Contacts of the helix formed by residues 102 - 118 (chain A) in PDB entry 1X3W
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU* 1.3 97.8 + - - +
103A ILE* 1.3 52.6 + - - +
104A TYR* 2.6 19.9 + - - -
105A THR* 2.9 28.8 + - + +
106A ASP* 4.1 1.4 + - - +
226A ASN* 3.3 26.9 - - + +
227A PHE* 3.8 22.6 - - - +
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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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92A PHE* 3.5 22.0 - - + -
96A GLY 4.6 1.3 - - - -
97A HIS* 3.6 31.4 - - + +
99A GLU 4.4 11.2 - - - +
101A GLU 3.1 8.8 - - - +
102A ASN* 1.3 75.5 - - - +
104A TYR* 1.3 63.7 + - - +
105A THR 3.3 0.2 - - - -
106A ASP* 3.3 30.7 + - + +
107A TYR* 3.0 40.7 - - + -
110A LYS* 6.3 0.7 - - - +
227A PHE* 3.4 43.2 - - + -
228A LEU* 5.2 0.7 - - + -
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.4 35.3 - + - -
88A VAL* 3.7 24.4 - - + +
89A ASP* 3.1 29.4 + - - -
92A PHE* 3.6 48.2 - + + -
101A GLU 3.9 4.4 + - - +
102A ASN* 2.6 8.1 + - - +
103A ILE* 1.3 78.2 - - - +
105A THR* 1.3 69.2 + - + +
107A TYR* 3.0 15.8 + - - +
108A LEU* 3.0 14.1 + - + -
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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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102A ASN* 3.0 28.3 - - + +
104A TYR* 1.3 80.3 - - + +
106A ASP* 1.3 59.8 + - - +
108A LEU* 2.9 27.7 - - - +
109A VAL* 3.0 9.9 + - - +
207A LEU* 4.3 13.4 - - - +
223A TYR* 3.1 21.9 + - - +
226A ASN* 5.6 9.0 - - - +
227A PHE 6.0 0.2 - - - +
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Residues in contact with ASP 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 ASN 4.7 1.3 - - - +
103A ILE* 3.3 27.6 + - + +
104A TYR 3.1 0.4 - - - -
105A THR* 1.3 76.4 - - - +
107A TYR* 1.3 60.1 + - + +
109A VAL* 2.9 6.9 + - - +
110A LYS* 2.7 44.4 + - - +
223A TYR* 2.6 30.5 + - - -
225A SER* 2.9 16.9 + - - -
227A PHE* 3.9 5.6 + - - +
228A LEU* 3.1 27.2 - - - +
241A PHE* 4.3 14.6 - - + -
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.6 16.6 - - + +
91A GLU* 3.1 51.1 - - + -
92A PHE* 3.7 11.7 - + + -
95A ASP* 4.3 4.9 + - + +
96A GLY* 3.5 9.8 + - - -
97A HIS* 3.0 29.8 + - + +
103A ILE* 3.0 47.3 - - + -
104A TYR* 3.0 9.2 + - - +
106A ASP* 1.3 81.2 - - + +
108A LEU* 1.3 52.7 + - - +
110A LYS* 3.6 17.7 - - + +
111A GLU* 2.7 35.9 + - - +
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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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84A ILE* 4.2 3.6 - - + -
85A TYR* 4.2 16.4 - - + +
88A VAL* 3.5 24.5 - - + +
104A TYR* 3.0 13.6 + - + +
105A THR* 2.9 23.3 - - - +
107A TYR* 1.3 73.5 - - - +
109A VAL* 1.3 55.2 + - - +
111A GLU* 2.9 4.3 + - - +
112A LEU* 2.6 61.8 + - + +
205A PHE* 3.9 31.0 - - + -
207A LEU* 4.2 25.1 - - + -
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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 THR 3.3 13.2 - - - +
106A ASP 2.9 7.1 + - - +
108A LEU* 1.3 70.8 - - - +
110A LYS* 1.3 55.0 + - - +
112A LEU* 2.8 13.3 + - - +
113A LEU* 2.7 51.3 + - + +
202A LEU* 4.1 17.9 - - + -
207A LEU* 3.6 21.8 - - + -
223A TYR* 3.4 42.4 - - + -
234A VAL* 4.6 7.0 - - + -
241A PHE* 4.2 6.5 - - + -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 6.3 0.8 - - - +
106A ASP* 2.7 26.6 + - + +
107A TYR* 3.6 18.1 - - + +
109A VAL* 1.3 71.6 - - - +
111A GLU* 1.3 58.2 + - - +
113A LEU* 2.9 26.9 - - - +
114A ARG* 3.3 5.7 + - - +
239A GLN* 4.8 1.9 + - - -
241A PHE* 3.5 56.6 - - + -
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Residues in contact with GLU 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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84A ILE* 4.4 10.6 - - + +
