Contacts of the helix formed by residues 101 - 117 (chain A) in PDB entry 1B3U
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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLU 3.0 3.6 + - - +
100A GLU* 1.3 79.6 + - - +
102A VAL* 1.3 69.2 + - - +
104A ARG* 2.9 40.9 + - - +
105A ASP* 2.9 34.7 + - - -
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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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66A LEU* 3.7 28.9 - - + +
100A GLU* 3.0 23.2 + - + +
101A THR* 1.3 86.9 + - - +
103A VAL* 1.3 62.5 + - + +
105A ASP* 3.6 10.5 + - + +
106A LYS* 3.4 15.6 + - + +
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Residues in contact with VAL 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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62A ASP* 3.7 29.8 - - + +
65A LEU* 4.0 26.5 - - + +
66A LEU* 4.1 15.7 - - + +
69A ALA* 4.6 2.2 - - + +
95A LEU* 3.9 25.8 - - + +
98A VAL* 4.6 9.2 - - + -
100A GLU* 2.8 28.0 + - + +
102A VAL* 1.3 76.6 - - + +
104A ARG* 1.3 66.8 - - - +
106A LYS* 3.1 12.8 + - - +
107A ALA* 3.1 11.8 + - - +
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Residues in contact with ARG 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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95A LEU 3.7 10.1 - - - +
96A ALA* 3.4 25.6 - - - +
98A VAL 3.0 29.3 + - - +
99A GLU* 2.6 31.9 + - - +
100A GLU 3.7 2.7 - - - +
101A THR* 2.9 45.0 + - - +
103A VAL* 1.3 77.4 - - - +
105A ASP* 1.3 60.3 + - - +
107A ALA* 3.4 2.8 + - - +
108A VAL* 3.0 34.0 + - - +
140A PHE* 5.3 4.9 - - - -
141A THR* 3.7 32.3 + - - +
144A THR* 4.3 9.3 + - - +
145A SER* 3.9 12.3 + - - +
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Residues in contact with ASP 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 THR* 2.9 28.1 + - - +
102A VAL* 3.7 9.0 - - - +
103A VAL 3.1 0.2 - - - -
104A ARG* 1.3 78.2 - - - +
106A LYS* 1.3 59.0 + - - +
108A VAL* 3.3 9.9 + - - +
109A GLU* 2.9 27.7 + - - +
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Residues in contact with LYS 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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66A LEU* 3.3 34.3 - - + +
69A ALA* 3.9 11.4 - - + -
70A GLU* 3.9 43.0 + - + +
102A VAL 3.4 3.5 + - - +
103A VAL 3.1 8.3 + - - +
105A ASP* 1.3 74.1 - - - +
107A ALA* 1.3 61.6 + - - +
109A GLU* 2.8 32.2 + - - +
110A SER* 2.8 34.5 + - - +
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Residues in contact with ALA 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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69A ALA* 4.0 4.8 - - + +
92A LEU* 3.8 35.7 - - + +
95A LEU* 3.9 11.9 - - + -
96A ALA* 3.8 16.8 - - + +
103A VAL 3.1 11.4 + - - +
104A ARG 3.6 7.9 - - - +
106A LYS* 1.3 76.0 - - - +
108A VAL* 1.3 52.1 + - - +
110A SER* 3.1 3.5 + - - -
111A LEU* 2.7 40.1 + - - +
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Residues in contact with VAL 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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96A ALA* 4.7 5.8 - - + -
104A ARG 3.0 20.0 + - - +
105A ASP* 3.5 13.7 - - - +
107A ALA* 1.3 78.1 - - - +
109A GLU* 1.3 58.0 + - - +
111A LEU* 3.2 10.1 + - + +
112A ARG* 2.9 40.5 + - - +
145A SER* 4.0 34.3 - - - +
148A GLY* 4.5 12.1 - - - +
149A LEU* 4.2 15.9 - - + -
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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 ASP 2.9 14.3 + - - +
106A LYS* 2.8 44.8 + - - +
108A VAL* 1.3 78.9 - - - +
110A SER* 1.3 61.1 + - - +
112A ARG* 3.3 11.0 + - - +
113A ALA* 3.1 21.5 + - + +
315B ASP* 5.3 7.4 - - - +
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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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69A ALA 2.8 27.2 + - - -
