Contacts of the helix formed by residues 97 - 119 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN* 2.9 16.4 + - - +
96B PRO* 1.3 77.2 - - + +
98B PRO* 1.3 71.2 - - - +
99B ALA* 3.0 25.5 + - - +
100B ALA* 3.0 22.2 + - + +
101B ARG* 3.2 12.8 + - - +
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Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PRO 3.4 8.7 - - - +
97B ASP* 1.3 90.5 - - - +
99B ALA* 1.3 55.1 + - - +
101B ARG* 3.3 33.6 + - - +
102B ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 3.0 16.5 + - - +
98B PRO* 1.3 76.9 - - - +
100B ALA* 1.3 61.6 + - - +
102B ALA* 3.4 7.3 + - - +
103B ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 4.7 10.3 - - + +
88B TRP* 2.9 22.3 + - + +
92B ALA 4.5 0.9 - - - -
95B ASN* 3.3 36.6 - - - +
97B ASP* 3.0 14.5 + - + +
99B ALA* 1.3 76.4 - - - +
101B ARG* 1.3 57.6 + - - +
103B ALA* 3.3 3.7 + - - -
104B ALA* 2.9 24.4 + - - +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU* 5.3 6.1 + - - -
92B ALA 3.4 21.2 - - - +
93B PHE* 3.1 24.0 - - - +
95B ASN 2.8 42.3 + - - +
96B PRO* 3.6 17.8 + - - +
97B ASP 3.2 4.2 + - - +
98B PRO* 3.3 30.9 + - - +
100B ALA* 1.3 77.2 - - - +
102B ALA* 1.3 57.5 + - - +
104B ALA* 3.3 3.1 + - - +
105B PHE* 3.0 27.2 + - - +
108B MSE 5.4 0.5 - - - +
146B LEU* 3.7 31.4 - - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO 3.0 13.6 + - - +
99B ALA* 3.6 11.2 - - - +
101B ARG* 1.3 77.6 - - - +
103B ALA* 1.3 56.9 + - - +
105B PHE* 3.2 10.5 + - - +
106B GLU* 3.0 32.3 + - + +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.5 34.3 - - - +
88B TRP* 3.6 7.8 - - + -
99B ALA 2.9 17.4 + - - +
100B ALA* 3.6 5.4 - - - +
102B ALA* 1.3 74.5 - - - +
104B ALA* 1.3 64.1 + - - +
106B GLU* 3.3 9.5 + - - +
107B LEU* 3.1 18.9 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 4.6 4.0 - - + -
88B TRP* 3.5 26.1 - - + +
92B ALA* 3.8 31.2 - - + -
93B PHE* 5.4 0.2 - - - -
100B ALA 2.9 9.3 + - - +
101B ARG 3.6 7.9 - - - +
102B ALA 3.3 0.2 - - - -
103B ALA* 1.3 76.0 - - - +
105B PHE* 1.3 64.1 + - - +
107B LEU* 3.2 3.2 + - - +
108B MSE 3.0 37.3 + - + +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG 3.0 13.0 + - - +
102B ALA* 3.2 10.5 + - - +
104B ALA* 1.3 75.4 - - - +
106B GLU* 1.3 79.9 + - - +
108B MSE 3.1 13.2 + - + +
109B HIS* 2.8 61.2 + + + +
150B GLY 5.3 1.3 - - - -
153B ASP* 3.8 30.3 - - + -
154B LEU* 3.8 27.4 - - + -
157B ALA* 4.1 11.4 - - + -
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 3.0 19.1 + - + +
103B ALA* 3.6 10.5 - - - +
104B ALA 3.2 0.6 - - - -
105B PHE* 1.3 96.5 - - - +
107B LEU* 1.3 56.8 + - - +
109B HIS* 3.7 11.4 - - - +
110B GLU* 2.9 30.0 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 3.9 20.4 - - + +
55B PRO* 3.8 30.3 - - + -
81B PRO* 4.2 6.3 - - + -
82B GLU 4.0 26.5 - - - +
83B ILE* 4.2 6.1 - - + -
88B TRP* 3.7 32.5 - - + -
103B ALA 3.1 12.6 + - - +
104B ALA 3.2 6.7 + - - +
106B GLU* 1.3 76.5 - - - +
108B MSE 1.3 58.9 + - - +
110B GLU* 3.2 8.9 + - + +
111B SER* 2.8 25.6 + - - -
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Residues in contact with MSE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.8 11.9 - - + -
83B ILE* 3.6 30.1 - - + -
93B PHE* 3.4 51.8 - - + -
101B ARG 5.4 0.4 - - - +
104B ALA* 3.0 39.0 + - + +
105B PHE* 3.8 9.2 - - + +
107B LEU* 1.3 71.7 - - - +
109B HIS* 1.3 66.0 + - - +
111B SER* 2.8 22.7 + - - -
112B ALA* 3.1 10.0 + - - +
123B VAL* 4.8 2.4 - - + +
125B VAL* 4.6 5.2 - - - -
154B LEU* 3.7 30.1 - - + +
