Contacts of the helix formed by residues 105 - 122 (chain A) in PDB entry 1CVU
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 ILE 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.3 35.2 - - - +
103A VAL 2.8 3.4 + - - +
105A ASN* 1.3 80.9 - - - +
106A PRO* 1.3 54.6 - - - +
107A PHE* 3.1 9.2 + - - +
108A LEU* 2.5 74.2 + - + +
109A ARG* 2.8 10.0 + - - -
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Residues in contact with PRO 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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104A ASN 5.3 0.9 - - - +
105A ILE* 1.3 97.9 - - - +
107A PHE* 1.3 61.9 + - - +
109A ARG* 3.7 9.9 - - + +
110A SER* 2.8 33.3 + - - +
360A LYS* 5.9 2.9 - - - +
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Residues in contact with PHE 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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105A ILE* 2.9 10.5 + - - +
106A PRO* 1.3 78.6 - - - +
108A LEU* 1.3 63.4 + - + +
110A SER* 3.5 5.8 + - - -
111A LEU* 2.9 55.3 + - + +
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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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102A ILE* 5.0 4.5 - - + -
103A VAL* 4.1 26.5 - - + -
105A ILE* 2.5 51.3 + - + +
107A PHE* 1.3 77.0 - - + +
109A ARG* 1.3 56.0 + - - +
111A LEU* 3.0 21.8 + - + +
112A ILE* 2.8 50.5 + - + +
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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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103A VAL* 3.8 13.3 + - - +
104A ASN* 4.0 24.3 + - - +
105A ILE 2.8 6.0 + - - +
106A PRO* 3.7 12.8 - - + +
108A LEU* 1.3 76.7 - - - +
110A SER* 1.3 58.2 + - - +
112A ILE 3.2 0.7 + - - -
113A MET* 2.9 28.5 + - - +
346A GLU* 4.1 11.7 + - - -
357A PHE* 3.3 31.9 - - + -
358A LYS* 2.9 33.7 + - - +
359A LEU 2.9 27.3 + - - -
360A LYS* 3.5 34.1 - - + +
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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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106A PRO* 2.8 22.2 + - - +
107A PHE* 3.7 5.8 - - - -
109A ARG* 1.3 75.3 - - - +
111A LEU* 1.3 65.0 + - - +
113A MET* 3.2 5.6 + - - +
114A LYS* 2.9 25.6 + - - +
360A LYS* 3.0 27.0 + - - +
362A ASP* 4.8 0.2 + - - -
365A LEU* 3.9 23.9 - - - +
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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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107A PHE* 2.9 44.0 + - + +
108A LEU* 3.1 22.0 - - + +
110A SER* 1.3 79.3 - - - +
112A ILE* 1.3 72.6 + - + +
114A LYS* 3.3 10.5 + - - +
115A TYR* 3.3 18.7 + - + +
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Residues in contact with ILE 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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93A LEU* 5.2 3.6 - - + -
100A TRP* 4.2 20.6 - - + -
103A VAL* 3.9 21.5 - - + -
108A LEU* 2.8 30.0 + - + +
109A ARG 3.6 0.4 - - - +
111A LEU* 1.3 82.1 - - + +
113A MET* 1.3 64.4 + - - +
115A TYR* 2.9 22.4 + - + +
116A VAL* 2.8 23.2 + - + +
357A PHE* 3.4 31.9 - - + -
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Residues in contact with MET 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 ARG 2.9 20.1 + - - +
110A SER* 3.7 4.3 - - - +
112A ILE* 1.3 73.2 - - - +
114A LYS* 1.3 63.0 + - - +
116A VAL* 3.4 17.9 + - + +
117A LEU* 3.0 52.9 + - + +
345A ILE* 4.6 2.2 - - + -
357A PHE* 3.5 6.9 - - + -
359A LEU* 3.8 22.0 - - + -
360A LYS* 3.2 52.0 - - + +
365A LEU* 3.6 18.4 - - + -
701A ACD 4.2 16.8 - - + -
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Residues in contact with LYS 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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110A SER 2.9 13.0 + - - +
111A LEU* 3.3 14.4 - - - +
113A MET* 1.3 77.6 - - - +
115A TYR* 1.3 57.0 + - - +
117A LEU* 3.1 10.1 + - + +
118A THR* 2.8 43.1 + - + +
