Contacts of the helix formed by residues 101 - 116 (chain A) in PDB entry 3CEI
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU 4.8 0.4 - - - -
96A GLU* 3.9 16.0 + - - +
99A PHE* 3.2 5.0 + - - +
100A GLY* 1.3 79.7 - - - +
102A LEU* 1.3 62.8 + - - +
103A GLU* 3.0 22.8 + - - +
104A LYS* 3.1 20.1 + - - +
105A PHE* 3.0 21.9 + - - +
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Residues in contact with LEU 102 (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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87A LEU* 4.1 20.9 - - + -
92A LYS* 4.3 28.9 - - + +
95A LEU* 3.9 36.3 - - + -
96A GLU* 4.3 18.2 + - + +
101A SER* 1.3 73.0 - - - +
103A GLU* 1.3 69.9 + - - +
105A PHE* 3.1 8.8 + - + +
106A LYS* 2.9 28.6 + - - +
178A TYR* 4.3 3.1 + - - -
183A TRP* 6.4 0.2 - - + -
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Residues in contact with GLU 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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101A SER* 3.0 25.3 + - - +
102A LEU* 1.3 84.8 + - - +
104A LYS* 1.3 57.0 + - - +
106A LYS* 3.5 9.6 + - - +
107A GLU* 3.0 28.0 + - - +
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Residues in contact with LYS 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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99A PHE* 3.3 26.0 - - - +
100A GLY 4.9 0.4 - - - -
101A SER* 3.1 19.1 + - - +
103A GLU* 1.3 74.5 - - - +
105A PHE* 1.3 62.0 + - - +
107A GLU* 3.1 27.5 + - - +
108A ASP* 2.8 68.1 + - - +
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Residues in contact with PHE 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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95A LEU* 4.0 28.9 - - + -
99A PHE* 3.6 43.2 - + + +
101A SER 3.0 12.3 + - - +
102A LEU* 3.1 12.3 + - + +
104A LYS* 1.3 77.1 - - - +
106A LYS* 1.3 52.3 + - - +
108A ASP* 3.0 3.2 + - - +
109A PHE* 2.7 53.0 + + + +
124A ALA* 3.9 25.1 - - + -
133A ILE* 4.9 1.1 - - + -
135A ILE* 3.8 25.6 - - + -
153A LEU* 4.5 7.4 - - + -
178A TYR* 3.2 25.6 - + - -
183A TRP* 4.1 16.8 - + - -
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Residues in contact with LYS 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 LEU 2.9 10.7 + - - +
103A GLU* 3.6 12.8 - - - +
105A PHE* 1.3 75.9 - - - +
107A GLU* 1.3 58.8 + - - +
109A PHE* 3.2 0.3 + - - +
110A ILE* 2.8 50.5 + - + +
175A GLU* 3.0 38.2 + - - -
178A TYR* 3.3 52.7 + - + +
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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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103A GLU 3.0 15.0 + - - +
104A LYS* 3.1 35.1 - - - +
106A LYS* 1.3 81.7 - - - +
108A ASP* 1.3 63.8 + - - +
110A ILE* 4.1 3.7 - - - +
111A LYS* 3.0 27.1 + - + +
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Residues in contact with ASP 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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99A PHE* 3.6 19.2 - - + +
104A LYS* 2.8 56.9 + - - +
105A PHE* 3.6 1.3 - - - +
107A GLU* 1.3 74.3 - - - +
109A PHE* 1.3 63.6 + - - +
111A LYS* 3.5 6.9 + - - +
112A SER* 3.0 25.1 + - - -
135A ILE* 3.5 18.3 - - + +
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Residues in contact with PHE 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 PHE* 2.7 46.7 + + + +