163B PHE* 4.8 0.5 - - - -
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Residues in contact with HIS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PHE* 2.8 43.4 + + + +
106B GLU* 3.7 12.8 - - - +
108B MSE 1.3 76.7 - - - +
110B GLU* 1.3 61.5 + - - +
112B ALA* 3.2 14.2 + - - +
113B GLY* 3.4 7.8 + - - -
116B ARG* 4.9 2.1 + - - -
154B LEU* 3.8 6.4 - - + +
157B ALA* 4.0 17.0 - - + -
158B ASN* 2.9 42.6 + - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 2.4 38.3 + - + +
106B GLU 2.9 19.3 + - - +
107B LEU* 3.2 11.5 + - - +
109B HIS* 1.3 78.8 - - - +
111B SER* 1.3 57.1 + - - +
113B GLY* 2.9 19.2 + - - +
114B ILE* 3.1 13.5 + - + +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 4.3 8.3 - - - -
79B ILE* 4.0 17.7 - - - +
81B PRO* 3.5 21.0 - - - +
107B LEU 2.8 13.5 + - - -
108B MSE 2.8 18.0 + - - -
110B GLU* 1.3 78.3 - - - +
112B ALA* 1.3 54.9 + - - +
114B ILE* 3.1 13.6 + - - +
115B VAL* 2.9 31.0 + - - +
123B VAL* 3.5 21.6 - - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MSE 3.1 11.3 + - - +
109B HIS 3.4 11.0 - - - +
110B GLU 3.2 0.2 - - - -
111B SER* 1.3 75.9 + - - +
113B GLY* 1.3 62.4 + - - +
115B VAL* 3.3 5.4 + - - +
116B ARG* 3.0 30.3 + - - +
123B VAL* 3.6 19.5 - - + -
158B ASN* 3.7 28.7 - - - +
161B VAL* 4.1 7.9 - - + +
163B PHE* 4.1 7.6 - - + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B HIS 3.4 5.6 + - - -
110B GLU* 2.9 10.0 + - - -
112B ALA* 1.3 78.7 - - - +
114B ILE* 1.3 57.4 + - - +
116B ARG* 3.2 20.4 + - - +
117B GLU* 2.9 32.1 + - - +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 3.6 41.3 - - + +
56B PHE* 4.3 8.7 - - + -
62B LEU* 4.3 29.4 - - + -
79B ILE* 3.9 18.4 - - + -
110B GLU* 3.1 15.4 + - + +
111B SER* 3.1 10.6 + - - +
113B GLY* 1.3 73.0 - - - +
115B VAL* 1.3 66.8 + - - +
117B GLU* 3.1 5.8 + - + +
118B LEU* 2.9 45.0 + - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 3.6 19.5 - - + -
111B SER 2.9 17.1 + - - +
112B ALA* 3.3 10.3 + - - +
114B ILE* 1.3 76.1 - - - +
116B ARG* 1.3 63.2 + - - +
119B GLY* 2.9 20.3 + - - -
120B ALA* 3.0 37.2 + - + +
121B ASN 4.7 0.9 - - - -
122B TYR 3.4 26.9 - - - +
123B VAL* 3.5 15.3 - - + -
161B VAL* 4.1 20.6 - - + -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B HIS* 4.9 2.0 + - - -
112B ALA* 3.0 8.9 + - - +
113B GLY* 3.2 35.1 + - - +
115B VAL* 1.3 77.7 - - - +
117B GLU* 1.3 65.1 + - + +
119B GLY* 3.4 8.9 + - - -
157B ALA 5.0 0.4 + - - -
158B ASN* 2.9 29.3 + - - +
160B ASP* 2.8 41.8 + - - +
161B VAL* 3.6 20.5 - - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.9 25.8 - - + -
66B LYS* 3.0 35.0 + - - -
113B GLY 2.9 18.3 + - - +
114B ILE* 3.5 9.4 - - + +
116B ARG* 1.3 79.7 - - + +
118B LEU* 1.3 59.9 + - + +
119B GLY 3.8 0.5 + - - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.7 2.2 - - + -
56B PHE* 4.8 2.0 - - + -
62B LEU* 4.0 17.5 - - + -
65B VAL* 4.5 13.0 - - + -
66B LYS* 3.5 36.3 - - + +
69B LEU* 4.5 12.8 - - + -
75B LYS* 5.8 1.4 - - - +
76B ALA* 4.0 27.8 + - + +
79B ILE* 3.9 14.8 - - + -
114B ILE* 2.9 34.6 + - + +
115B VAL 4.5 1.1 - - - +
117B GLU* 1.3 75.9 - - - +
119B GLY* 1.3 62.4 + - - +
120B ALA* 3.2 3.9 + - + +
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ALA 4.2 2.5 - - - +
115B VAL 2.9 7.2 + - - -
116B ARG* 3.4 9.3 + - - -
117B GLU 3.4 0.8 + - - -
118B LEU* 1.3 78.8 - - - +
120B ALA* 1.3 65.0 + - - +
121B ASN* 4.0 3.6 + - - +
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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