Contacts of the helix formed by residues 88 - 100 (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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA 4.1 0.2 + - - -
87A LEU* 1.3 76.5 - - - +
89A ASP* 1.3 64.4 + - - +
90A GLU* 3.6 22.8 + - - +
91A LEU* 3.1 23.6 + - - +
92A LYS* 2.9 21.5 + - - +
187A SER* 2.9 27.8 + - - -
190A TYR* 5.1 0.3 - - - -
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Residues in contact with ASP 89 (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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87A LEU 4.5 3.6 - - - +
88A SER* 1.3 74.1 - - - +
90A GLU* 1.3 57.8 + - + +
92A LYS* 3.6 8.4 - - - +
93A GLY* 2.8 27.2 + - - -
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Residues in contact with GLU 90 (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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88A SER* 3.9 18.2 + - - +
89A ASP* 1.3 76.7 - - + +
91A LEU* 1.3 54.4 + - - +
93A GLY* 3.2 1.4 + - - -
94A ALA* 2.7 36.7 + - - +
187A SER 5.4 1.0 - - - +
190A TYR* 3.9 6.6 + - + -
191A GLU* 3.9 35.3 - - - +
194A LYS* 3.0 31.4 + - - +
195A LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 91 (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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87A LEU* 4.0 8.5 - - + -
88A SER* 3.1 19.0 + - - +
90A GLU* 1.3 77.2 - - - +
92A LYS* 1.3 66.0 + - - +
94A ALA* 3.1 2.5 + - - +
95A LEU* 2.8 45.6 + - + +
133A ILE* 4.3 11.0 - - + -
152A LEU* 4.8 2.5 - - + -
183A TRP* 3.9 19.3 - - + +
186A VAL* 3.7 31.2 - - + -
187A SER* 3.4 22.2 - - - +
190A TYR* 3.9 34.2 - - + -
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Residues in contact with LYS 92 (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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87A LEU* 4.3 20.1 - - + +
88A SER 2.9 17.0 + - - +
89A ASP* 3.6 7.9 - - - +
91A LEU* 1.3 78.4 - - - +
93A GLY* 1.3 64.9 + - - +
95A LEU* 3.0 1.7 + - - +
96A GLU* 2.9 59.4 + - + +
102A LEU* 4.3 23.4 - - + +
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Residues in contact with GLY 93 (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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89A ASP 2.8 19.3 + - - -
90A GLU* 3.6 3.4 - - - -
92A LYS* 1.3 73.6 - - - +
94A ALA* 1.3 57.4 + - - +
96A GLU* 3.2 11.9 + - - +
97A LYS* 2.9 30.2 + - - +
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Residues in contact with ALA 94 (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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90A GLU 2.7 17.7 + - - +
91A LEU 3.5 4.0 - - - +
93A GLY* 1.3 74.3 - - - +
95A LEU* 1.3 56.8 + - - +
97A LYS* 3.4 12.6 + - - +
98A ASP* 2.9 38.8 + - - +
133A ILE* 4.0 11.4 - - + -
190A TYR* 3.1 36.6 - - + +
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Residues in contact with LEU 95 (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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87A LEU* 3.9 18.4 - - + -
91A LEU* 2.8 44.2 + - + +
92A LYS 3.6 3.4 - - - +
94A ALA* 1.3 69.9 - - - +
96A GLU* 1.3 61.5 + - - +
99A PHE* 2.8 42.7 + - + +
101A SER 4.4 1.5 + - - -
102A LEU* 3.9 15.7 - - + -
105A PHE* 4.0 41.1 - - + -
133A ILE* 3.8 23.1 - - + -
183A TRP* 4.2 14.4 - - + -
186A VAL* 6.0 0.2 - - + -
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Residues in contact with GLU 96 (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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92A LYS* 2.9 51.8 + - + +
93A GLY* 3.7 9.5 - - - +
95A LEU* 1.3 76.9 - - - +
97A LYS* 1.3 56.9 + - - +
100A GLY* 2.6 45.7 + - - +
101A SER* 4.0 13.7 - - - +
102A LEU* 4.3 13.4 + - + +
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Residues in contact with LYS 97 (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 GLY 2.9 15.5 + - - +
94A ALA* 3.7 11.0 - - - +
96A GLU* 1.3 80.7 - - - +
98A ASP* 1.3 92.1 + - - +
99A PHE 3.4 0.2 + - - -
100A GLY* 4.2 1.7 + - - -
131A GLN 4.2 9.1 + - - -
132A LYS* 3.7 21.9 + - - +
190A TYR* 6.0 0.7 - - - -
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Residues in contact with ASP 98 (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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94A ALA* 2.9 22.8 + - - +
97A LYS* 1.3 104.6 + - - +
99A PHE* 1.3 85.9 + - + +
131A GLN 4.6 0.7 - - - +
132A LYS* 3.0 31.8 + - - +
133A ILE* 2.9 37.6 + - + +
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Residues in contact with PHE 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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95A LEU* 2.8 21.5 + - + +
98A ASP* 1.3 89.9 - - + +
100A GLY* 1.3 59.5 + - - +
101A SER 3.2 6.6 + - - +
104A LYS* 3.3 22.2 - - - +
105A PHE* 3.6 40.4 - + + +
108A ASP* 3.6 21.2 - - + +
133A ILE* 3.3 39.9 - - + -
134A GLU* 4.6 0.4 - - - -
135A ILE* 3.6 39.3 - - + -
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Residues in contact with GLY 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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96A GLU* 2.6 31.4 + - - +
97A LYS 4.2 2.0 + - - -
98A ASP 3.9 0.4 - - - -
99A PHE* 1.3 72.8 - - - +
101A SER* 1.3 62.2 + - - +
104A LYS* 5.1 0.7 - - - -
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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