Contacts of the helix formed by residues 90 - 109 (chain A) in PDB entry 3L32
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 1.3 58.8 + - - +
92A LEU* 3.4 9.4 + - - +
93A PHE* 3.0 29.6 + - + +
94A GLN* 2.9 34.0 + - - +
128A TYR* 4.3 2.0 + - - -
133A PHE* 3.5 31.1 - - - -
126B VAL* 4.1 24.2 - - + +
130B THR* 5.2 5.4 + - - +
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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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90A ASN* 1.3 73.9 + - - +
92A LEU* 1.3 59.3 + - - +
94A GLN* 4.3 17.0 - - - +
95A SER* 2.8 41.2 + - - +
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Residues in contact with LEU 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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90A ASN* 3.3 5.8 + - - +
91A LEU* 1.3 80.0 - - - +
93A PHE* 1.3 57.7 + - - +
95A SER* 3.1 10.4 + - - +
96A TYR* 3.0 26.0 + - - +
128A TYR* 3.2 20.6 - - + +
132A ASN* 4.4 13.0 - - - +
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASN* 3.0 24.2 + - + +
92A LEU* 1.3 72.9 - - - +
94A GLN* 1.3 66.9 + - - +
96A TYR* 3.2 4.7 + + - +
97A LEU* 2.9 41.6 + - + +
125A ILE* 4.3 7.9 - - + -
128A TYR* 3.2 45.4 + + + +
129A VAL* 3.8 19.3 - - + -
133A PHE* 4.4 11.7 - + + -
125B ILE* 3.8 26.0 - - + -
126B VAL* 3.8 22.7 - - + -
129B VAL* 3.9 25.8 - - + -
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Residues in contact with GLN 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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90A ASN 2.9 24.1 + - - +
91A LEU* 3.7 17.5 - - - +
93A PHE* 1.3 76.5 - - - +
95A SER* 1.3 57.5 - - - +
97A LEU* 3.2 3.3 + - - +
98A ASP* 2.8 46.3 + - - +
122B VAL* 4.1 17.9 - - + -
126B VAL* 4.2 15.5 - - + +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 2.8 29.0 + - - +
92A LEU* 3.1 17.2 + - - +
94A GLN* 1.3 74.0 - - - +
96A TYR* 1.3 65.6 + - - +
98A ASP* 3.2 13.3 + - - +
99A ASN* 3.0 21.1 + - - +
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Residues in contact with TYR 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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92A LEU 3.0 14.8 + - - +
93A PHE* 3.4 16.8 - + - +
95A SER* 1.3 77.3 + - - +
97A LEU* 1.3 59.5 + - + +
99A ASN* 3.1 11.3 + - + +
100A VAL* 2.9 45.1 + - + +
124A GLU* 2.9 44.3 + - + +
125A ILE* 4.4 4.5 - - + -
127A SER* 5.3 0.9 - - - -
128A TYR* 3.5 48.8 + + + +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 2.9 39.6 + - + +
94A GLN 3.8 3.4 - - - +
96A TYR* 1.3 74.9 - - + +
98A ASP* 1.3 65.4 + - - +
100A VAL* 3.2 6.6 + - + +
101A GLY 3.0 9.0 + - - -
125A ILE* 3.8 37.0 - - + -
118B TRP* 2.9 29.3 + - + -
122B VAL* 3.8 21.8 - - + +
125B ILE* 3.8 23.1 - - + -
126B VAL* 3.8 29.4 - - + -
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Residues in contact with ASP 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 GLN* 2.8 33.5 + - - +
95A SER* 3.5 15.1 - - - +
97A LEU* 1.3 76.3 - - - +
99A ASN* 1.3 62.4 + - - +
101A GLY* 3.2 9.7 + - - -
102A VAL* 3.3 18.8 + - - +
118B TRP* 4.3 7.2 + - - +
119B SER* 6.1 0.5 - - - -
122B VAL* 4.1 17.7 - - - +
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Residues in contact with ASN 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 SER 3.0 12.3 + - - +
96A TYR* 3.3 13.2 - - + +
98A ASP* 1.3 76.1 - - - +
100A VAL* 1.3 63.4 + - + +
102A VAL* 3.0 10.3 + - - +
103A GLN* 2.8 47.1 + - - +
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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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96A TYR* 2.9 36.3 + - + +
97A LEU* 3.4 15.3 - - + +
99A ASN* 1.3 75.0 - - - +
101A GLY* 1.3 62.2 + - - +
