Contacts of the helix formed by residues 90 - 111 (chain A) in PDB entry 3U0V
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 5.4 2.3 + - - -
79A ASP* 3.4 41.4 + - + +
80A ARG* 4.7 1.9 - - - +
81A PHE* 3.6 36.7 - + + -
88A PRO 3.7 0.4 + - - -
89A GLU* 1.3 70.7 - - - +
91A LEU* 1.3 66.2 + - - +
92A GLU* 3.5 22.3 - - + +
93A SER* 2.7 53.5 + - - -
94A ILE* 3.2 15.0 + - - +
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Residues in contact with LEU 91 (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 GLU* 3.2 36.5 + - + +
90A HIS* 1.3 75.4 - - - +
92A GLU* 1.4 66.8 + - - +
94A ILE* 3.3 7.6 + - + -
95A ASP* 2.8 56.1 + - - +
136A ARG* 3.4 34.3 - - - +
156A ALA* 3.8 11.9 - - + -
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Residues in contact with GLU 92 (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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81A PHE* 5.8 1.4 - - - -
89A GLU 5.0 0.5 - - - +
90A HIS* 3.5 28.0 + - + +
91A LEU* 1.4 88.0 + - - +
93A SER* 1.3 58.9 + - - +
95A ASP* 3.4 5.5 + - - +
96A VAL* 3.1 28.4 + - + +
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Residues in contact with SER 93 (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 ARG* 3.7 22.4 - - - +
77A TRP 4.3 0.7 - - - +
78A PHE* 3.4 6.5 - - - +
79A ASP* 2.9 28.8 + - - -
90A HIS* 2.7 38.0 + - - +
92A GLU* 1.3 73.7 - - - +
94A ILE* 1.3 67.1 + - - +
96A VAL* 3.3 9.3 + - - +
97A MET* 3.1 23.7 + - - +
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Residues in contact with ILE 94 (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 PHE* 3.7 39.5 - - + -
89A GLU* 3.9 25.4 - - + -
90A HIS 3.2 17.2 + - - +
91A LEU* 3.3 8.3 + - - +
93A SER* 1.3 83.3 + - - +
95A ASP* 1.4 56.5 + - - +
97A MET* 3.3 4.3 + - - -
98A CYS* 2.8 29.1 + - - -
128A CYS* 5.0 1.8 - - - -
129A MET* 3.8 7.8 - - + +
132A HIS* 3.5 54.7 - - + +
136A ARG* 3.7 11.2 - - - +
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Residues in contact with ASP 95 (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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91A LEU* 2.8 33.8 + - - +
92A GLU* 3.9 5.4 - - - +
94A ILE* 1.4 73.2 - - - +
96A VAL* 1.3 69.4 + - + +
98A CYS* 3.2 10.0 + - - +
99A GLN* 3.1 20.6 + - - +
136A ARG* 2.8 40.9 + - - -
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Residues in contact with VAL 96 (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 ARG* 6.3 1.3 - - - +
92A GLU* 3.1 20.9 + - + +
93A SER* 3.6 11.0 - - - +
94A ILE 3.3 0.2 - - - -
95A ASP* 1.3 77.6 - - - +
97A MET* 1.3 67.6 + - + +
99A GLN* 3.0 20.8 + - - +
100A VAL* 3.1 23.9 + - + +
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Residues in contact with MET 97 (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 PRO* 4.0 26.9 - - + -
64A ARG* 6.0 3.6 - - - -
76A VAL 4.9 2.2 - - - +
77A TRP* 3.2 58.8 - - + +
93A SER 3.1 10.3 + - - +
94A ILE 3.9 0.2 - - - +
96A VAL* 1.3 84.0 - - + +
98A CYS* 1.4 63.1 + - - +
100A VAL* 3.8 26.7 - - + -
101A LEU* 2.9 29.9 + - + +
129A MET* 3.7 23.8 - - - -
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Residues in contact with CYS 98 (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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94A ILE* 2.8 35.5 + - - -
95A ASP* 3.2 13.2 + - - +
97A MET* 1.4 72.7 - - - +
99A GLN* 1.4 58.2 + - - +
102A THR* 2.8 34.3 + - - +
129A MET* 3.6 17.9 - - - +
132A HIS* 4.2 11.2 - - - -
133A LEU* 3.7 8.1 - - + +
136A ARG* 4.3 7.0 - - - -
137A ASN* 3.6 32.3 - - - +
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Residues in contact with GLN 99 (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 ASP 3.1 10.2 + - - +
96A VAL* 3.0 10.9 + - - +
98A CYS* 1.4 77.6 - - - +
100A VAL* 1.3 65.1 + - + +
102A THR* 3.2 16.9 + - - +
103A ASP* 2.9 50.4 + - - +
106A ASP* 5.7 0.2 + - - -
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Residues in contact with VAL 100 (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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9A LEU* 3.7 38.2 - - + +
62A PRO* 5.4 2.9 - - + -
96A VAL* 3.1 21.8 + - + +
97A MET* 3.8 24.2 - - + +
99A GLN* 1.3 78.1 - - + +
101A LEU* 1.4 61.5 + - - +
103A ASP* 3.2 26.1 + - - +
104A LEU* 3.4 6.2 + - - +
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Residues in contact with LEU 101 (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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9A LEU* 3.6 25.8 - - + -
