Contacts of the helix formed by residues 96 - 110 (chain A) in PDB entry 2K4I
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.9 5.8 - - - -
20A ARG* 3.4 26.7 - - + +
22A ARG 4.0 7.4 - - - +
23A PRO* 3.6 26.5 - - + +
94A VAL* 3.8 11.3 - - - +
95A LYS* 1.3 83.6 - - - +
97A THR* 1.3 64.2 + - - +
98A GLU* 3.0 10.5 + - - +
99A GLY* 2.8 33.4 + - - +
100A ALA* 3.5 13.3 + - - +
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Residues in contact with THR 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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20A ARG 2.9 10.0 + - - -
21A LEU* 2.9 29.7 + - - +
29A TYR* 3.0 29.6 + - - +
80A ASN* 3.9 40.3 - - + +
84A VAL* 4.4 5.2 - - + -
96A ASP* 1.3 72.9 - - - +
98A GLU* 1.3 67.7 + - - +
100A ALA* 3.1 8.8 + - - +
101A LYS* 3.1 22.9 + - + +
300A PBU 4.6 2.4 + - - +
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Residues in contact with GLU 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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23A PRO* 4.4 25.5 - - + +
96A ASP* 3.0 12.8 + - - +
97A THR* 1.3 79.3 - - + +
99A GLY* 1.3 63.5 + - - +
101A LYS* 3.0 32.7 + - + +
102A GLN* 3.2 15.1 + - - +
300A PBU 5.7 3.6 - - - +
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Residues in contact with GLY 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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94A VAL* 3.8 9.6 - - - -
95A LYS 5.5 1.3 - - - -
96A ASP* 2.8 22.5 + - - -
97A THR 3.3 0.2 - - - -
98A GLU* 1.3 73.0 - - - +
100A ALA* 1.3 60.6 + - - +
102A GLN* 3.2 8.2 + - - +
103A ILE* 3.1 29.1 + - - +
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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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83A CYS* 4.1 11.9 - - + +
84A VAL* 3.9 23.6 - - + -
87A CYS* 4.0 4.4 - - - -
94A VAL* 3.4 32.1 - - + +
96A ASP 3.5 5.1 + - - +
97A THR 3.1 9.9 + - - +
99A GLY* 1.3 73.8 - - - +
101A LYS* 1.3 64.1 + - - +
104A VAL* 2.9 34.6 + - - +
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Residues in contact with LYS 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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68A VAL* 6.3 1.6 - - - -
79A PHE* 4.1 20.4 - - + -
80A ASN* 3.6 31.3 + - - +
83A CYS* 3.9 28.7 - - + +
97A THR* 3.1 12.2 + - + +
98A GLU* 3.0 26.0 + - + +
100A ALA* 1.3 76.9 - - - +
102A GLN* 1.3 61.4 + - - +
104A VAL* 4.2 0.7 - - - +
105A ARG* 3.2 25.5 + - - +
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Residues in contact with GLN 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 GLU* 3.2 12.6 + - - +
99A GLY* 3.5 10.3 - - - +
100A ALA 3.2 0.4 - - - -
101A LYS* 1.3 75.5 - - - +
103A ILE* 1.3 68.0 + - + +
105A ARG* 3.1 6.3 + - + +
106A ARG* 2.9 34.3 + - + +
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Residues in contact with ILE 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 CYS* 4.1 5.2 - - - -
92A GLU* 3.2 43.3 - - + +
93A LYS 3.6 12.3 - - - +
94A VAL* 3.2 30.7 - - + -
99A GLY 3.1 11.1 + - - +
100A ALA 4.1 3.4 - - - +
102A GLN* 1.3 77.4 - - + +
104A VAL* 1.3 62.1 + - - +
106A ARG* 3.4 7.1 + - - +
107A HIS* 2.9 38.1 + - + +
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Residues in contact with VAL 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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61A LEU* 3.2 31.9 - - + -
83A CYS* 3.0 37.5 - - - +
86A TRP* 4.2 17.7 - - + -
87A CYS* 3.8 10.8 - - - -
100A ALA 2.9 22.8 + - - +
101A LYS 4.2 0.2 - - - +
103A ILE* 1.3 76.3 - - - +
105A ARG* 1.3 63.7 + - - +
107A HIS* 2.9 20.0 + - - +
108A LEU* 2.9 26.9 + - + +
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Residues in contact with ARG 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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65A ASP* 3.9 30.6 + - - +
79A PHE* 6.0 1.6 - - - -
101A LYS 3.2 18.3 + - - +
102A GLN* 3.1 6.0 + - - +
104A VAL* 1.3 79.0 - - - +
106A ARG* 1.3 60.1 + - + +
108A LEU* 2.7 31.3 + - + +
109A VAL* 2.9 34.8 + - + +
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Residues in contact with ARG 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 GLN* 2.9 26.4 + - + +
103A ILE* 3.6 7.2 - - - +
105A ARG* 1.3 78.5 - - + +
107A HIS* 1.3 64.5 + - + +
109A VAL* 3.9 30.5 - - - +
110A ALA* 3.4 25.7 + - - +
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Residues in contact with HIS 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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58A GLN* 4.8 3.9 + - - -
86A TRP* 3.6 35.2 - + + -
92A GLU* 3.0 25.8 + - - +
103A ILE* 2.9 31.7 + - + +
104A VAL* 2.9 10.2 + - + +
106A ARG* 1.3 81.1 + - + +
108A LEU* 1.3 63.7 + - + +
110A ALA* 3.8 12.4 - - - +
111A GLU* 3.9 7.8 + - - +
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Residues in contact with LEU 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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58A GLN* 3.3 46.2 - - + +
61A LEU* 4.2 13.5 - - + -
62A THR* 5.2 3.1 - - - +
65A ASP* 3.4 26.7 - - - +
79A PHE* 6.1 0.4 - - + -
83A CYS* 6.1 0.2 - - - -
86A TRP* 6.0 2.7 - - + +
104A VAL* 2.9 35.1 + - + +
105A ARG* 2.7 17.3 + - + +
107A HIS* 1.3 71.0 - - + +
109A VAL* 1.3 61.6 + - + +
110A ALA 3.0 1.8 - - - -
111A GLU* 2.8 22.2 + - - +
112A THR* 3.0 17.7 + - - +
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Residues in contact with VAL 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 ARG* 2.9 40.6 + - + +
106A ARG* 3.9 28.3 - - - +
108A LEU* 1.3 76.3 - - + +
110A ALA* 1.3 56.6 + - - +
112A THR* 3.8 8.1 - - - +
113A GLY* 3.0 30.6 + - - -
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Residues in contact with ALA 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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106A ARG* 3.4 23.1 + - - +
107A HIS* 3.8 10.1 - - - +
108A LEU 3.0 0.6 - - - -
109A VAL* 1.3 81.0 - - - +
111A GLU* 1.3 58.8 + - - +
113A GLY 4.0 4.7 + - - -
114A THR* 4.0 15.4 + - - +
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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