103A GLN* 3.2 12.0 + - - +
104A ILE* 3.0 34.0 + - + +
121A THR* 4.2 18.4 - - + -
124A GLU* 3.5 22.9 - - - +
125A ILE* 4.6 13.2 - - + -
118B TRP* 4.0 17.0 - - + -
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Residues in contact with GLY 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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97A LEU 3.0 12.5 + - - -
98A ASP 3.2 1.9 + - - -
99A ASN 3.2 0.8 - - - -
100A VAL* 1.3 75.7 - - - +
102A VAL* 1.3 58.2 + - - +
104A ILE* 3.2 5.1 + - - +
105A VAL* 3.0 34.7 + - - +
114B PHE* 3.6 5.5 - - - -
115B LEU* 4.8 3.1 - - - -
118B TRP* 3.3 34.5 - - - +
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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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98A ASP 3.3 14.4 + - - +
99A ASN* 3.0 10.5 + - - +
101A GLY* 1.3 73.3 - - - +
103A GLN* 1.3 65.3 + - + +
105A VAL* 3.2 9.2 + - + +
106A ARG* 3.0 54.4 + - + +
115B LEU* 5.6 4.5 - - + -
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Residues in contact with GLN 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 ASN* 2.8 34.4 + - - +
100A VAL* 3.2 17.7 + - - +
102A VAL* 1.3 77.0 - - + +
104A ILE* 1.3 62.7 + - - +
106A ARG* 3.4 7.6 + - - +
107A GLN* 3.1 30.5 + - + +
121A THR* 4.4 11.7 - - + +
124A GLU* 2.6 42.5 + - - +
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Residues in contact with ILE 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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100A VAL* 3.0 26.7 + - + +
101A GLY 3.5 6.5 - - - +
103A GLN* 1.3 73.1 - - - +
105A VAL* 1.3 55.6 + - - +
107A GLN* 3.1 4.2 + - - +
108A MET* 2.9 41.5 + - + +
114A PHE* 3.7 19.7 - - + -
117A ILE* 4.2 15.0 - - + +
118A TRP* 3.8 31.2 - - + -
121A THR* 3.9 25.6 - - + +
114B PHE* 3.5 31.6 - - + -
118B TRP* 4.3 3.8 - - + -
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Residues in contact with VAL 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 GLY 3.0 14.4 + - - +
102A VAL* 3.2 11.4 + - + +
104A ILE* 1.3 75.5 - - - +
106A ARG* 1.3 69.2 + - + +
108A MET* 3.2 9.7 + - - +
109A ARG* 3.1 70.0 + - - +
114B PHE* 3.7 12.1 - - + -
115B LEU* 3.2 46.4 - - + -
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Residues in contact with ARG 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 VAL* 3.0 42.0 + - + +
103A GLN* 3.8 6.5 - - - +
105A VAL* 1.3 82.6 - - + +
107A GLN* 1.3 70.3 + - - +
109A ARG* 3.3 20.1 + - - +
110A SER* 3.5 9.4 + - - -
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Residues in contact with GLN 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 GLN* 3.1 19.2 + - + +
104A ILE 3.1 1.8 + - - +
106A ARG* 1.3 80.1 + - - +
108A MET* 1.3 65.4 + - - +
110A SER* 2.6 34.6 + - - -
112A GLU* 3.7 10.5 + - + +
117A ILE* 3.6 31.9 - - + -
120A GLN* 6.0 2.0 - - - +
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Residues in contact with MET 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 ILE* 2.9 23.3 + - + +
105A VAL* 3.2 10.0 + - - +
107A GLN* 1.3 74.6 - - - +
109A ARG* 1.3 59.6 + - + +
111A GLY* 3.0 20.6 + - - -
112A GLU 4.2 7.7 + - - +
114A PHE* 3.9 25.1 - - + +
117A ILE* 3.8 17.0 - - + -
108B MET* 4.0 23.3 - - + -
114B PHE* 3.9 26.9 - - + -
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Residues in contact with ARG 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 VAL* 3.1 40.5 + - - +
106A ARG* 3.6 15.8 - - - +
107A GLN 3.2 0.4 - - - -
108A MET* 1.3 78.9 - - + +
110A SER* 1.3 58.5 + - - +
111A GLY 3.2 1.9 + - - -
113B ARG* 6.0 2.2 - - - +
115B LEU* 4.5 11.3 - - - +
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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