Contacts of the helix formed by residues 99 - 112 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B THR* 4.9 1.8 + - - -
98B GLU* 1.3 77.1 + - - +
100B LYS* 1.3 65.2 + - + +
101B ALA* 3.0 41.1 - - + +
102B VAL* 2.8 21.0 + - + +
103B LEU 3.1 7.3 + - - -
146B MET* 3.7 7.5 - - - +
150B ASN* 3.7 10.3 + - - +
177B ASP* 4.2 5.1 + - - +
333B HIS* 4.9 2.9 - - - -
501B PLP 3.4 52.2 + + + +
503B CYS* 3.0 52.6 + - - -
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Residues in contact with LYS 100 (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 3.7 0.8 + - - -
99B HIS* 1.3 77.5 + - + +
101B ALA* 1.3 65.0 + - - +
102B VAL 3.1 0.2 - - - -
103B LEU* 3.8 13.1 - - + +
104B GLU* 2.9 53.3 + - + +
333B HIS* 4.2 32.7 + - + +
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Residues in contact with ALA 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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71B THR* 3.8 30.5 - - + +
74B ILE* 3.8 30.7 - - + +
75B ASN* 4.3 2.8 - - - +
99B HIS* 2.9 23.1 + - + -
100B LYS* 1.3 79.1 - - - +
102B VAL* 1.3 58.6 + - - +
104B GLU* 4.7 0.7 - - - +
105B THR* 2.8 26.0 + - - -
501B PLP 4.5 0.7 - - + -
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Residues in contact with VAL 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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74B ILE* 3.7 32.8 - - + -
78B LEU* 4.2 4.0 - - + -
94B THR* 4.0 13.5 - - - +
98B GLU* 3.8 24.5 - - + +
99B HIS 2.8 9.8 + - - +
101B ALA* 1.3 76.1 - - + +
103B LEU* 1.3 67.9 + - + +
105B THR* 3.0 5.0 + - - -
106B MET* 3.0 50.9 + - + +
144B SER* 4.1 13.0 - - - +
175B HIS* 4.9 0.7 - - + -
177B ASP* 4.2 11.7 - - + +
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Residues in contact with LEU 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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94B THR* 4.6 4.3 - - + -
95B THR 3.5 23.6 - - - +
96B PRO* 3.9 7.2 - - + +
98B GLU* 3.2 34.5 - - + +
99B HIS 3.1 4.8 + - - +
100B LYS* 4.1 9.9 - - + +
102B VAL* 1.3 79.1 - - - +
104B GLU* 1.3 60.9 + - + +
106B MET* 3.2 6.7 + - - +
107B LYS* 3.0 27.4 + - - +
118B TYR* 4.1 23.0 + - + +
333B HIS* 3.4 27.1 - - + +
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Residues in contact with GLU 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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100B LYS* 2.9 51.6 + - + +
101B ALA* 4.7 0.9 - - - +
103B LEU* 1.3 72.6 - - - +
105B THR* 1.3 64.6 + - - +
107B LYS* 3.5 25.6 + - - +
108B TYR* 3.2 18.9 + - - +
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Residues in contact with THR 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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75B ASN* 3.4 25.3 + - - +
78B LEU* 3.8 34.0 - - + +
79B LYS* 3.9 28.0 - - + +
101B ALA 2.8 19.3 + - - -
102B VAL 3.0 8.8 + - - -
104B GLU* 1.3 76.4 - - - +
106B MET* 1.3 61.4 + - - +
108B TYR* 2.9 10.5 + - - +
109B LEU* 2.9 30.4 + - + +
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Residues in contact with MET 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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78B LEU* 4.1 14.8 - - + -
92B ILE* 3.5 39.5 - - + -
94B THR* 3.7 24.5 - - + -
102B VAL* 3.0 30.9 + - + +
103B LEU* 3.4 8.7 - - - +
105B THR* 1.3 74.4 - - - +
107B LYS* 1.3 64.9 + - - +
109B LEU* 3.2 8.6 + - - +
110B SER* 2.9 27.0 + - - -
116B VAL* 3.7 14.8 - - + +
118B TYR* 3.9 16.2 - - - +
144B SER* 3.7 28.0 - - - -
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Residues in contact with LYS 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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103B LEU 3.0 13.2 + - - +
104B GLU* 3.5 31.6 - - - +
106B MET* 1.3 75.1 - - - +
108B TYR* 1.3 63.0 + - - +
110B SER* 3.3 9.8 + - - -
111B MET* 3.1 20.6 + - - +
118B TYR* 4.8 4.0 + - - +
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Residues in contact with TYR 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 LYS* 3.6 41.4 - - + +
104B GLU 3.2 12.5 + - - +
105B THR* 2.9 13.2 + - - +
107B LYS* 1.3 77.4 - - - +
109B LEU* 1.3 81.1 + - + +
111B MET* 3.0 31.2 + - - +
112B LYS* 3.1 46.8 + - + +
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Residues in contact with LEU 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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78B LEU* 3.9 21.8 - - + +
79B LYS* 4.5 11.0 - - + +
82B ALA* 3.8 24.2 - - + -
92B ILE* 3.4 27.6 - - + -
105B THR* 2.9 18.7 + - + +
106B MET* 3.2 12.5 + - - +
108B TYR* 1.3 96.1 - - + +
110B SER* 1.3 59.5 + - - +
112B LYS* 3.2 11.7 + - + +
113B GLY 3.4 0.9 + - - -
114B PHE* 3.0 46.1 + - + +
116B VAL* 4.9 1.3 - - + -
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Residues in contact with SER 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 MET 2.9 15.1 + - - -
107B LYS* 3.4 13.2 - - - -
109B LEU* 1.3 74.6 - - - +
111B MET* 1.3 57.6 + - - +
112B LYS 2.9 1.3 - - - -
113B GLY* 2.6 27.0 + - - -
114B PHE 3.6 13.5 + - - +
116B VAL* 3.3 21.2 + - - +
118B TYR* 5.3 1.2 + - - -
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Residues in contact with MET 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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107B LYS 3.1 8.4 + - - +
108B TYR* 3.0 23.3 + - - +
110B SER* 1.3 80.4 - - - +
112B LYS* 1.3 78.9 + - + +
113B GLY 3.2 3.1 + - - -
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Residues in contact with LYS 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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86B GLU* 5.6 1.9 - - - +
108B TYR* 3.1 53.3 + - + +
109B LEU* 3.5 13.9 - - + +
110B SER 2.9 1.4 + - - -
111B MET* 1.3 88.8 - - + +
113B GLY* 1.3 59.2 + - - +
114B PHE* 4.4 12.7 - - + -
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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