Contacts of the helix formed by residues 101 - 116 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LEU 4.8 0.2 - - - -
96B GLU* 3.9 15.4 + - - +
99B PHE* 3.3 4.8 + - - +
100B GLY* 1.3 78.6 - - - +
102B LEU* 1.3 64.3 + - - +
103B GLU* 3.0 19.7 + - - +
104B LYS* 3.1 24.4 + - - +
105B PHE* 3.0 22.2 + - - +
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Residues in contact with LEU 102 (chain B).
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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87B LEU* 4.2 22.0 - - + -
92B LYS* 4.2 30.3 - - + +
95B LEU* 3.9 35.7 - - + -
96B GLU* 4.2 18.9 + - + +
101B SER* 1.3 73.3 - - - +
103B GLU* 1.3 69.0 + - - +
105B PHE* 3.2 7.3 + - + +
106B LYS* 2.9 29.1 + - - +
178B TYR* 4.5 2.9 + - - -
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 3.0 24.2 - - - +
102B LEU* 1.3 85.4 + - - +
104B LYS* 1.3 56.2 + - - +
106B LYS* 3.5 9.2 + - - +
107B GLU* 3.0 26.9 + - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE 3.3 24.5 - - - +
100B GLY* 5.0 0.4 - - - -
101B SER* 3.1 19.5 + - - +
103B GLU* 1.3 73.5 - - - +
105B PHE* 1.3 61.8 + - - +
107B GLU* 3.1 27.4 + - - +
108B ASP* 2.8 67.9 + - - +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.0 30.7 - - + -
99B PHE* 3.4 49.9 - + + +
101B SER 3.0 13.3 + - - +
102B LEU* 3.5 11.0 - - + +
104B LYS* 1.3 76.7 - - - +
106B LYS* 1.3 51.4 + - - +
108B ASP* 3.1 1.9 + - - +
109B PHE* 2.7 52.3 + + + +
124B ALA* 3.9 25.1 - - + -
135B ILE* 3.8 20.4 - - + -
153B LEU* 4.5 7.6 - - + -
178B TYR* 3.2 27.8 - - - -
183B TRP* 4.1 13.7 - + - -
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU 2.9 11.3 + - - +
103B GLU* 3.6 12.8 - - - +
105B PHE* 1.3 76.4 - - - +
107B GLU* 1.3 65.4 + - - +
109B PHE* 3.1 1.0 + - - +
110B ILE* 2.8 51.6 + - + +
175B GLU* 2.9 29.9 + - - -
178B TYR* 3.5 50.2 - - + +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU 3.0 13.8 + - - +
104B LYS* 3.1 34.5 - - - +
106B LYS* 1.3 81.5 - - - +
108B ASP* 1.3 57.1 + - - +
110B ILE* 4.0 2.9 - - - +
111B LYS* 2.9 34.6 + - + +
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.8 17.4 - - + +
104B LYS* 2.8 57.9 + - - +
105B PHE* 3.6 2.0 - - - +
107B GLU* 1.3 74.6 - - - +
109B PHE* 1.3 62.6 + - - +
111B LYS* 3.6 8.1 + - - +
112B SER* 3.1 25.5 + - - -
135B ILE* 3.6 19.9 - - + +
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PHE* 2.7 46.6 + + + +
106B LYS* 3.6 5.6 - - - +
108B ASP* 1.3 73.3 - - - +
110B ILE* 1.3 67.5 + - + +
112B SER 3.4 1.4 + - - -
113B ALA* 3.0 20.3 + - + +
122B ASN* 3.0 52.0 + - - +
123B TRP 3.9 18.2 - - - -
124B ALA* 4.1 2.0 - - + -
135B ILE* 3.5 11.9 - - + +
153B LEU* 4.0 24.2 - - + -
155B VAL* 3.9 21.3 - - + -
174B LEU* 5.8 1.1 - - + -
177B PHE* 4.0 16.6 - + - -
178B TYR* 4.2 15.7 - + + -
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 2.8 55.1 + - + +
107B GLU* 4.1 3.6 - - - +
109B PHE* 1.3 73.3 - - + +
111B LYS* 1.3 60.2 + - - +
113B ALA* 3.1 7.3 + - - +
114B THR* 2.8 40.9 + - - +
171B PRO* 5.7 2.7 - - + +
174B LEU* 4.5 23.3 - - + +
175B GLU* 3.8 15.0 - - - +
177B PHE* 6.5 0.2 - - + -
178B TYR* 4.1 24.2 - - + -
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 2.9 21.6 + - + +
108B ASP* 4.0 7.4 - - - +
110B ILE* 1.3 78.1 - - - +
112B SER* 1.3 64.1 + - - +
114B THR* 3.1 9.7 + - - -
115B THR* 3.1 37.1 + - + +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASP 3.1 19.1 + - - -
109B PHE 3.6 3.8 - - - -
111B LYS* 1.3 77.8 - - - +
113B ALA* 1.3 61.3 + - - +
115B THR* 3.5 5.5 + - - -
116B LEU* 3.3 9.9 + - - +
122B ASN* 2.7 21.8 + - - +
135B ILE* 3.7 18.1 + - - +
137B GLN* 2.9 37.5 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 3.0 12.7 + - + +
110B ILE* 3.1 5.8 + - - +
112B SER* 1.3 77.0 - - - +
114B THR* 1.3 57.8 + - - +
116B LEU* 3.9 3.3 + - - +
122B ASN* 3.4 33.8 + - + +
155B VAL* 3.9 4.7 - - + -
157B VAL* 3.8 5.8 - - + +
170B ARG* 2.8 29.8 + - - -
174B LEU* 3.7 27.1 - - + -
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 2.8 26.8 + - - +
111B LYS* 3.1 12.3 + - - -
113B ALA* 1.3 79.5 - - - +
115B THR* 1.3 64.8 + - + +
116B LEU 4.3 0.3 - - - +
170B ARG* 3.5 15.5 + - - +
171B PRO* 4.5 22.7 - - + +
174B LEU* 3.3 16.3 - - - +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 3.1 32.2 + - + +
112B SER* 3.5 9.0 + - - -
114B THR* 1.3 81.9 - - + +
116B LEU* 1.3 70.4 + - - +
117B PHE* 2.9 10.0 + - - +
137B GLN* 4.1 6.4 + - - -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER 3.3 9.6 + - - +
113B ALA 4.1 2.9 - - - +
114B THR 3.5 1.7 - - - +
115B THR* 1.3 74.3 + - - +
117B PHE* 1.3 72.7 + - - +
118B GLY 4.0 8.7 - - - +
119B SER 4.1 11.7 - - - +
120B GLY* 4.1 4.9 - - - -
121B TRP 3.3 35.4 - - - +
122B ASN* 4.3 4.0 - - + +
137B GLN* 3.3 40.6 - - + +
138B THR 3.7 11.4 - - - +
139B SER* 5.0 2.7 - - - -
157B VAL* 4.0 8.3 - - + -
170B ARG* 2.7 38.6 + - - +
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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