Contacts of the helix formed by residues 109 - 127 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU 4.0 9.7 - - - +
82A ARG* 5.4 1.9 - - - -
83A ARG* 4.7 13.0 + - - +
55D CYS* 4.3 9.2 - - - -
56D THR* 5.1 3.6 + - - -
57D GLU* 2.8 41.3 - - - +
108D ASP* 1.3 78.0 - - + +
110D PRO* 1.3 74.2 - - + +
111D LEU* 4.3 14.3 - - + +
112D GLU* 3.0 28.4 + - + +
113D ARG* 3.0 13.8 + - - +
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Residues in contact with PRO 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP 3.6 4.5 - - - +
109D GLU* 1.3 85.2 - - + +
111D LEU* 1.3 56.9 + - + +
113D ARG* 3.2 33.4 - - - +
114D GLU* 2.7 53.2 + - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.8 22.7 - - - +
47D ALA 5.1 1.0 - - - +
50D ARG* 4.3 20.6 - - + +
51D TYR* 3.8 11.9 - - + +
54D LEU* 3.8 30.5 - - + +
55D CYS* 3.7 35.2 - - + +
109D GLU* 3.2 15.1 - - - +
110D PRO* 1.3 82.2 - - + +
112D GLU* 1.3 61.5 - - + +
114D GLU* 3.2 15.2 - - - +
115D CYS* 3.4 22.2 + - - +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TYR* 3.9 17.3 - - + -
55D CYS* 4.2 6.4 - - - -
57D GLU* 2.3 40.1 - - - +
62D GLN* 6.0 0.6 + - - -
105D CYS 3.1 22.9 - - - +
106D ASP* 3.1 19.2 - - - +
107D GLY* 3.2 22.4 - - - +
108D ASP 3.2 1.4 + - - -
109D GLU* 3.0 33.2 + - + +
111D LEU* 1.3 77.4 - - - +
113D ARG* 1.3 64.9 + - - +
115D CYS* 3.4 2.8 + - - +
116D ALA 3.2 12.6 + - - -
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ASP* 4.0 9.2 - - + +
107D GLY 3.0 22.9 - - - +
108D ASP* 3.4 21.0 + - - +
109D GLU 3.0 6.2 + - - +
110D PRO* 3.2 34.7 + - - +
112D GLU* 1.3 77.2 - - - +
114D GLU* 1.3 55.4 - - + +
116D ALA* 3.3 2.4 + - - +
117D GLY* 2.7 34.3 + - - -
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ALA* 3.7 8.8 - - + +
50D ARG* 5.9 5.6 + - - +
110D PRO* 2.7 45.4 + - + +
111D LEU* 3.2 18.3 - - - +
113D ARG* 1.3 79.3 - - + +
115D CYS* 1.3 56.7 + - - +
117D GLY* 4.4 1.3 - - - +
118D ALA* 2.8 32.7 + - - +
121D ARG* 4.2 8.3 + - - +
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Residues in contact with CYS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ALA* 3.8 13.8 - - - +
48D CYS* 3.8 33.8 - - - -
51D TYR* 4.2 21.5 - - + -
66D ALA* 4.7 0.2 - - - -
101D CYS* 4.0 17.0 - - - -
105D CYS* 4.2 13.2 - - + -
111D LEU 3.4 17.6 + - - +
112D GLU* 3.7 5.2 - - - +
113D ARG 3.3 0.4 - - - -
114D GLU* 1.3 78.8 - - - +
116D ALA* 1.3 64.8 + - - +
118D ALA* 3.7 2.4 - - - +
119D CYS* 3.0 26.0 + - - -
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA* 3.5 33.9 - - + +
106D ASP* 3.1 38.3 - - + +
112D GLU 3.2 3.4 + - - +
113D ARG 3.8 1.6 - - - +
115D CYS* 1.3 80.4 - - - +
117D GLY* 1.3 58.8 + - - +
119D CYS* 3.0 3.6 + - - +
120D ARG* 2.8 39.9 + - - +
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ARG 2.7 22.3 + - - -
114D GLU* 3.8 1.8 - - - -
116D ALA* 1.3 72.9 - - - +
118D ALA* 1.3 57.0 + - - +
120D ARG* 3.3 11.3 + - - +
121D ARG* 2.9 44.3 + - - +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA 4.2 2.8 - - - +
43D ALA* 3.8 6.5 - - + +
44D CYS* 3.6 20.4 - - - +
47D ALA* 3.4 22.9 - - + -
114D GLU 2.8 21.9 + - - +
115D CYS 3.7 1.3 - - - +
117D GLY* 1.3 72.4 - - - +
119D CYS* 1.3 56.9 + - - +
121D ARG* 3.5 24.4 + - - +
122D PHE* 3.0 28.4 + - - +
