Contacts of the helix formed by residues 97 - 123 (chain A) in PDB entry 1XD7
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 CYS 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PRO* 4.7 2.1 - - + +
96A LYS* 1.3 84.0 + - - +
98A PRO* 1.3 86.3 - - - +
99A VAL* 3.2 30.3 - - - -
100A GLY* 3.3 8.9 + - - +
101A LYS* 3.2 19.4 + - - +
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Residues in contact with PRO 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS 4.2 3.6 - - - +
97A CYS* 1.3 93.5 - - - +
99A VAL* 1.3 66.1 + - + +
101A LYS* 3.4 10.9 + - + +
102A LYS* 3.0 27.8 + - + +
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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
----------------------------------------------------------
97A CYS* 3.2 22.4 - - - -
98A PRO* 1.3 76.1 - - + +
100A GLY* 1.3 67.1 + - - +
102A LYS* 3.1 12.7 + - + +
103A ILE* 3.1 36.0 + - + +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.4 24.0 - - - +
97A CYS* 3.3 11.2 + - - +
98A PRO 3.3 0.2 - - - -
99A VAL* 1.3 82.2 - - - +
101A LYS* 1.3 56.0 + - - +
103A ILE* 3.2 10.8 + - - +
104A GLN* 2.8 27.2 + - - +
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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
----------------------------------------------------------
95A PRO* 3.6 23.8 - - + +
96A LYS* 4.5 8.1 - - - +
97A CYS 3.2 14.1 + - - +
98A PRO* 3.6 11.4 - - + +
99A VAL 3.2 0.2 - - - -
100A GLY* 1.3 73.2 - - - +
102A LYS* 1.3 67.5 + - - +
104A GLN* 2.9 24.3 + - + +
105A ASN* 2.9 14.1 + - - +
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Residues in contact with LYS 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 PRO* 3.0 20.4 + - + +
99A VAL* 3.1 11.9 + - + +
101A LYS* 1.3 74.5 - - + +
103A ILE* 1.3 57.4 + - + +
105A ASN* 2.7 39.0 + - + +
106A ALA* 3.1 8.5 + - - +
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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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99A VAL* 3.1 27.6 + - + +
100A GLY* 3.5 9.9 - - - +
102A LYS* 1.3 79.5 - - + +
104A GLN* 1.3 65.7 + - - +
106A ALA* 2.8 9.7 + - + +
107A LEU* 2.8 45.6 + - + +
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN 5.3 2.9 + - - -
95A PRO* 4.7 16.5 - - + +
100A GLY 2.8 14.1 + - - +
101A LYS* 2.9 20.4 - - - +
103A ILE* 1.3 78.0 - - - +
105A ASN* 1.3 53.7 + - - +
107A LEU* 3.0 13.5 + - - +
108A ASP* 2.6 62.4 + - - +
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Residues in contact with ASN 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 LYS* 2.9 19.7 + - - +
102A LYS* 2.7 25.8 + - + +
104A GLN* 1.3 71.8 - - - +
106A ALA* 1.3 69.2 + - - +
108A ASP* 3.2 14.2 + - - +
109A GLU* 3.2 21.4 + - - +
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Residues in contact with ALA 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 LYS 3.1 5.8 + - - +
103A ILE* 2.8 16.6 + - + +
105A ASN* 1.3 73.9 - - - +
107A LEU* 1.3 73.0 + - + +
109A GLU* 2.4 40.3 - - - +
110A THR* 4.0 1.1 - - - -
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Residues in contact with LEU 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 ILE* 2.8 43.5 + - + +
104A GLN* 3.2 18.2 - - - +
106A ALA* 1.3 76.4 - - + +
108A ASP* 1.3 65.4 + - - +
110A THR* 2.9 21.3 + - + +
111A PHE* 3.0 49.8 + - + -
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Residues in contact with ASP 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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104A GLN* 2.6 47.6 + - - +
105A ASN* 3.4 18.2 - - - +
106A ALA 3.2 0.2 + - - -
107A LEU* 1.3 74.2 - - - +
109A GLU* 1.3 62.9 + - - +
111A PHE* 3.6 12.9 + - - +
112A GLU* 3.5 19.5 + - - +
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Residues in contact with GLU 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 ASN 3.2 9.1 + - - +
106A ALA* 2.4 24.9 - - - +
108A ASP* 1.3 76.4 - - - +
110A THR* 1.3 99.1 + - - +
112A GLU* 2.7 36.5 + - + +
113A SER* 3.0 9.2 + - - -
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Residues in contact with THR 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 ALA 3.2 6.8 + - - -
107A LEU* 2.9 12.6 + - + +
109A GLU* 1.3 110.9 + - - +
111A PHE* 1.3 63.9 + - + +
112A GLU 2.8 1.0 + - - -
113A SER* 2.6 32.2 + - - +
114A VAL* 2.9 21.4 + - + +
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Residues in contact with PHE 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 LEU* 3.0 45.9 + - + -
