Contacts of the helix formed by residues 98 - 116 (chain A) in PDB entry 1CIP
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 ALA 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE* 4.9 4.7 + - - -
96A GLY 4.2 1.4 + - - -
97A ASP* 1.3 71.8 - - - +
99A ALA* 1.3 61.7 + - - +
100A ARG 3.0 1.8 + - - -
101A ALA* 3.2 21.2 + - - +
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Residues in contact with ALA 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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97A ASP* 3.2 3.7 + - + +
98A ALA* 1.3 77.9 - - - +
100A ARG* 1.3 87.2 + - - +
101A ALA 3.2 0.8 + - - -
102A ASP* 3.4 16.7 + - - +
103A ASP* 3.7 6.9 + - - +
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Residues in contact with ARG 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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95A PHE* 3.6 21.1 - - + -
97A ASP* 3.3 38.5 + - - +
98A ALA 3.0 1.4 - - - -
99A ALA* 1.3 95.9 + - - +
101A ALA* 1.3 58.9 + - - +
103A ASP* 2.9 32.9 + - - +
104A ALA* 2.8 29.8 + - - +
129A ARG* 3.5 49.0 + - - +
130A LEU* 3.7 9.0 - - + +
133A ASP* 3.3 23.1 - - + +
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Residues in contact with ALA 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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95A PHE* 4.2 21.0 - - + -
98A ALA 3.2 13.7 + - - +
99A ALA 3.2 0.6 - - - -
100A ARG* 1.3 79.2 - - - +
102A ASP* 1.3 61.9 + - - +
104A ALA* 3.4 4.8 + - - +
105A ARG* 3.1 40.8 + - - +
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Residues in contact with ASP 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 ALA 4.7 0.2 + - - -
99A ALA* 3.4 11.4 + - - +
100A ARG 3.2 0.6 - - - -
101A ALA* 1.3 75.7 - - - +
103A ASP* 1.3 62.9 + - - +
105A ARG* 2.7 39.5 + - - +
106A GLN* 2.9 28.1 + - - +
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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 ALA 3.7 3.5 + - - -
100A ARG* 2.9 39.9 + - - +
102A ASP* 1.3 78.6 - - - +
104A ALA* 1.3 58.7 + - - +
106A GLN* 3.1 5.0 + - - +
107A LEU* 2.9 24.3 + - - +
126A VAL* 3.2 22.3 - - + +
129A ARG* 2.9 44.1 + - - +
130A LEU* 4.0 16.8 - - + -
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Residues in contact with ALA 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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85A ILE* 4.9 12.8 - - + -
95A PHE* 3.9 23.3 - - + -
100A ARG 2.8 12.1 + - - +
101A ALA* 3.5 10.5 - - - +
102A ASP 3.2 0.2 - - - -
103A ASP* 1.3 77.2 - - - +
105A ARG* 1.3 61.3 + - - +
107A LEU* 3.2 17.2 + - - +
108A PHE* 3.3 23.4 - - + -
130A LEU* 4.1 9.1 - - + +
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Residues in contact with ARG 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 ALA* 3.1 32.6 + - - +
102A ASP* 2.7 44.9 + - - +
103A ASP 3.2 0.4 - - - -
104A ALA* 1.3 77.0 - - + +
106A GLN* 1.3 64.0 + - - +
107A LEU 3.2 1.0 + - - -
108A PHE* 3.3 16.7 + - - +
109A VAL* 3.5 15.0 + - + +
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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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102A ASP 2.9 16.0 + - - +
103A ASP* 3.1 6.5 + - - +
105A ARG* 1.3 77.6 - - - +
107A LEU* 1.3 62.7 + - - +
109A VAL* 3.3 22.3 + - - +
110A LEU* 3.0 49.1 + - + +
122A GLU* 3.4 20.8 + - - +
126A VAL* 4.3 13.5 - - + -
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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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78A ILE* 4.9 3.8 - - + -
81A ILE* 4.3 18.8 - - + -
82A ILE* 4.1 22.4 - - + -
85A ILE* 3.4 33.2 - - + -
103A ASP 2.9 12.8 + - - +
104A ALA* 3.3 12.3 - - - +
105A ARG 3.1 0.2 - - - -
106A GLN* 1.3 78.1 - - - +
108A PHE* 1.3 60.6 + - + +
110A LEU* 3.6 0.7 - - - +
