Contacts of the helix formed by residues 96 - 112 (chain B) in PDB entry 3RK6
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 SER 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B HIS* 3.5 22.0 + - - -
90B LEU* 3.7 9.3 - - - +
93B GLN* 2.8 33.7 + - - +
95B GLY* 1.3 76.6 - - - +
97B PHE* 1.3 67.3 + - - +
98B GLU 3.3 0.6 + - - -
99B THR* 3.4 8.7 + - - -
100B GLU* 3.1 45.4 + - - +
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Residues in contact with PHE 97 (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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90B LEU* 3.8 18.5 - - + +
94B PRO 3.4 9.0 + - - +
95B GLY 3.3 1.6 - - - -
96B SER* 1.3 76.7 + - - +
98B GLU* 1.3 63.1 + - + +
100B GLU* 5.4 0.4 - - - -
101B ILE* 2.9 76.1 + - + +
138B MET* 3.5 24.7 - - + -
141B ARG* 3.5 54.5 - - + +
142B LEU* 3.9 23.3 - - + -
145B TYR* 4.0 21.1 - + + -
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Residues in contact with GLU 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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98A GLU* 5.4 2.9 - - - +
137A TYR* 5.0 8.3 + - - -
141A ARG* 5.8 1.6 + - - -
94B PRO 4.5 1.2 - - - +
95B GLY* 3.3 21.2 - - - +
96B SER 3.4 0.2 - - - -
97B PHE* 1.3 81.2 + - + +
99B THR* 1.3 63.3 + - + +
101B ILE* 4.0 11.4 + - - +
102B GLU* 5.1 5.7 + - - +
141B ARG* 2.7 33.4 + - - +
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Residues in contact with THR 99 (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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95B GLY 4.7 2.7 + - - -
96B SER* 3.7 14.4 + - - -
98B GLU* 1.3 80.7 - - + +
100B GLU* 1.3 67.0 + - - +
101B ILE 3.7 0.2 - - - -
102B GLU* 5.1 3.4 + - - +
103B GLN* 5.5 1.9 + - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.8 19.7 - - + -
89B HIS* 2.6 41.6 + - - -
93B GLN* 4.7 0.9 - - - +
96B SER* 3.1 23.5 + - - +
99B THR* 1.3 86.3 + - - +
101B ILE* 1.3 65.9 + - - +
102B GLU 3.3 3.0 + - - -
103B GLN* 3.5 9.7 + - - +
104B PHE* 3.2 20.4 + - - +
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Residues in contact with ILE 101 (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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86B PHE* 4.1 17.9 - - + -
97B PHE* 2.9 49.5 + - + +
98B GLU* 4.0 11.2 - - - +
100B GLU* 1.3 78.5 - - - +
102B GLU* 1.3 67.7 + - + +
104B PHE* 3.2 7.2 + - + +
105B ALA* 3.0 21.5 + - - +
142B LEU* 3.5 31.9 - - + -
145B TYR* 3.4 42.0 - - + +
146B LEU* 5.1 0.4 - - + -
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Residues in contact with GLU 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 GLU 5.1 5.1 + - - +
99B THR 5.1 2.9 + - - +
100B GLU 3.3 1.0 - - - -
101B ILE* 1.3 85.6 - - + +
103B GLN* 1.3 58.0 + - - +
105B ALA* 3.3 4.1 + - - +
106B GLU* 3.0 28.0 + - - +
145B TYR* 3.4 21.8 - - + +
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Residues in contact with GLN 103 (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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82B TYR* 5.0 2.7 - - - +
99B THR 5.5 1.5 + - - +
100B GLU* 3.5 11.5 + - + +
101B ILE 3.4 0.2 - - - -
102B GLU* 1.3 75.1 - - - +
104B PHE* 1.3 67.1 + - - +
106B GLU* 3.6 26.6 + - - +
107B THR* 2.9 54.3 + - - +
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Residues in contact with PHE 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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82B TYR* 3.5 40.8 + + - -
