Contacts of the helix formed by residues 109 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A CYS* 3.8 12.8 - - - -
56A THR* 4.7 5.0 + - - +
57A GLU* 3.8 15.7 + - + +
108A ASP* 1.3 79.9 - - - +
110A PRO* 1.3 87.1 - - + +
111A LEU* 3.3 37.7 + - + +
112A GLU* 2.8 46.8 + - + +
113A ARG* 3.1 10.0 + - - +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASP 4.0 1.1 - - - +
109A GLU* 1.3 99.3 - - + +
111A LEU* 1.3 61.7 + - + +
113A ARG* 3.1 34.0 + - - +
114A GLU* 2.9 45.3 + - + +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA 5.2 0.7 - - - +
50A ARG* 4.1 28.7 - - + +
51A TYR* 3.9 8.7 - - + +
54A LEU* 3.4 26.7 - - + +
55A CYS* 3.3 33.2 - - + +
109A GLU* 3.2 29.5 + - + +
110A PRO* 1.3 79.6 - - + +
112A GLU* 1.3 61.0 + - - +
114A GLU* 3.4 13.5 + - - +
115A CYS* 3.5 21.1 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.9 9.8 - - + -
55A CYS* 3.8 17.5 - - - -
57A GLU* 2.4 43.9 - - - +
62A GLN* 5.0 7.3 + - - -
105A CYS 3.2 26.7 - - - +
106A ASP 4.8 0.7 - - - -
107A GLY* 3.1 28.3 - - - +
108A ASP 3.3 1.4 + - - -
109A GLU* 2.8 20.9 + - + +
111A LEU* 1.3 76.9 - - - +
113A ARG* 1.3 65.3 + - - +
115A CYS* 3.4 3.6 + - - +
116A ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASP* 3.5 12.5 + - - +
107A GLY 2.9 24.0 - - - +
108A ASP* 3.3 20.8 + - - +
109A GLU 3.1 2.2 + - - +
110A PRO* 3.1 41.4 - - + +
112A GLU* 1.3 76.4 - - - +
114A GLU* 1.3 59.6 + - + +
116A ALA* 3.2 4.0 + - - +
117A GLY* 2.8 28.1 + - - -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.1 7.6 - - + +
50A ARG* 5.5 10.3 + - - +
110A PRO* 2.9 35.2 + - + +
111A LEU* 3.4 17.7 + - - +
113A ARG* 1.3 77.3 - - + +
115A CYS* 1.3 55.5 + - - +
117A GLY* 3.5 1.9 + - - +
118A ALA* 2.9 30.8 + - - +
121A ARG* 4.7 4.1 + - - +
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Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.0 13.6 - - - +
48A CYS* 3.9 19.5 - - - -
51A TYR* 4.1 31.0 - - + -
66A ALA* 4.7 0.2 - - - -
101A CYS* 3.8 28.3 - - - -
105A CYS* 4.5 6.5 - - + -
111A LEU 3.5 17.8 + - - +
112A GLU* 3.4 5.8 + - - +
113A ARG 3.2 0.6 - - - -
114A GLU* 1.3 74.5 - - - +
116A ALA* 1.3 66.4 + - - +
118A ALA* 3.1 3.1 + - - +
119A CYS* 2.9 25.9 + - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA* 4.0 23.8 - - + +
105A CYS 5.7 0.2 - - - -
106A ASP* 3.4 44.1 - - + +
112A GLU 3.1 5.6 + - - +
113A ARG 3.5 5.4 - - - +
115A CYS* 1.3 80.0 - - - +
117A GLY* 1.3 58.0 + - - +
119A CYS* 3.2 2.0 + - - +
120A ARG* 2.8 39.1 + - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG 2.8 19.2 + - - -
114A GLU* 3.8 0.4 - - - -
116A ALA* 1.3 74.2 - - - +
118A ALA* 1.3 51.8 + - - +
120A ARG* 3.3 7.4 + - - +
121A ARG* 2.7 59.7 + - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 5.0 1.4 - - - +
43A ALA* 4.3 6.5 - - + +
44A CYS* 3.9 19.2 - - - +
47A ALA* 3.8 20.6 - - + -
114A GLU 2.9 18.1 + - - +
115A CYS 3.5 3.6 - - - +
117A GLY* 1.3 74.6 - - - +
119A CYS* 1.3 58.7 + - - +
121A ARG* 3.3 18.5 + - - +
122A PHE* 2.8 30.3 + - - +
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Residues in contact with CYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A CYS* 3.6 26.0 - - - -
