Contacts of the helix formed by residues 101 - 116 (chain A) in PDB entry 1RZR
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER 2.6 20.3 + - - +
99A ASP* 2.8 24.9 + - - +
100A GLN* 1.3 77.9 - - - +
102A GLN* 1.3 64.8 + - - +
103A ASP 3.3 0.2 - - - -
104A LYS* 2.8 22.1 - - - +
105A GLU* 3.0 24.7 + - - +
704A MG 2.0 30.5 - - - -
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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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100A GLN 3.8 3.2 + - - -
101A ASN* 1.3 72.3 - - - +
103A ASP* 1.3 105.3 + - - +
105A GLU* 3.7 12.9 - - - +
106A LEU* 3.1 33.5 + - + +
128A THR* 5.9 3.1 - - + -
131A HIS* 3.9 20.4 - - + +
704A MG 4.0 0.9 - - - -
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Residues in contact with ASP 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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101A ASN* 3.2 0.7 - - - +
102A GLN* 1.3 93.9 + - - +
104A LYS* 1.3 86.9 + - - +
106A LEU* 2.9 7.9 + - - +
107A HIS* 2.9 21.6 + - - +
704A MG 2.3 30.7 - - - -
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Residues in contact with LYS 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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96A SER* 4.7 5.2 - - - -
97A ASN 3.2 27.0 + - - +
98A SER* 4.2 8.1 - - - +
99A ASP* 4.8 6.6 + - + +
101A ASN* 2.8 23.9 + - - +
103A ASP* 1.3 89.4 + - - +
105A GLU* 1.3 57.3 + - - +
107A HIS* 3.1 16.2 + - + +
108A LEU* 2.7 46.6 + - + +
704A MG 4.0 0.4 - - - -
946A SO4 5.9 0.7 - - - -
80D ARG* 5.3 1.2 - - - +
83D GLU* 4.7 5.1 + - - -
84D ASP* 5.0 8.3 + - - -
87D THR* 4.3 25.4 - - - +
17Y ARG* 6.0 1.6 - - - +
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Residues in contact with GLU 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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66A ILE* 4.2 9.0 - - + +
98A SER* 3.4 32.1 + - - -
100A GLN* 3.5 14.6 - - - +
101A ASN 3.0 29.7 + - - +
102A GLN* 3.7 6.7 - - - +
103A ASP 3.1 0.2 - - - -
104A LYS* 1.3 76.9 - - - +
106A LEU* 1.3 60.2 + - - +
108A LEU* 3.5 4.9 - - - +
109A LEU* 2.9 26.0 + - - +
122A PHE* 3.7 19.1 - - + -
124A SER* 3.1 29.0 + - - -
131A HIS* 3.3 29.9 + - + -
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Residues in contact with LEU 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* 3.1 19.2 + - + +
103A ASP* 2.9 5.9 + - - +
105A GLU* 1.3 76.4 - - + +
107A HIS* 1.3 60.5 + - - +
109A LEU* 3.6 12.8 + - + +
110A ASN* 2.4 39.6 + - - +
122A PHE* 5.7 4.7 - - + -
130A GLU* 3.6 29.6 - - - +
131A HIS* 3.9 22.7 - - + +
134A GLU* 3.6 29.8 - - + -
135A LEU* 5.8 1.6 - - + -
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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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103A ASP 2.9 12.7 + - - +
104A LYS* 3.1 20.6 + - + +
106A LEU* 1.3 75.9 - - - +
108A LEU* 1.3 58.2 + - + +
110A ASN* 2.6 40.8 + - - +
111A ASN* 3.0 17.7 + - + -
946A SO4 3.4 29.6 + - - -
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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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66A ILE* 3.8 15.3 - - + -
96A SER* 3.3 50.7 - - - +
97A ASN 4.1 5.8 - - - +
98A SER* 3.9 25.4 - - - -
104A LYS* 2.7 29.2 + - + +
105A GLU 3.5 4.7 - - - +
107A HIS* 1.3 74.9 - - + +
109A LEU* 1.3 64.8 + - - +
110A ASN 3.0 0.7 + - - -
111A ASN* 3.3 5.6 + - - +
112A MSE 3.2 38.7 + - + +
946A SO4 4.0 21.3 - - - +
92D ASN* 5.8 0.7 - - - +
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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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66A ILE* 3.8 21.5 - - + +