87A ASN* 3.1 34.8 + - + +
88A VAL* 3.8 16.8 - - + +
91A GLU* 6.3 2.2 - - + -
107A TYR 2.7 23.7 + - - +
108A LEU 3.4 3.6 - - - +
110A LYS* 1.3 69.9 - - - +
112A LEU* 1.3 69.8 + - - +
113A LEU 2.7 2.7 + - - -
114A ARG* 2.6 60.1 + - + +
115A TYR* 2.9 12.0 + - - +
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Residues in contact with LEU 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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79A LEU* 4.5 1.8 - - + -
84A ILE* 3.8 28.2 - - + +
108A LEU* 2.6 62.3 + - + +
109A VAL* 2.8 10.1 + - - +
111A GLU* 1.3 73.4 + - - +
113A LEU* 1.3 64.5 + - - +
115A TYR* 3.2 8.0 + - + +
116A PHE* 2.9 26.0 + - - +
198A PHE* 3.6 15.3 - - + -
201A ILE* 3.8 24.9 - - + -
202A LEU* 4.4 14.6 - - + -
205A PHE* 4.1 17.5 - - + -
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Residues in contact with LEU 113 (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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109A VAL* 2.7 40.1 + - + +
110A LYS* 2.9 18.2 - - - +
111A GLU 2.7 3.4 + - - -
112A LEU* 1.3 73.1 - - - +
114A ARG* 1.3 60.3 + - - +
116A PHE* 3.2 3.5 + - - +
117A LYS* 3.2 15.9 + - - +
198A PHE* 3.5 22.4 - - + -
234A VAL* 4.3 15.0 - - + -
235A ASP 3.9 4.3 - - - +
236A SER* 3.6 31.1 - - - +
239A GLN* 3.7 25.9 - - + +
240A SER 4.4 12.8 - - - +
241A PHE* 4.8 6.1 - - + +
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Residues in contact with ARG 114 (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 LEU* 4.7 3.8 - - - +
87A ASN* 3.5 13.7 - - - +
110A LYS 3.3 2.9 + - - +
111A GLU* 2.6 66.1 + - + +
113A LEU* 1.3 71.4 - - - +
115A TYR* 1.3 84.4 + - - +
117A LYS 2.9 0.7 + - - -
118A GLN* 2.8 47.9 + - - +
119A ASP* 2.4 42.6 + - - +
239A GLN* 3.2 29.0 - - - +
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Residues in contact with TYR 115 (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 THR 4.8 0.9 + - - -
79A LEU* 3.7 18.6 - - + -
80A ASP* 3.3 29.3 + - + +
83A LEU* 3.8 25.6 - - + -
84A ILE* 3.8 23.8 - - + -
111A GLU* 2.9 22.9 + - - +
112A LEU* 3.6 13.0 - - + +
114A ARG* 1.3 90.0 - - - +
116A PHE* 1.3 61.8 + + - +
119A ASP* 2.7 29.6 - - + +
120A PHE* 2.7 61.1 + + + -
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Residues in contact with PHE 116 (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 LEU* 5.9 0.7 - - + -
112A LEU 2.9 16.7 + - - +
113A LEU 3.6 2.7 - - - +
115A TYR* 1.3 80.5 - + + +
117A LYS* 1.3 60.7 + - - +
120A PHE* 3.1 34.5 + + + -
121A PHE* 2.8 55.8 + + + +
194A TRP* 3.6 34.5 - + - -
197A LEU* 3.5 20.2 - - + -
198A PHE* 3.4 23.6 - + + -
201A ILE* 3.2 32.5 - - + -
236A SER* 3.9 11.7 - - - +
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Residues in contact with LYS 117 (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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113A LEU 3.2 8.9 + - - +
114A ARG 2.9 5.7 + - - +
116A PHE* 1.3 79.4 - - - +
118A GLN* 1.3 63.5 + - + +
119A ASP 2.6 17.2 + - - -
121A PHE 3.7 12.6 - - - +
194A TRP* 5.0 13.2 - - + -
236A SER 4.6 7.2 - - - +
237A CYS 3.5 21.9 + - - +
238A GLU* 4.7 2.2 + - - +
239A GLN* 3.8 32.0 - - + +
1C GLC 4.7 10.3 + - - -
2D FRU 4.0 23.6 + - - -
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Residues in contact with GLN 118 (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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114A ARG* 2.8 34.1 + - - +
117A LYS* 1.3 88.9 - - + +
119A ASP* 1.3 70.0 + - - +
239A GLN* 2.9 29.3 + - - +
2D FRU 5.7 2.6 - - - -
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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