Contacts of the helix formed by residues 103 - 117 (chain A) in PDB entry 4RBO
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A VAL 4.3 0.4 + - - -
102A PHE* 1.3 76.6 - - - +
104A SER* 1.3 64.2 + - - +
105A THR* 3.2 23.0 + - - -
106A GLN* 3.1 22.7 + - - +
107A LEU* 3.1 23.7 + - - +
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Residues in contact with SER 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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103A SER* 1.3 73.6 - - - +
105A THR* 1.3 64.9 + - - +
107A LEU* 3.6 6.7 + - - +
108A CYS* 3.3 22.7 + - - +
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Residues in contact with THR 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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103A SER* 3.2 16.5 - - - -
104A SER* 1.3 80.5 - - - +
106A GLN* 1.3 67.4 + - - +
108A CYS* 3.3 17.2 - - - +
109A VAL* 3.7 8.3 + - - +
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Residues in contact with GLN 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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101A VAL 4.9 0.5 - - - +
102A PHE* 3.5 21.5 - - + -
103A SER* 3.1 39.4 + - - +
104A SER 3.2 0.4 - - - -
105A THR* 1.3 79.2 - - - +
107A LEU* 1.3 67.0 + - - +
108A CYS 3.0 2.1 + - - -
109A VAL* 3.2 10.6 - - - +
110A LEU* 2.9 28.8 + - + +
132A LEU* 2.9 44.7 + - + +
134A LEU* 3.4 26.2 - - + +
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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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102A PHE* 3.3 43.3 - - + +
103A SER 3.1 16.1 + - - +
104A SER* 4.0 7.2 - - - +
106A GLN* 1.3 75.7 - - - +
108A CYS* 1.3 56.5 + - - +
110A LEU* 4.1 6.7 - - + -
111A ASN* 2.8 51.6 + - - +
142A TRP* 5.0 11.2 - - - +
5C A 4.8 7.6 - - - +
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Residues in contact with CYS 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 SER 3.3 11.5 + - - +
105A THR* 3.3 15.5 - - - +
106A GLN 3.0 0.6 - - - -
107A LEU* 1.3 78.2 - - - +
109A VAL* 1.3 64.5 + - - +
111A ASN* 3.7 3.1 - - - +
112A ASP* 2.8 33.6 + - - +
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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 THR 4.0 8.5 - - - +
106A GLN* 3.2 11.4 - - - +
108A CYS* 1.3 81.8 - - - +
110A LEU* 1.3 60.7 + - + +
112A ASP* 3.7 7.1 - - + +
113A ARG* 2.8 32.2 + - + +
128A LEU* 4.1 18.8 - - + -
131A ILE* 5.5 4.3 - - + -
132A LEU* 3.7 32.1 - - + -
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Residues in contact with LEU 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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102A PHE* 5.1 13.7 - - + -
106A GLN* 2.9 23.4 + - + +
107A LEU* 3.7 5.4 - - + +
109A VAL* 1.3 82.4 - - + +
111A ASN* 1.3 57.3 + - - +
113A ARG* 3.6 4.7 - - - +
114A PHE* 2.8 30.3 + - - +
128A LEU* 4.4 18.2 - - + -
132A LEU* 3.2 35.0 - - + -
134A LEU* 5.2 4.5 - - + -
139A VAL* 5.4 9.0 - - + -
142A TRP* 3.3 57.3 - - + +
143A PHE* 4.7 1.5 - - + -
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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 LEU* 2.8 46.4 + - - +
108A CYS* 3.8 3.1 - - - +
110A LEU* 1.3 73.4 - - - +
112A ASP* 1.3 56.9 + - - +
114A PHE* 3.3 6.5 + - - +
115A GLN* 2.8 32.0 + - - +
142A TRP* 3.2 23.4 - - - -
146A GLN* 4.2 9.4 + - - +
149A LYS* 5.8 1.4 + - - -
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Residues in contact with ASP 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 CYS* 2.8 24.6 + - - +
109A VAL* 3.7 8.5 - - + +
111A ASN* 1.3 75.3 - - - +
113A ARG* 1.3 63.6 + - - +
115A GLN* 3.4 8.0 + - - +
116A ARG* 2.7 57.4 + - - +
12F C 3.8 17.7 - - - +
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Residues in contact with ARG 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 VAL* 2.8 21.9 + - + +
110A LEU* 3.6 4.9 - - - +
112A ASP* 1.3 78.9 + - - +
114A PHE* 1.3 53.0 + - - +
116A ARG* 3.2 6.1 + - - +
117A GLN* 2.8 55.5 + - - +
120A LEU* 3.1 27.5 - - + +
124A GLN* 3.6 28.7 + - - +
127A GLU* 5.1 8.7 + - - +
128A LEU* 4.2 30.8 - - + +
143A PHE* 4.2 18.8 - - + -
12F C 5.2 20.1 + - - +
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Residues in contact with PHE 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 LEU 2.8 16.8 + - - +
111A ASN* 3.3 6.9 + - - +
113A ARG* 1.3 76.9 - - - +
115A GLN* 1.3 66.9 + - + +
116A ARG 3.1 1.0 + - - -
117A GLN 3.2 15.0 + - - +
118A LYS* 3.2 47.9 - - + +
142A TRP* 3.8 12.6 - + + -
143A PHE* 3.9 20.6 - + + -
146A GLN* 3.4 59.5 - - + -
147A ARG* 3.9 10.1 - - + -
150A SER* 4.1 14.6 - - - -
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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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111A ASN 2.8 20.6 + - - +
112A ASP* 3.7 8.7 - - - +
113A ARG 3.3 0.2 - - - -
114A PHE* 1.3 77.9 - - + +
116A ARG* 1.3 70.6 + - + +
118A LYS* 2.7 26.6 + - - +
3E C 5.7 0.3 - - - +
4E C 5.4 3.6 + - - +
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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 ASP* 2.7 53.9 + - - +
113A ARG* 3.2 6.8 + - - +
114A PHE 3.1 0.2 - - - -
115A GLN* 1.3 91.5 + - + +
117A GLN* 1.3 62.1 + - + +
118A LYS* 5.1 1.8 - - - -
2E G 5.1 8.7 + - - +
3E C 4.2 22.3 + - - +
4E C 6.1 3.3 - - - +
11F C 6.1 1.1 + - - -
12F C 3.9 37.8 + - - +
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Residues in contact with GLN 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 ARG* 2.8 40.0 + - - +
114A PHE* 3.2 11.2 + - - +
116A ARG* 1.3 81.8 - - + +
118A LYS* 1.3 59.2 + - - +
119A TYR 2.9 27.5 + - - +
120A LEU* 3.2 27.3 - - + +
121A SER 4.6 0.2 - - - +
124A GLN* 3.0 30.5 + - - +
143A PHE* 4.0 0.7 - - - -
1E G 5.3 5.6 + - - -
2E G 5.8 6.8 + - - +
3E C 5.6 5.8 - - - -
12F C 5.2 4.9 - - - +
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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