105A GLU 2.9 17.5 + - - +
106A LEU* 3.7 14.8 - - + +
107A HIS 3.1 0.4 + - - -
108A LEU* 1.3 76.9 - - - +
110A ASN* 1.3 60.8 + - - +
112A MSE 3.8 3.8 + - - +
113A LEU* 3.2 42.3 + - + +
120A ILE* 4.0 21.4 - - + +
122A PHE* 4.4 7.4 - - + -
134A GLU* 4.3 30.3 - - + +
135A LEU* 3.7 34.3 - - + -
138A SER* 5.7 3.1 - - - -
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Residues in contact with ASN 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 LEU* 2.4 32.3 + - - +
107A HIS* 2.6 21.7 + - - +
109A LEU* 1.3 72.9 - - - +
111A ASN* 1.3 64.2 + - - +
112A MSE 2.9 2.6 + - - -
113A LEU* 2.9 13.3 + - - +
114A GLY* 2.8 23.0 + - - -
134A GLU* 6.0 0.6 + - - -
47D ARG* 5.1 11.2 + - + +
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Residues in contact with ASN 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 HIS* 3.0 22.4 + - + +
108A LEU* 3.7 13.8 - - - +
110A ASN* 1.3 74.8 - - - +
112A MSE 1.3 57.0 + - + +
114A GLY* 3.5 2.8 + - - -
115A LYS* 3.0 30.6 + - - +
946A SO4 1.9 41.2 + - - +
50D ALA* 5.5 0.2 - - - +
92D ASN* 3.3 28.9 + - - +
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Residues in contact with MSE 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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64A GLY* 3.4 31.6 - - - -
65A VAL 4.1 9.2 - - - +
66A ILE* 3.2 35.4 - - + -
94A ILE* 4.4 17.3 - - + -
96A SER* 4.6 6.5 - - - +
108A LEU* 3.2 35.4 + - + +
109A LEU* 3.8 4.0 - - - +
110A ASN 2.9 1.0 + - - -
111A ASN* 1.3 79.1 - - + +
113A LEU* 1.3 66.0 + - - +
114A GLY 2.9 1.1 - - - -
115A LYS* 2.8 21.2 + - + +
116A GLN 2.9 8.5 + - - -
117A VAL* 3.4 22.3 + - + +
120A ILE* 5.1 6.5 - - + -
92D ASN* 5.3 3.4 - - - +
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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 LEU* 3.2 27.5 + - + +
110A ASN* 2.9 16.4 + - - +
112A MSE 1.3 73.6 - - - +
114A GLY* 1.3 51.7 + - - +
116A GLN* 2.5 40.1 + - - -
117A VAL* 4.6 3.8 - - + +
120A ILE* 3.7 25.1 - - + -
137A LYS 5.2 0.7 - - - +
138A SER* 3.9 11.7 - - - +
139A PRO* 3.8 33.2 - - + -
140A VAL* 4.4 10.5 - - + -
47D ARG* 4.1 28.7 - - - +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ASN 2.8 13.7 + - - -
111A ASN* 3.8 2.7 - - - -
113A LEU* 1.3 73.9 - - - +
115A LYS* 1.3 53.3 + - - +
116A GLN* 2.7 32.5 + - - +
47D ARG* 4.7 10.4 - - - +
48D PRO* 3.5 18.5 - - - +
50D ALA* 3.2 17.5 + - - -
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Residues in contact with LYS 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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60A THR* 4.6 3.8 + - - +
94A ILE* 4.1 21.8 - - + -
111A ASN* 3.0 21.1 + - - +
112A MSE 3.0 16.4 - - - +
114A GLY* 1.3 72.2 - - - +
116A GLN* 1.3 71.6 + - - +
117A VAL* 3.6 6.8 + - + +
50D ALA* 3.8 23.8 - - + +
51D VAL* 3.8 12.2 - - - +
60D THR* 3.1 9.3 + - - -
61D THR* 2.8 30.3 + - - -
62D THR* 3.5 15.7 - - - -
92D ASN* 2.9 31.3 + - - +
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Residues in contact with GLN 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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58A LYS 5.1 3.8 - - - +
60A THR* 2.7 23.5 + - + +
112A MSE 2.9 2.2 + - - -
113A LEU 2.5 37.9 + - - -
114A GLY* 2.7 16.7 + - - +
115A LYS* 1.3 82.9 - - - +
117A VAL* 1.3 66.4 + - - +
118A ASP* 4.0 0.9 - - - +
2D ASN* 6.0 3.4 - - - +
47D ARG* 5.1 8.9 + - - +
48D PRO 4.8 0.6 + - - -
49D ASN* 2.6 36.9 + - + +
51D VAL* 4.3 15.9 - - + -
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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