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Residues in contact with CYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D CYS* 3.7 25.8 - - - -
48D CYS* 4.2 3.1 - - - -
69D CYS* 3.8 13.9 - - - -
98D ALA* 3.3 26.8 - - - +
101D CYS* 3.9 17.0 - - - -
102D ALA* 3.6 6.7 - - + -
115D CYS 3.0 20.7 + - - -
116D ALA 3.0 9.3 + - - +
118D ALA* 1.3 74.6 - - - +
120D ARG* 1.3 65.9 + - - +
122D PHE* 3.0 4.5 + - - +
123D VAL* 3.0 27.4 + - - +
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Residues in contact with ARG 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 5.2 12.7 + - + +
102D ALA* 3.3 39.8 + - + +
103D GLU* 4.2 12.9 - - - +
106D ASP* 3.5 20.2 + - - -
116D ALA* 2.8 27.6 + - - +
117D GLY* 3.8 7.5 - - - +
119D CYS* 1.3 71.8 - - - +
121D ARG* 1.3 63.5 + - + +
123D VAL* 3.0 11.2 + - - +
124D GLU* 2.9 25.0 + - - +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA* 4.3 7.0 - - + +
43D ALA* 4.5 17.2 - - - +
114D GLU* 4.2 8.7 + - - +
117D GLY* 2.9 22.0 + - - +
118D ALA* 3.5 34.6 - - - +
120D ARG* 1.3 76.2 - - - +
122D PHE* 1.3 62.7 + - - +
124D GLU* 3.4 7.9 + - - +
125D ALA* 3.0 24.3 + - - +
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D CYS* 3.9 14.4 - - - -
40D ALA* 3.8 15.7 - - + +
41D ALA* 3.5 39.3 - - + -
44D CYS* 4.2 4.7 - - + -
73D CYS* 3.9 14.6 - - - -
76D ALA* 4.4 11.9 - - + -
80D MSE 5.6 0.2 - - - -
91D CYS* 4.4 2.7 - - - -
94D ALA* 3.6 22.4 - - + -
95D ALA* 3.6 24.0 - - - -
98D ALA* 3.8 17.9 - - + -
118D ALA 3.0 15.5 + - - +
119D CYS 3.0 6.9 + - - +
121D ARG* 1.3 77.0 - - - +
123D VAL* 1.3 63.8 + - - +
125D ALA* 3.1 3.6 + - - +
126D CYS* 3.1 46.3 + - - -
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Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ALA* 3.7 22.2 - - + +
98D ALA* 3.6 23.1 - - + -
99D LEU* 3.7 32.1 - - + +
119D CYS 3.0 18.4 - - - +
120D ARG* 3.4 6.1 - - - +
122D PHE* 1.3 77.2 - - - +
124D GLU* 1.3 57.9 + - - +
126D CYS* 2.8 30.9 + - - +
127D ARG* 3.4 11.5 + - + +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ARG 2.9 15.5 + - - +
121D ARG* 3.7 8.7 - - - +
123D VAL* 1.3 77.0 - - - +
125D ALA* 1.3 59.2 + - - +
127D ARG* 3.0 54.6 + - - +
128D PRO* 3.6 7.3 - - - +
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO 4.2 1.4 - - - +
36D ARG* 4.3 17.5 - - - +
37D CYS* 3.5 37.5 - - - +
40D ALA* 3.8 10.3 - - + -
121D ARG 3.0 17.6 + - - +
122D PHE 3.5 5.4 - - - +
123D VAL 3.0 0.4 - - - -
124D GLU* 1.3 75.3 - - - +
126D CYS* 1.3 61.4 + - - +
127D ARG 3.4 0.4 - - - -
128D PRO* 3.4 18.1 - - - +
129D LEU* 3.7 1.9 - - - +
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Residues in contact with CYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D CYS* 4.0 11.7 - - - -
91D CYS* 3.9 15.6 - - + +
95D ALA* 3.8 20.4 - - + -
122D PHE* 3.1 58.0 + - - -
123D VAL 2.8 8.2 + - - +
125D ALA* 1.3 79.9 - - - +
127D ARG* 1.3 64.3 + - - +
128D PRO 3.4 0.2 - - - -
129D LEU* 2.9 19.7 + - - +
130D LEU* 3.3 17.0 + - + +
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D VAL* 3.6 11.7 - - + +
124D GLU* 3.0 47.0 + - - +
126D CYS* 1.3 72.5 - - - +
128D PRO* 1.3 58.6 - - + +
129D LEU 2.7 16.7 + - - -
130D LEU* 3.0 22.1 + - - +
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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