Contacts of the helix formed by residues 97 - 119 (chain A) in PDB entry 3KTC
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 ASP 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASN* 2.9 15.9 + - - +
96A PRO* 1.3 77.4 - - + +
98A PRO* 1.3 71.8 - - - +
99A ALA* 3.0 24.7 + - - +
100A ALA* 3.0 24.5 + - + +
101A ARG* 3.2 12.0 + - - +
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Residues in contact with PRO 98 (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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96A PRO 3.4 10.1 - - - +
97A ASP* 1.3 90.2 - - - +
99A ALA* 1.3 59.6 + - - +
101A ARG* 3.2 33.7 + - - +
102A ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 99 (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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97A ASP* 3.0 17.6 + - - +
98A PRO* 1.3 78.8 - - - +
100A ALA* 1.3 57.2 + - - +
102A ALA* 3.4 7.7 + - - +
103A ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 100 (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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87A LYS* 4.7 9.0 - - + +
88A TRP* 2.9 34.5 + - + +
92A ALA 4.5 0.4 - - - -
95A ASN* 3.3 31.0 - - - +
97A ASP* 3.0 20.4 + - + +
99A ALA* 1.3 77.5 - - - +
101A ARG* 1.3 59.2 + - - +
103A ALA* 3.3 3.9 + - - -
104A ALA* 2.9 13.0 + - - +
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Residues in contact with ARG 101 (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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92A ALA 3.5 19.7 - - - +
93A PHE* 3.1 23.9 - - - +
95A ASN* 2.8 42.3 + - + +
96A PRO* 3.6 17.0 + - - +
97A ASP 3.2 4.0 + - - +
98A PRO* 3.2 32.3 + - - +
100A ALA* 1.3 76.4 - - - +
102A ALA* 1.3 57.2 + - - +
104A ALA* 3.3 4.2 + - - +
105A PHE* 3.0 27.0 + - - +
146A LEU* 3.8 30.5 - - - +
309B GLU* 5.5 5.3 + - - -
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Residues in contact with ALA 102 (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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98A PRO 3.0 13.2 + - - +
99A ALA* 3.6 11.7 - - - +
101A ARG* 1.3 73.9 - - - +
103A ALA* 1.3 60.6 + - - +
105A PHE* 3.2 9.8 + - - +
106A GLU* 3.0 33.7 + - + +
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Residues in contact with ALA 103 (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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87A LYS* 3.5 33.7 - - - +
88A TRP* 3.6 8.6 - - + -
99A ALA 3.0 17.4 + - - +
100A ALA* 3.3 5.6 + - - +
102A ALA* 1.3 73.6 - - - +
104A ALA* 1.3 65.9 + - - +
106A GLU* 3.3 9.0 + - - +
107A LEU* 3.1 19.1 + - - +
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Residues in contact with ALA 104 (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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83A ILE* 4.8 3.1 - - + -
88A TRP* 3.5 21.2 - - + +
92A ALA* 3.9 31.4 - - + -
93A PHE* 5.4 0.2 - - - -
100A ALA 2.9 13.4 + - - +
101A ARG 3.5 8.7 - - - +
102A ALA 3.3 0.2 - - - -
103A ALA* 1.3 74.1 - - - +
105A PHE* 1.3 66.0 + - - +
107A LEU* 3.2 3.7 + - - +
108A MSE 3.0 36.6 + - + +
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Residues in contact with PHE 105 (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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101A ARG 3.0 13.9 + - - +
102A ALA* 3.2 11.6 + - - +
104A ALA* 1.3 76.1 - - - +
106A GLU* 1.3 81.5 + - - +
108A MSE 3.2 12.7 + - + +
109A HIS* 2.8 62.3 + + + +
150A GLY 5.4 1.1 - - - -
153A ASP* 3.8 30.3 - - + -
154A LEU* 3.9 27.4 - - + -
157A ALA* 4.1 11.9 - - + -
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Residues in contact with GLU 106 (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* 3.0 20.1 + - + +
103A ALA* 3.7 10.1 - - - +
104A ALA 3.2 0.4 - - - -
105A PHE* 1.3 97.2 - - - +
107A LEU* 1.3 57.6 + - - +
109A HIS* 3.7 11.8 - - - +
110A GLU* 3.0 30.2 + - - +
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Residues in contact with LEU 107 (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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54A TYR* 3.9 19.3 - - + +
55A PRO* 3.8 29.4 - - + -
81A PRO* 4.2 6.1 - - + -
82A GLU 3.9 27.1 - - - +
83A ILE* 4.2 5.8 - - + -
88A TRP* 3.7 33.2 - - + -
103A ALA 3.1 12.8 + - - +
104A ALA 3.7 6.1 - - - +
106A GLU* 1.3 75.0 - - - +
108A MSE 1.3 58.4 + - - +
110A GLU* 3.3 9.5 + - + +
111A SER* 2.9 25.6 + - - -
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Residues in contact with MSE 108 (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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81A PRO* 3.8 11.0 - - + -
83A ILE* 3.7 29.8 - - + -
93A PHE* 3.3 52.3 - - + -
101A ARG 5.5 0.2 - - - +
104A ALA* 3.0 37.3 + - + +
105A PHE* 3.8 9.0 - - + +
107A LEU* 1.3 75.8 - - - +
109A HIS* 1.3 62.5 + - - +
111A SER* 2.7 24.0 + - - +
112A ALA* 3.0 10.4 + - - +
123A VAL* 4.7 3.2 - - + +
125A VAL* 4.5 4.7 - - - -
154A LEU* 3.7 29.2 - - + +
