 + - - +
130C LEU* 3.2 28.4 + - + +
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Residues in contact with ARG 127 (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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123C VAL 3.5 4.8 + - - +
124C GLU* 3.3 15.1 + - - +
126C CYS* 1.3 77.0 - - - +
128C PRO* 1.3 65.0 - - + +
129C LEU 2.8 6.8 + - - -
130C LEU* 3.0 39.5 + - + +
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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