106A LYS* 3.7 4.5 - - - +
108A ASP* 1.3 74.9 - - - +
110A ILE* 1.3 69.6 + - + +
112A SER 3.3 0.2 + - - -
113A ALA* 3.0 19.8 + - + +
122A ASN* 3.0 52.1 + - - +
123A TRP 3.9 19.5 - - - -
124A ALA* 4.2 1.3 - - + -
135A ILE* 3.4 11.9 - - + +
153A LEU* 3.9 24.7 - - + -
155A VAL* 3.8 21.3 - - + -
174A LEU* 5.8 1.1 - - + -
177A PHE* 4.0 16.4 - + - -
178A TYR* 4.2 15.5 - + + -
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Residues in contact with ILE 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 LYS* 2.8 46.4 + - + +
107A GLU* 4.1 2.9 - - - +
109A PHE* 1.3 75.9 - - + +
111A LYS* 1.3 53.9 + - - +
113A ALA* 3.1 6.6 + - - +
114A THR* 2.7 45.5 + - - +
171A PRO* 5.6 2.5 - - + +
174A LEU* 3.9 23.7 - - + +
175A GLU* 3.6 25.8 - - + +
177A PHE* 6.5 0.2 - - + -
178A TYR* 4.0 24.2 - - + -
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Residues in contact with LYS 111 (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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107A GLU* 3.0 20.1 + - + +
108A ASP* 3.8 6.7 - - - +
109A PHE 3.3 0.2 - - - -
110A ILE* 1.3 77.3 - - - +
112A SER* 1.3 63.6 + - - +
114A THR* 3.2 9.0 + - - -
115A THR* 3.1 37.0 + - + +
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Residues in contact with SER 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 ASP 3.0 18.2 + - - -
109A PHE 3.6 3.1 - - - -
111A LYS* 1.3 77.6 - - - +
113A ALA* 1.3 62.6 + - - +
115A THR* 3.6 5.3 + - - -
116A LEU* 3.3 10.0 + - - +
122A ASN* 2.9 21.0 + - - +
135A ILE* 3.7 19.0 + - - +
137A GLN* 2.9 37.8 + - - +
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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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109A PHE* 3.0 18.2 + - + +
110A ILE* 3.6 7.2 - - - +
112A SER* 1.3 77.4 - - - +
114A THR* 1.3 52.6 + - - +
116A LEU* 3.9 3.2 + - - +
122A ASN* 3.4 27.3 + - + +
155A VAL* 4.0 4.7 - - + -
157A VAL* 3.8 5.9 - - + +
170A ARG* 2.7 36.0 + - - -
174A LEU* 3.7 26.7 - - + -
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Residues in contact with THR 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 ILE* 2.7 29.6 + - - +
111A LYS* 3.2 9.9 + - - -
113A ALA* 1.3 79.4 - - - +
115A THR* 1.3 65.9 + - + +
116A LEU 4.3 0.3 - - - +
170A ARG* 3.6 16.3 + - + +
171A PRO* 4.4 23.8 - - + +
174A LEU* 3.4 16.4 - - - +
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Residues in contact with THR 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 LYS* 3.1 31.8 + - + +
112A SER* 3.7 8.0 + - - -
113A ALA 3.5 0.2 - - - -
114A THR* 1.3 82.2 - - + +
116A LEU* 1.3 69.1 + - - +
117A PHE* 2.9 10.0 + - - +
137A GLN* 4.2 6.0 + - - +
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Residues in contact with LEU 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 SER 3.3 15.2 + - - +
113A ALA 4.0 2.5 - - - +
114A THR 3.4 1.5 - - - +
115A THR* 1.3 75.0 + - - +
117A PHE* 1.3 73.2 - - - +
118A GLY 3.8 11.0 - - - +
119A SER 4.2 2.5 - - - +
120A GLY* 4.0 13.7 - - - -
121A TRP 3.1 38.1 - - - +
122A ASN* 4.3 3.8 - - + +
137A GLN* 3.5 32.8 - - + +
138A THR 3.7 11.0 - - - +
139A SER* 5.2 2.5 - - - -
157A VAL* 3.8 7.6 - - + -
170A ARG* 2.8 39.4 + - - +
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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