Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 1ECX
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 HIS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A THR* 5.3 1.0 + - - -
97A ILE 3.9 0.8 + - - -
98A GLU* 1.3 74.2 + - - +
100A LYS* 1.3 67.7 + - + +
101A ALA* 3.1 39.2 + - + +
102A VAL* 2.8 22.3 + - + +
103A LEU 3.0 9.9 + - - -
146A MET* 4.2 5.7 - - - +
150A ASN* 3.5 10.1 + - - +
177A ASP* 4.2 4.5 + - - +
333A HIS* 5.1 2.0 - - - -
500A PLP 3.5 51.4 + + + +
502A CYS* 3.4 50.0 + - + -
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Residues in contact with LYS 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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98A GLU 3.7 1.4 + - - -
99A HIS* 1.3 81.7 + - + +
101A ALA* 1.3 64.7 + - - +
103A LEU* 3.6 12.6 - - + +
104A GLU* 2.7 51.4 + - + +
333A HIS* 4.6 25.8 + - + +
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Residues in contact with ALA 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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71A THR* 4.1 31.2 - - + +
74A ILE* 3.8 28.2 - - + +
75A ASN* 4.3 2.3 - - - +
99A HIS* 2.9 22.8 + - + -
100A LYS* 1.3 78.1 - - - +
102A VAL* 1.3 59.4 + - - +
104A GLU* 4.7 0.7 - - - +
105A THR* 3.0 26.2 + - - -
500A PLP 4.6 1.1 - - + -
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Residues in contact with VAL 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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74A ILE* 3.7 32.3 - - + -
78A LEU* 4.2 3.4 - - + -
94A THR* 4.0 20.9 - - + +
98A GLU* 3.8 24.7 - - + +
99A HIS* 2.8 11.2 + - + +
101A ALA* 1.3 76.7 - - + +
103A LEU* 1.3 65.9 + - - +
105A THR* 3.1 4.9 + - - -
106A MET* 2.9 40.7 + - + +
144A SER* 4.0 17.9 - - - +
175A HIS* 5.0 0.9 - - + -
177A ASP* 4.5 11.4 - - + +
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Residues in contact with LEU 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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94A THR* 4.8 3.1 - - + -
95A THR 3.6 22.7 - - - +
96A PRO* 3.8 8.3 - - + +
98A GLU* 3.2 32.5 - - + +
99A HIS 3.0 9.4 + - - +
100A LYS* 4.1 8.1 - - + +
102A VAL* 1.3 75.3 - - + +
104A GLU* 1.3 62.5 + - - +
106A MET* 3.3 5.0 + - - +
107A LYS* 2.9 26.7 + - - +
118A TYR* 3.9 23.6 + - + +
333A HIS* 3.4 26.7 - - + +
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Residues in contact with GLU 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 LYS* 2.7 50.2 + - + +
101A ALA* 4.7 1.3 - - - +
103A LEU* 1.3 73.5 - - - +
105A THR* 1.3 59.4 - - - +
107A LYS* 3.2 25.3 + - - +
108A TYR* 2.9 27.7 + - - +
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Residues in contact with THR 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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74A ILE 4.6 1.3 - - - +
75A ASN* 3.1 27.4 + - - -
78A LEU* 3.3 38.6 - - + -
79A LYS* 4.2 22.4 - - + +
101A ALA 3.0 21.5 + - - -
102A VAL 3.1 5.0 + - - -
104A GLU* 1.3 78.2 - - - +
106A MET* 1.3 56.3 + - - +
108A TYR* 3.0 9.7 - - - +
109A LEU* 3.0 29.8 + - + +
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Residues in contact with MET 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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78A LEU* 3.7 28.5 - - + -
92A ILE* 3.5 39.5 - - + -
94A THR* 4.1 17.5 - - + -
102A VAL* 2.9 25.8 + - + +
103A LEU* 3.4 10.5 - - - +
105A THR* 1.3 72.5 - - - +
107A LYS* 1.3 66.1 + - - +
108A TYR 3.0 2.0 + - - -
109A LEU* 3.1 7.7 + - - +
110A SER* 2.9 26.9 + - - -
116A VAL* 3.8 15.6 - - + +
118A TYR* 3.7 15.3 - - - +
144A SER* 3.7 23.6 - - - -
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Residues in contact with LYS 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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103A LEU 2.9 14.6 + - - +
104A GLU* 3.5 29.4 - - - +
106A MET* 1.3 74.3 - - - +
108A TYR* 1.3 62.7 + - - +
110A SER* 3.4 9.0 + - - -
111A MET* 3.2 22.4 + - + +
118A TYR* 4.6 4.2 + - - +
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Residues in contact with TYR 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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79A LYS* 3.6 41.6 - - + +
104A GLU 2.9 12.9 + - - +
105A THR* 3.0 12.6 - - - +
107A LYS* 1.3 75.7 - - - +
109A LEU* 1.3 81.5 + - + +
111A MET* 3.2 19.3 + - + +
112A LYS* 3.1 61.1 + - + +
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Residues in contact with LEU 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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78A LEU* 4.1 16.8 - - + +
79A LYS* 4.4 10.8 - - - +
82A ALA* 4.0 25.1 - - + -
92A ILE* 3.4 27.6 - - + -
105A THR* 3.0 25.9 + - + +
106A MET* 3.1 12.8 + - - +
108A TYR* 1.3 91.2 - - + +
110A SER* 1.3 66.8 + - - +
112A LYS* 3.0 14.4 + - + +
113A GLY 3.2 0.9 + - - -
114A PHE* 3.0 40.3 + - + -
116A VAL* 4.9 0.9 - - + -
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Residues in contact with SER 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 MET 2.9 9.8 + - - -
107A LYS* 3.5 11.0 - - - -
109A LEU* 1.3 75.1 - - - +
111A MET* 1.3 56.1 + - - +
113A GLY* 2.7 26.7 + - - -
114A PHE 3.4 16.7 + - - +
116A VAL* 3.0 28.5 + - - +
118A TYR* 4.9 1.6 + - - -
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Residues in contact with MET 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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107A LYS* 3.2 9.5 + - + +
108A TYR* 3.2 22.8 + - + +
110A SER* 1.3 78.2 - - - +
112A LYS* 1.3 83.6 + - + +
113A GLY 3.2 2.7 + - - -
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Residues in contact with LYS 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 TYR* 3.1 56.9 + - + +
109A LEU* 3.0 15.5 + - + +
110A SER 3.0 1.2 - - - -
111A MET* 1.3 95.4 - - - +
113A GLY* 1.3 57.3 + - - +
114A PHE* 3.6 15.1 + - + -
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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