Contacts of the helix formed by residues 91 - 106 (chain A) in PDB entry 2K21
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ILE* 4.6 12.1 - - - +
84A SER* 6.2 0.2 - - - -
87A TRP* 4.7 11.3 + - - -
88A GLN 5.4 1.2 + - - -
89A GLU* 2.9 30.7 + - - +
90A LYS* 1.4 78.3 - - - +
92A LYS* 1.4 50.6 + - - +
93A ALA 3.3 1.6 - - - -
94A TYR* 2.8 45.8 + - + +
95A VAL* 2.7 43.7 + - + -
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Residues in contact with LYS 92 (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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89A GLU* 5.5 3.7 - - + +
90A LYS* 3.1 19.2 - - + +
91A ASP* 1.4 74.0 - - - +
93A ALA* 1.4 56.1 + - - +
95A VAL* 4.3 7.6 - - + -
96A GLN* 3.0 54.5 + - - +
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Residues in contact with ALA 93 (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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78A PHE* 5.7 1.5 - - - -
91A ASP 3.1 0.4 + - - -
92A LYS* 1.4 80.5 - - - +
94A TYR* 1.4 80.8 + - + +
96A GLN* 4.0 4.5 - - - +
97A ALA* 3.6 18.2 + - - +
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Residues in contact with TYR 94 (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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78A PHE* 3.6 54.7 - + + -
82A ILE* 3.8 36.2 - - + +
89A GLU* 4.8 14.0 - - + +
91A ASP* 2.8 43.3 + - + +
93A ALA* 1.4 90.6 - - + +
95A VAL* 1.4 53.5 + - + +
96A GLN 3.3 0.9 - - - -
97A ALA* 3.1 8.5 + - - +
98A ARG* 2.7 45.0 + - + +
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Residues in contact with VAL 95 (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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90A LYS 3.9 7.2 - - - +
91A ASP* 2.7 44.1 + - + +
92A LYS* 4.3 6.1 - - + -
94A TYR* 1.4 67.1 - - + +
96A GLN* 1.4 51.3 + - - +
98A ARG* 3.3 6.4 + - - -
99A VAL* 2.4 57.8 + - + +
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Residues in contact with GLN 96 (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 LYS* 3.0 45.1 + - - +
93A ALA* 4.0 7.0 - - - +
94A TYR 3.2 0.2 + - - -
95A VAL* 1.4 77.6 - - - +
97A ALA* 1.4 58.9 + - - +
99A VAL* 3.9 10.0 + - - +
100A LEU* 3.8 17.5 + - - +
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Residues in contact with ALA 97 (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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78A PHE* 5.0 16.8 - - + -
93A ALA 3.6 10.1 + - - +
94A TYR* 3.1 9.2 + - - +
96A GLN* 1.4 74.3 - - - +
98A ARG* 1.4 68.6 + - + +
100A LEU* 3.7 8.0 + - - +
101A GLU* 3.5 18.4 + - - +
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Residues in contact with ARG 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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76A ASP* 4.6 16.6 + - - -
77A PRO* 6.2 0.4 - - - +
78A PHE* 3.9 32.8 - - + -
94A TYR* 2.7 33.1 + - + +
95A VAL* 3.8 5.8 - - - +
97A ALA* 1.4 72.3 + - - +
99A VAL* 1.4 55.8 + - - +
101A GLU* 3.0 40.8 + - - +
102A SER* 2.5 44.9 + - - +
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Residues in contact with VAL 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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95A VAL* 2.4 56.3 + - + +
96A GLN* 4.0 10.8 - - - +
97A ALA 3.6 0.4 - - - -
98A ARG* 1.4 66.7 - - - +
100A LEU* 1.4 58.8 + - + +
102A SER* 3.5 7.0 - - - -
103A TYR* 2.5 45.3 + - + +
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Residues in contact with LEU 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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96A GLN 3.8 8.1 + - - +
97A ALA* 3.7 8.6 + - - +
98A ARG 3.4 0.4 - - - -
99A VAL* 1.4 80.7 - - + +
101A GLU* 1.4 59.6 + - - +
103A TYR* 3.9 14.2 - - + +
104A LYS* 3.5 21.3 + - - +
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Residues in contact with GLU 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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97A ALA 3.5 10.8 + - - +
98A ARG* 3.0 38.6 + - - +
100A LEU* 1.4 76.2 - - - +
102A SER* 1.4 57.2 + - - +
104A LYS* 3.5 20.8 + - - +
105A SER* 3.1 27.0 + - - -
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Residues in contact with SER 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 ARG* 2.5 46.3 + - - +
99A VAL* 3.0 10.7 + - - +
101A GLU* 1.4 63.9 - - - +
103A TYR* 1.4 51.5 + - - +
105A SER* 3.0 8.6 + - - -
106A CYS* 2.5 48.0 + - - +
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Residues in contact with TYR 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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99A VAL* 2.5 43.7 + - + +
100A LEU* 3.9 14.1 - - + +
102A SER* 1.4 68.0 + - - +
104A LYS* 1.4 63.6 + - + +
106A CYS* 3.8 16.8 + - + +
107A TYR* 4.1 6.4 + - - +
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Residues in contact with LYS 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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100A LEU 3.5 16.1 + - - +
101A GLU* 3.7 22.7 + - - +
102A SER 3.3 0.2 - - - -
103A TYR* 1.4 82.3 - - + +
105A SER* 1.4 63.8 + - - +
106A CYS 3.5 0.2 - - - -
107A TYR* 3.5 18.8 - - - +
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Residues in contact with SER 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 GLU 3.1 16.4 + - - -
102A SER* 3.0 9.0 + - - -
104A LYS* 1.4 79.1 + - - +
106A CYS* 1.4 55.7 + - - +
107A TYR 3.2 6.5 + - - -
108A VAL* 2.9 31.3 + - - +
124A GLU* 5.5 3.3 + - - -
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Residues in contact with CYS 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 SER* 2.5 39.2 + - - +
103A TYR* 3.9 13.5 - - + +
104A LYS 3.5 0.8 - - - -
105A SER* 1.4 65.6 - - - +
107A TYR* 1.4 62.1 + - - +
108A VAL 3.5 6.4 + - - +
109A VAL* 4.9 5.7 - - - +
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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