163A PHE* 4.8 0.7 - - - -
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Residues in contact with HIS 109 (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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105A PHE* 2.8 47.7 + + + +
106A GLU* 3.7 13.7 - - - +
108A MSE 1.3 70.4 - - - +
110A GLU* 1.3 65.0 + - - +
112A ALA* 3.2 14.0 + - - +
113A GLY* 3.4 7.6 + - - -
116A ARG* 4.9 2.7 + - - -
154A LEU* 3.8 5.7 - - - +
157A ALA* 3.9 17.3 - - + -
158A ASN* 2.9 41.8 + - - +
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Residues in contact with GLU 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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54A TYR* 2.6 36.1 + - + +
106A GLU 3.0 19.3 + - - +
107A LEU* 3.5 9.9 - - - +
109A HIS* 1.3 78.0 - - - +
111A SER* 1.3 58.7 + - - +
113A GLY* 3.0 18.1 + - - -
114A ILE* 3.1 14.5 + - + +
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Residues in contact with SER 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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54A TYR* 4.3 9.1 - - - -
79A ILE* 4.0 18.0 - - - +
81A PRO* 3.5 15.7 - - - +
107A LEU 2.9 14.0 + - - -
108A MSE 2.7 23.1 + - - -
110A GLU* 1.3 75.4 - - - +
112A ALA* 1.3 57.3 + - - +
114A ILE* 3.0 13.4 + - - +
115A VAL* 2.9 30.0 + - - +
123A VAL* 3.5 20.1 - - - +
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Residues in contact with ALA 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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108A MSE 3.0 11.0 + - - +
109A HIS 3.2 10.3 + - - +
111A SER* 1.3 75.6 + - - +
113A GLY* 1.3 63.2 + - - +
115A VAL* 3.2 5.3 + - - +
116A ARG* 3.0 29.7 + - - +
123A VAL* 3.5 21.3 - - + -
158A ASN* 3.7 28.0 - - + +
161A VAL* 4.1 8.1 - - + +
163A PHE* 4.1 7.0 - - + -
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Residues in contact with GLY 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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109A HIS 3.4 5.2 + - - -
110A GLU* 3.0 10.9 + - - -
112A ALA* 1.3 79.0 - - - +
114A ILE* 1.3 56.9 + - - +
116A ARG* 3.2 21.6 + - - +
117A GLU* 2.9 33.6 + - - +
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Residues in contact with ILE 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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54A TYR* 3.7 41.3 - - + +
56A PHE* 4.3 12.1 - - + -
62A LEU* 4.3 26.2 - - + -
79A ILE* 3.7 29.6 - - + -
110A GLU* 3.1 15.3 + - + +
111A SER* 3.0 9.1 + - - +
113A GLY* 1.3 72.4 - - - +
115A VAL* 1.3 67.2 + - - +
117A GLU* 3.2 4.8 + - + +
118A LEU* 2.9 36.4 + - + +
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Residues in contact with VAL 115 (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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79A ILE* 3.6 17.0 - - + -
111A SER 2.9 16.3 + - - +
112A ALA* 3.2 10.1 + - - +
114A ILE* 1.3 76.5 - - - +
116A ARG* 1.3 59.1 + - - +
119A GLY* 2.9 26.0 + - - -
120A ALA* 3.0 41.5 + - + +
121A ASN 4.6 0.7 - - - +
122A TYR* 3.4 26.7 - - - +
123A VAL* 3.6 16.2 - - + -
161A VAL* 4.2 19.7 - - + -
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Residues in contact with ARG 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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109A HIS* 4.9 2.6 + - - -
112A ALA* 3.0 14.0 + - - +
113A GLY* 3.2 34.3 + - - +
115A VAL* 1.3 78.0 - - - +
117A GLU* 1.3 63.7 + - + +
119A GLY* 3.4 8.5 + - - -
157A ALA 5.0 0.4 + - - -
158A ASN* 2.9 28.7 + - - +
160A ASP* 2.8 41.2 + - - +
161A VAL* 3.6 20.6 - - + +
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Residues in contact with GLU 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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62A LEU* 4.0 29.9 - - + +
66A LYS* 3.3 28.5 + - - -
113A GLY 2.9 19.4 + - - +
114A ILE* 3.6 9.4 - - + +
116A ARG* 1.3 79.1 - - + +
118A LEU* 1.3 62.1 + - + +
119A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 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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52A LEU* 4.6 1.8 - - + -
56A PHE* 4.9 1.8 - - + -
62A LEU* 4.0 15.3 - - + -
65A VAL* 4.5 14.1 - - + -
66A LYS* 3.6 38.8 - - + -
69A LEU* 4.5 11.9 - - + -
75A LYS* 5.8 1.6 - - - +
76A ALA* 4.0 28.9 + - + +
79A ILE* 3.9 14.8 - - + -
114A ILE* 2.9 34.1 + - + +
115A VAL 4.4 0.7 - - - +
117A GLU* 1.3 75.4 - - - +
119A GLY* 1.3 63.3 + - - +
120A ALA* 3.3 3.7 + - + +
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Residues in contact with GLY 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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76A ALA 4.2 3.2 - - - +
115A VAL 2.9 7.9 + - - -
116A ARG 3.4 6.3 + - - -
117A GLU 3.4 4.2 - - - -
118A LEU* 1.3 78.0 - - - +
120A ALA* 1.3 64.7 + - - +
121A ASN* 4.6 4.9 + - - -
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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