365A LEU* 3.1 42.8 - - + +
368A ASN* 3.1 29.9 + - - +
369A GLN* 3.1 18.8 + - - +
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Residues in contact with TYR 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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84A PRO* 4.9 6.8 - - - +
89A VAL* 4.0 34.7 - - + +
93A LEU* 5.8 4.3 - - + -
111A LEU* 3.3 9.2 + - + +
112A ILE* 2.9 19.1 + - + +
114A LYS* 1.3 78.7 - - - +
116A VAL* 1.3 59.4 + - + +
118A THR* 3.4 7.7 + - - -
119A SER* 2.5 64.5 + - - -
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Residues in contact with VAL 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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93A LEU* 6.1 7.6 - - + -
112A ILE* 2.8 22.9 - - + +
113A MET* 3.5 36.1 - - + +
115A TYR* 1.3 85.2 - - + +
117A LEU* 1.3 64.6 + - - +
119A SER* 2.8 16.5 + - - -
120A ARG* 3.7 20.6 + - - +
355A TYR* 6.2 2.5 - - + -
357A PHE* 4.3 13.7 - - + -
359A LEU* 4.6 3.6 - - + -
701A ACD 4.1 24.3 - - + +
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Residues in contact with LEU 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 MET* 3.0 56.7 + - + +
114A LYS* 3.3 5.4 - - - +
116A VAL* 1.3 78.5 - - + +
118A THR* 1.3 66.7 + - + +
120A ARG 3.2 10.9 + - - -
121A SER* 3.3 13.1 + - - -
360A LYS 5.1 1.8 - - - +
362A ASP 5.1 2.7 - - - +
365A LEU* 4.0 23.6 - - + -
366A LEU* 4.3 24.0 - - + -
531A LEU* 3.5 33.0 - - + +
535A MET* 4.7 7.6 - - + -
701A ACD 3.9 14.8 - - + -
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Residues in contact with THR 118 (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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114A LYS* 2.8 31.8 + - + +
115A TYR* 3.4 9.0 + - - -
117A LEU* 1.3 73.1 - - + +
119A SER* 1.3 66.2 + - - +
120A ARG 3.2 0.9 + - - -
121A SER* 3.2 25.8 - - - +
122A TYR* 4.4 3.8 + - - -
366A LEU* 4.7 5.2 - - + -
369A GLN* 3.4 40.2 - - + +
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Residues in contact with SER 119 (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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115A TYR* 2.5 55.5 + - - -
116A VAL* 2.8 20.8 + - - -
118A THR* 1.3 73.8 + - - +
120A ARG* 1.3 68.9 + - - +
122A TYR* 3.6 22.3 - - - -
123A LEU* 4.2 1.7 - - - +
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Residues in contact with ARG 120 (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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116A VAL* 3.7 19.2 + - - +
117A LEU 3.2 2.8 + - - +
118A THR 3.1 0.2 - - - -
119A SER* 1.3 89.5 + - - +
121A SER* 1.3 68.0 + - - +
122A TYR 3.1 0.7 + - - -
123A LEU* 2.9 32.8 + - - +
355A TYR* 4.6 7.7 + - - -
523A VAL* 4.4 7.5 - - - +
524A GLU* 3.2 34.7 + - - -
527A ALA* 3.7 32.4 - - + +
528A PRO* 4.3 23.6 - - + +
531A LEU* 3.5 22.7 - - + -
701A ACD 4.0 25.0 - - + +
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Residues in contact with SER 121 (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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117A LEU 3.3 13.7 + - - -
118A THR* 3.2 22.4 - - - +
120A ARG* 1.3 75.7 - - - +
122A TYR* 1.3 54.2 + - - -
123A LEU 2.5 15.4 + - - -
124A ILE* 3.6 12.3 + - - +
366A LEU* 5.2 3.6 - - - +
369A GLN* 5.8 1.0 - - - +
370A GLN 5.3 6.6 + - - -
371A PHE* 4.6 15.2 - - - -
528A PRO* 6.1 0.2 - - - +
531A LEU* 4.0 10.4 - - - +
532A LYS* 6.0 1.7 - - - +
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Residues in contact with TYR 122 (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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44A ARG* 3.7 14.6 + - - -
83A LYS* 3.7 17.3 + - + +
118A THR 4.4 2.4 + - - -
119A SER* 3.6 24.5 - - - -
120A ARG 3.1 2.4 + - - -
121A SER* 1.3 73.6 - - - +
123A LEU* 1.3 83.8 + - + +
124A ILE 3.9 1.7 - - - +
471A SER* 3.1 25.2 + - - -
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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