111A ALA* 2.7 46.1 + - + +
123A LEU* 4.2 19.1 - - + -
126A VAL* 4.0 11.0 - - + -
127A ILE* 4.3 11.0 - - + -
130A LEU* 4.1 5.2 - - + -
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Residues in contact with PHE 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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82A ILE* 4.0 45.1 - - + -
85A ILE* 4.7 18.2 - - + -
104A ALA* 3.3 26.0 - - + -
105A ARG* 3.3 9.0 + - - +
107A LEU* 1.3 84.1 - - + +
109A VAL* 1.3 64.9 + - + +
110A LEU 3.4 0.3 + - - -
111A ALA* 3.7 11.5 + - + +
112A GLY 4.7 2.1 + - - -
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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 ARG 3.5 14.1 + - - +
106A GLN* 3.3 33.3 + - - +
108A PHE* 1.3 78.4 - - + +
110A LEU* 1.3 66.4 + - + +
112A GLY 4.8 1.7 + - - -
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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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106A GLN* 3.0 45.9 + - + +
109A VAL* 1.3 85.8 - - + +
111A ALA* 1.3 64.6 + - - +
112A GLY 3.0 4.5 + - - -
113A ALA* 3.3 15.1 + - - +
120A THR* 5.3 4.0 - - + +
122A GLU* 3.7 39.5 - - + +
123A LEU* 3.8 39.5 - - + +
126A VAL* 4.5 3.1 - - + -
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Residues in contact with ALA 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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78A ILE* 4.1 22.7 - - + +
82A ILE* 4.6 9.4 - - + -
107A LEU* 2.7 27.4 + - + +
108A PHE* 3.7 10.9 + - + +
109A VAL 3.7 1.0 - - - -
110A LEU* 1.3 73.0 - - - +
112A GLY* 1.3 62.0 + - - +
113A ALA 3.2 1.0 + - - -
114A ALA* 3.4 11.1 + - - +
115A GLU* 3.1 23.4 - - - +
123A LEU* 4.7 8.5 - - - -
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Residues in contact with GLY 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 PHE 4.7 2.8 + - - -
109A VAL 4.8 2.2 + - - -
110A LEU 3.0 2.4 + - - -
111A ALA* 1.3 79.1 - - - +
113A ALA* 1.3 61.4 + - - +
115A GLU* 3.5 21.2 - - - +
116A GLU* 3.6 14.8 - - - +
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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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110A LEU 3.3 11.5 + - - +
111A ALA 3.2 0.8 + - - -
112A GLY* 1.3 73.6 - - - +
114A ALA* 1.3 57.5 + - - +
115A GLU 3.1 2.0 - - - -
116A GLU* 2.7 30.5 + - - +
118A PHE* 3.2 34.3 + - + +
120A THR* 5.5 9.0 - - + -
123A LEU* 5.3 2.9 - - + -
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Residues in contact with ALA 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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71A ALA 4.4 1.6 - - - +
74A TYR* 3.3 27.1 - - + +
78A ILE* 3.5 34.3 - - + -
110A LEU 4.5 0.6 + - - -
111A ALA 3.4 10.5 + - - +
113A ALA* 1.3 73.7 - - - +
115A GLU* 1.3 56.7 + - + +
117A GLY* 2.6 27.7 + - - -
118A PHE 2.9 17.4 + - - +
119A MET* 5.1 1.3 - - - -
123A LEU* 4.1 8.9 - - + +
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Residues in contact with GLU 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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71A ALA* 4.1 12.9 - - - +
75A SER* 4.9 23.6 + - - +
78A ILE* 3.7 22.1 - - + +
79A GLN* 4.7 9.4 - - - +
82A ILE* 5.1 1.7 - - - +
111A ALA* 3.1 28.5 - - - +
112A GLY* 3.5 13.4 + - - +
114A ALA* 1.3 77.0 - - + +
116A GLU* 1.3 65.4 + - - +
117A GLY 3.6 0.9 + - - -
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Residues in contact with GLU 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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71A ALA* 4.6 3.8 - - - +
112A GLY 3.6 15.6 - - - +
113A ALA* 2.7 19.9 + - - +
115A GLU* 1.3 79.6 - - - +
117A GLY* 1.3 55.7 + - - -
118A PHE* 3.2 27.8 - - + -
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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