70A GLU* 4.2 4.5 + - - -
73A GLY* 3.6 20.7 - - - -
92A LEU* 3.9 14.4 - - - -
106A LYS* 2.8 14.4 + - - +
107A ALA 3.5 7.0 - - - -
109A GLU* 1.3 74.4 + - - +
111A LEU* 1.3 66.4 + - - +
113A ALA* 3.1 7.8 + - - +
114A ILE* 3.1 28.3 + - - +
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Residues in contact with LEU 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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89A LEU* 3.8 26.5 - - + -
92A LEU* 3.7 41.7 - - + +
93A GLU* 4.9 1.3 - - - +
96A ALA* 4.6 10.5 - - + -
107A ALA 2.7 27.7 + - - +
108A VAL* 3.2 7.2 + - + +
110A SER* 1.3 74.4 - - - +
112A ARG* 1.3 62.3 + - - +
114A ILE* 3.7 5.1 - - + +
115A SER* 3.1 25.1 + - - -
127A PHE* 3.7 9.3 - - + -
130A LEU* 4.0 19.7 - - + -
134A LEU* 5.1 1.3 - - + -
149A LEU* 3.8 26.9 - - + -
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Residues in contact with ARG 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 VAL* 2.9 29.4 + - - +
109A GLU* 3.6 8.5 - - + +
111A LEU* 1.3 77.4 - - - +
113A ALA* 1.3 61.3 + - - +
115A SER* 2.6 24.6 + - - -
116A HIS* 3.2 14.8 + - - +
148A GLY* 3.2 26.8 + - - +
149A LEU* 4.5 6.1 - - + -
151A SER* 3.5 17.0 + - - -
152A VAL* 3.6 26.4 - - + +
187A LYS* 5.2 3.4 - - - +
190A GLU* 3.1 33.7 + - - -
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Residues in contact with ALA 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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73A GLY* 4.7 7.9 - - - +
109A GLU 3.1 13.9 + - - +
110A SER* 3.4 12.6 - - - +
112A ARG* 1.3 79.4 - - - +
114A ILE* 1.3 65.5 + - + +
116A HIS* 3.4 22.8 + - - +
117A GLU* 4.4 4.0 + - - +
315B ASP* 3.9 31.0 - - - +
319B ASN* 5.1 6.6 + - - +
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Residues in contact with ILE 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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72A LEU 4.3 10.8 - - - +
73A GLY* 4.0 19.1 - - - +
76A THR* 3.9 20.2 - - - +
85A VAL* 4.8 3.8 - - + +
88A LEU* 4.2 17.3 - - + -
89A LEU* 4.1 21.8 - - + -
92A LEU* 3.7 26.9 - - + -
110A SER 3.1 13.2 + - - +
111A LEU* 3.7 7.0 - - + +
113A ALA* 1.3 71.6 - - - +
115A SER* 1.3 59.3 + - - +
116A HIS 3.0 2.9 - - - -
117A GLU* 2.7 32.3 + - + +
118A HIS* 2.9 22.9 - - - +
127A PHE* 5.4 0.2 - - + -
319B ASN* 6.2 1.1 - - - +
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Residues in contact with SER 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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111A LEU 3.1 17.7 + - - -
112A ARG 2.6 20.8 + - - -
114A ILE* 1.3 78.0 - - - +
116A HIS* 1.3 61.4 + - - +
117A GLU 3.0 0.2 - - - -
118A HIS* 3.0 31.2 + - - +
123A LEU* 3.9 7.5 - - - +
127A PHE* 3.6 25.1 - - - -
152A VAL* 3.6 23.3 + - - +
156A ARG* 3.2 11.9 + - - -
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Residues in contact with HIS 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 ARG* 3.2 24.3 + - - +
113A ALA* 3.4 15.3 - - - +
114A ILE 3.0 0.4 - - - -
115A SER* 1.3 88.6 + - - +
117A GLU* 1.3 63.2 + - + +
118A HIS 3.3 1.1 - - - +
152A VAL* 4.4 24.6 + - + +
156A ARG* 3.7 20.9 + - - +
279B LYS* 6.0 1.8 + - - -
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Residues in contact with GLU 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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76A THR* 4.0 21.5 - - + +
82A PRO* 3.9 32.7 - - - +
85A VAL* 3.6 22.7 - - + +
113A ALA 4.7 1.8 - - - +
114A ILE* 2.7 20.7 + - + +
116A HIS* 1.3 80.8 - - + +
118A HIS* 1.3 62.8 + - - +
119A SER 3.7 1.9 + - - -
318B GLU 4.7 0.2 - - - +
319B ASN* 2.7 53.8 - - - +
322B MET* 5.9 0.9 - - - +
323B SER* 5.2 6.9 - - - -
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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