108A ASP* 3.7 13.5 - - - +
109A GLU 3.2 0.2 - - - -
110A THR* 1.3 81.4 - - + +
112A GLU* 1.3 56.4 + - - +
114A VAL* 4.2 10.5 - - + +
115A GLN* 2.9 28.2 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP 3.5 9.1 + - - +
109A GLU* 2.7 21.9 + - - +
111A PHE* 1.3 76.9 - - - +
113A SER* 1.3 59.8 + - - +
115A GLN* 3.5 5.1 - - + +
116A ARG* 2.9 63.7 + - + +
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Residues in contact with SER 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 GLU* 3.0 8.5 + - - -
110A THR* 2.6 25.0 + - - -
112A GLU* 1.3 70.2 - - - +
114A VAL* 1.3 65.8 + - - +
116A ARG* 3.3 7.2 + - - +
117A ALA* 3.0 22.1 + - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 2.9 23.8 + - + +
111A PHE* 4.2 10.3 - - + +
113A SER* 1.3 76.1 - - - +
115A GLN* 1.3 62.5 + - - +
117A ALA* 3.1 9.5 + - + +
118A MET* 2.8 30.4 + - + +
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Residues in contact with GLN 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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77A TYR* 4.6 10.9 + - - -
81A GLN* 5.1 3.6 - - - +
111A PHE 2.9 23.7 + - - +
112A GLU* 3.5 9.4 - - + +
114A VAL* 1.3 78.6 - - - +
116A ARG* 1.3 80.5 + - - +
118A MET* 3.1 30.7 + - - +
119A GLU* 2.8 57.3 + - - +
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Residues in contact with ARG 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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112A GLU* 2.9 55.7 + - + +
113A SER* 3.3 7.4 + - - +
115A GLN* 1.3 93.9 - - - +
117A ALA* 1.3 52.2 - - - +
119A GLU* 2.5 40.6 + - - +
120A ASN* 2.6 50.7 + - - +
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Residues in contact with ALA 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 SER 3.0 13.2 + - - +
114A VAL* 3.1 13.4 + - + +
116A ARG* 1.3 72.6 - - - +
118A MET* 1.3 69.0 + - - +
120A ASN* 2.7 20.3 + - - +
121A GLU* 3.2 12.0 + - - +
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Residues in contact with MET 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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77A TYR* 4.0 27.1 - - + +
114A VAL* 2.8 18.1 + - + +
115A GLN* 3.3 34.8 - - - +
117A ALA* 1.3 75.7 - - - +
119A GLU* 1.3 63.2 + - - +
120A ASN 3.0 0.3 + - - -
121A GLU* 3.1 15.4 + - - +
122A LEU* 3.4 35.6 + - + +
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Residues in contact with GLU 119 (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 LEU* 3.7 32.4 - - + +
77A TYR* 4.9 8.6 - - + -
78A ARG* 5.5 5.4 - - - +
115A GLN* 2.8 33.9 + - - +
116A ARG* 2.5 53.6 + - - +
118A MET* 1.3 75.9 - - + +
120A ASN* 1.3 66.6 + - - +
122A LEU* 3.7 5.0 + - + -
123A ALA* 3.4 21.3 + - - +
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Residues in contact with ASN 120 (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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116A ARG* 2.6 34.2 + - - +
117A ALA* 2.7 12.8 + - - +
119A GLU* 1.3 75.7 + - - +
121A GLU* 1.3 66.0 + - - +
123A ALA* 3.4 9.1 + - - +
124A SER* 3.4 14.9 + - - -
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Residues in contact with GLU 121 (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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117A ALA 3.2 8.7 + - - +
118A MET* 3.1 10.1 + - - +
120A ASN* 1.3 72.4 - - - +
122A LEU* 1.3 57.1 + - + +
123A ALA 2.7 4.5 + - - -
124A SER* 2.4 56.4 + - - -
125A LYS* 3.3 26.8 + - - +
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Residues in contact with LEU 122 (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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8A LEU* 4.1 18.8 - - + -
73A LEU* 3.1 35.9 + - + +
74A LEU* 2.6 43.3 + - + +
77A TYR* 4.1 31.6 - - + -
118A MET* 3.4 34.0 + - + +
119A GLU* 3.9 4.7 - - - +
120A ASN 3.4 0.2 - - - -
121A GLU* 1.3 79.7 - - + +
123A ALA* 1.3 56.8 + - - +
125A LYS* 3.7 4.9 - - - +
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Residues in contact with ALA 123 (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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72A SER* 4.2 12.7 - - - +
74A LEU* 3.7 16.6 - - + -
119A GLU 3.4 15.2 + - - +
120A ASN* 3.7 10.5 - - - +
121A GLU 2.7 3.0 + - - -
122A LEU* 1.3 76.8 - - - +
124A SER* 1.3 63.3 + - - +
125A LYS 3.5 4.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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