83B VAL* 4.2 24.9 - - + -
86B PHE* 3.4 63.3 - + + -
87B LEU* 5.5 0.9 - - + -
100B GLU 3.2 6.8 + - - +
101B ILE* 3.2 18.6 + - + +
103B GLN* 1.3 77.5 - - - +
105B ALA* 1.3 65.1 + - - +
107B THR* 3.3 1.4 + - - -
108B LEU* 3.0 54.1 + - + +
121B LEU* 4.5 2.2 - - + -
125B ILE* 5.7 0.2 - - + -
142B LEU* 4.2 18.8 - - + -
146B LEU* 4.3 9.4 - - + -
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Residues in contact with ALA 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 ILE 3.0 13.1 + - - +
102B GLU 3.8 6.3 - - - +
104B PHE* 1.3 76.6 - - - +
106B GLU* 1.3 51.6 + - - +
108B LEU* 3.3 6.5 + - - +
109B ASN* 2.8 42.4 + - - +
145B TYR* 3.8 22.0 - - + +
146B LEU* 4.4 13.7 - - + -
149B HIS* 4.0 21.5 - - + +
150B LEU* 4.7 0.9 - - + -
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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 GLU 3.0 17.0 + - - +
103B GLN* 3.6 26.9 + - - +
105B ALA* 1.3 74.8 - - - +
107B THR* 1.3 63.4 + - - +
109B ASN* 3.2 18.7 + - + +
110B GLY* 3.3 10.0 + - - -
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Residues in contact with THR 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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82B TYR* 3.3 40.8 + - + +
103B GLN* 2.9 32.2 + - - +
106B GLU* 1.3 71.5 - - - +
108B LEU* 1.3 67.1 + - - +
110B GLY* 3.2 4.2 + - - -
111B CYS* 3.1 27.4 + - + +
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Residues in contact with LEU 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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79B LEU* 3.7 29.8 - - + -
82B TYR* 4.2 9.6 - - + -
83B VAL* 4.0 13.7 - - + -
104B PHE* 3.0 55.4 + - + +
105B ALA 3.6 4.0 - - - +
107B THR* 1.3 76.8 - - - +
109B ASN* 1.3 58.5 + - - +
111B CYS* 3.2 3.5 + - - -
112B VAL* 2.8 43.4 + - + +
121B LEU* 3.9 21.5 - - + -
146B LEU* 4.2 13.0 - - + -
150B LEU* 3.9 11.0 - - + -
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Residues in contact with ASN 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 ALA* 2.8 25.2 + - - +
106B GLU* 3.2 10.1 + - + +
108B LEU* 1.3 73.6 - - - +
110B GLY* 1.3 61.1 + - - +
112B VAL 4.4 8.9 - - - +
113B THR* 5.2 2.3 - - - +
149B HIS 3.0 21.4 + - - -
150B LEU* 3.1 13.6 - - - +
151B THR* 2.8 49.9 + - + +
152B ILE* 4.5 2.3 + - - +
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Residues in contact with GLY 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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106B GLU 3.3 8.6 + - - -
107B THR* 3.2 7.8 + - - -
109B ASN* 1.3 79.0 - - - +
111B CYS* 1.3 59.3 + - - +
113B THR* 4.2 11.2 - - - +
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Residues in contact with CYS 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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79B LEU* 4.1 29.5 - - - +
82B TYR* 5.7 2.5 - - - -
107B THR* 3.1 25.7 + - + +
108B LEU* 4.1 7.9 - - - -
110B GLY* 1.3 78.8 - - - +
112B VAL* 1.3 62.5 + - - +
113B THR* 3.3 12.6 + - - +
117B ALA* 5.0 3.6 - - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 4.0 31.9 - - + -
108B LEU* 2.8 39.3 + - + +
109B ASN* 4.4 6.6 - - - +
111B CYS* 1.3 71.7 - - - +
113B THR* 1.3 61.3 + - - +
114B THR 4.4 0.2 - - - +
117B ALA* 3.9 5.8 - - + +
118B LEU* 3.6 47.3 - - + +
121B LEU* 4.6 9.2 - - + -
150B LEU* 6.0 2.0 - - + -
152B ILE* 3.3 24.7 - - + +
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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