25A ILE* 5.3 1.8 - - + -
27A LEU* 4.1 13.9 - - + -
59A PRO* 4.3 6.3 - - + -
77A TRP* 4.0 14.6 - - + -
97A MET* 2.9 34.7 + - + +
100A VAL* 1.4 70.1 - - - +
102A THR* 1.3 65.9 + - - +
104A LEU* 3.1 19.8 + - + +
105A ILE* 2.9 28.0 + - + +
129A MET* 3.5 32.3 - - + -
133A LEU* 3.4 26.7 - - + -
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Residues in contact with THR 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 CYS* 2.8 23.7 + - - +
99A GLN* 3.2 22.2 + - - +
101A LEU* 1.3 79.4 - - - +
103A ASP* 1.3 58.7 + - - +
105A ILE* 3.2 3.7 + - - +
106A ASP* 2.8 43.5 + - - +
133A LEU* 3.6 4.6 - - - +
137A ASN* 4.7 4.2 - - - +
138A HIS* 2.7 38.5 + - + +
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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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99A GLN* 2.9 39.6 + - - +
100A VAL* 3.2 13.7 + - - +
102A THR* 1.3 78.2 - - - +
104A LEU* 1.3 56.3 + - - +
106A ASP* 3.4 9.6 + - - +
107A GLU* 2.9 30.1 + - - +
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Residues in contact with LEU 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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9A LEU* 4.4 8.7 - - + -
11A ARG* 3.3 27.1 - - - +
25A ILE* 4.1 23.6 - - + -
57A ILE* 4.2 17.7 - - + -
59A PRO* 3.9 32.3 - - + -
100A VAL 3.4 4.4 + - - +
101A LEU* 3.1 22.1 + - + +
103A ASP* 1.3 74.1 - - - +
105A ILE* 1.4 66.0 + - - +
107A GLU* 2.8 47.3 - - - +
108A GLU* 3.2 8.4 + - - +
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Residues in contact with ILE 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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25A ILE* 3.7 26.0 - - + -
101A LEU 2.9 18.9 + - - +
102A THR* 3.6 5.8 - - - +
104A LEU* 1.4 74.1 - - - +
106A ASP* 1.3 60.2 + - - +
108A GLU* 3.1 6.9 + - - +
109A VAL* 3.0 26.0 + - - +
115A LYS* 3.5 35.0 - - + -
118A ILE* 3.9 14.1 - - + -
120A ILE* 5.2 10.3 - - + -
133A LEU* 3.8 20.4 - - + -
138A HIS* 3.7 33.9 - - + +
141A VAL* 5.6 1.1 - - + -
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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 THR* 2.8 37.1 + - - +
103A ASP* 3.7 10.9 - - - +
105A ILE* 1.3 80.9 - - - +
107A GLU* 1.3 60.5 + - - +
109A VAL* 3.9 7.7 - - - +
110A LYS* 3.0 31.5 + - - +
115A LYS* 4.8 9.5 - - - -
138A HIS* 4.9 2.3 - - - -
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Residues in contact with GLU 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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11A ARG* 2.4 41.1 + - - -
103A ASP 2.9 12.6 + - - +
104A LEU* 2.8 40.0 + - + +
106A ASP* 1.3 74.8 - - - +
108A GLU* 1.4 68.7 + - - +
110A LYS* 3.5 11.4 + - - +
111A SER* 3.3 22.2 + - - -
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Residues in contact with GLU 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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20A HIS* 3.3 7.6 - - - -
23A SER* 2.5 32.9 + - - +
25A ILE* 5.1 3.6 - - + -
55A LYS* 3.0 33.1 + - - -
57A ILE* 3.6 22.5 - - + +
104A LEU* 3.2 12.6 + - + +
105A ILE* 3.1 12.5 + - - +
107A GLU* 1.4 80.6 - - + +
109A VAL* 1.3 66.7 + - - +
110A LYS 3.1 1.6 - - - -
111A SER* 3.1 22.8 + - - -
113A ILE* 3.2 17.1 + - + +
118A ILE* 3.8 15.9 - - + -
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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 ILE 3.0 20.7 + - - +
106A ASP* 3.9 9.2 - - - +
108A GLU* 1.3 75.0 - - - +
110A LYS* 1.3 58.6 + - - +
112A GLY* 3.0 22.2 + - - -
113A ILE 3.1 20.7 + - - +
114A LYS* 5.2 2.2 - - - -
115A LYS* 4.1 31.4 - - + +
118A ILE* 3.8 13.2 - - + -
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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
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106A ASP 3.0 19.0 + - - +
107A GLU* 3.7 10.1 - - - +
108A GLU 3.1 0.2 - - - -
109A VAL* 1.3 78.3 - - - +
111A SER* 1.4 57.3 + - - +
112A GLY 3.3 1.0 + - - -
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Residues in contact with SER 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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20A HIS* 5.6 4.0 - - - -
55A LYS* 5.6 1.8 + - - -
107A GLU 3.3 12.3 + - - -
108A GLU* 3.1 21.5 + - - -
109A VAL 3.1 0.2 - - - -
110A LYS* 1.4 76.9 - - - +
112A GLY* 1.3 56.2 + - - +
113A ILE* 4.6 8.5 - - - +
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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