48A CYS* 4.0 5.8 - - - -
69A CYS* 3.8 6.3 - - - -
98A ALA* 3.3 26.0 - - + +
101A CYS* 3.8 29.8 - - - -
102A ALA* 4.1 4.7 - - + -
115A CYS 2.9 17.7 + - - -
116A ALA 3.5 7.0 - - - +
118A ALA* 1.3 76.7 - - - +
120A ARG* 1.3 53.3 + - - +
122A PHE* 3.1 4.3 + - - +
123A VAL* 2.7 39.0 + - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.6 25.9 - - + +
102A ALA* 3.6 26.3 + - + +
103A GLU* 3.8 24.0 - - - +
106A ASP* 4.8 8.1 + - - +
116A ALA* 2.8 31.1 + - - +
117A GLY* 3.7 5.8 - - - +
119A CYS* 1.3 68.8 - - - +
121A ARG* 1.3 61.9 + - - +
123A VAL* 3.1 10.4 + - - +
124A GLU* 2.8 29.5 + - - +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA* 4.5 5.6 - - + +
43A ALA* 6.2 1.6 - - - +
114A GLU* 4.7 4.6 + - - +
117A GLY* 2.7 48.4 + - - +
118A ALA* 3.5 15.5 - - - +
120A ARG* 1.3 72.4 - - - +
122A PHE* 1.3 62.1 + - - +
124A GLU* 3.3 12.2 + - + +
125A ALA* 3.1 20.8 + - - +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A CYS* 3.9 14.8 - - - -
40A ALA* 3.8 13.6 - - + +
41A ALA* 3.4 36.6 - - + -
44A CYS* 4.1 9.6 - - + -
73A CYS* 3.5 27.4 - - - -
76A ALA* 4.8 7.2 - - + -
80A MSE 5.8 0.2 - - - -
91A CYS* 4.9 1.8 - - + -
94A ALA* 3.7 32.1 - - + -
95A ALA 4.0 0.4 - - - -
98A ALA* 3.8 16.6 - - + -
118A ALA 2.8 14.5 + - - +
119A CYS 3.3 6.3 - - - +
121A ARG* 1.3 74.9 - - - +
123A VAL* 1.3 65.3 + - - +
125A ALA* 3.0 11.3 + - - +
126A CYS* 3.1 39.9 + - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA* 3.8 35.8 - - + +
98A ALA* 3.8 10.8 - - + -
99A LEU* 3.9 28.9 - - + +
119A CYS 2.7 31.7 + - - +
120A ARG* 3.4 10.8 - - - +
122A PHE* 1.3 74.2 - - - +
124A GLU* 1.3 65.7 + - - +
126A CYS* 3.1 16.9 + - - +
127A ARG* 3.6 9.3 + - + +
130A LEU* 6.0 0.2 - - - +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ARG 2.8 12.7 + - - +
121A ARG* 3.3 15.3 - - + +
123A VAL* 1.3 77.5 - - - +
125A ALA* 1.3 64.3 + - - +
127A ARG* 3.1 43.7 + - - +
128A PRO* 3.8 2.9 - - - +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO 4.5 1.0 - - - +
36A ARG* 4.4 9.8 - - + +
37A CYS* 3.7 27.9 - - - +
40A ALA* 3.9 12.3 - - + -
121A ARG 3.1 11.5 + - - +
122A PHE 3.0 10.1 + - - +
124A GLU* 1.3 79.2 - - + +
126A CYS* 1.3 58.8 + - - +
127A ARG 3.3 0.2 - - - -
128A PRO* 3.2 19.4 - - - +
129A LEU* 3.4 10.0 - - - +
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Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A CYS* 3.8 7.6 - - - -
91A CYS* 3.6 34.5 - - + +
95A ALA* 4.1 10.3 - - + -
122A PHE* 3.1 49.5 + - - -
123A VAL 3.1 9.8 + - - +
125A ALA* 1.3 76.1 - - - +
127A ARG* 1.3 67.0 + - - +
129A LEU* 2.9 16.7 + - - +
130A LEU* 3.1 19.4 + - + +
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.6 10.1 + - + +
124A GLU* 3.1 32.8 + - - +
126A CYS* 1.3 76.1 - - - +
128A PRO* 1.3 65.7 - - + +
130A LEU* 2.7 39.8 + - + +
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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
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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