Contacts of the helix formed by residues 91 - 105 (chain A) in PDB entry 3ECS
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 LYS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A CYS 3.0 24.0 + - - +
90A LYS* 1.3 75.1 - - - +
92A ILE* 1.3 67.3 + - + +
93A MSE 2.9 4.0 - - - -
94A ILE* 2.7 30.4 + - - +
95A GLU* 3.0 24.9 + - + +
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Residues in contact with ILE 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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89A CYS* 3.1 26.0 - - - +
91A LYS* 1.3 82.2 - - + +
93A MSE 1.3 59.6 + - + +
95A GLU* 2.7 21.3 - - + +
96A ARG* 3.0 43.0 + - + +
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Residues in contact with MSE 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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34A LEU* 3.8 16.2 - - + +
43A GLN* 4.3 22.9 - - - +
76A ILE* 3.3 30.9 - - + +
77A SER* 3.3 36.8 - - - +
89A CYS 5.0 1.8 - - - +
90A LYS* 3.5 50.5 - - + -
91A LYS 2.9 0.4 - - - -
92A ILE* 1.3 78.3 - - + +
94A ILE* 1.3 58.9 + - - +
95A GLU 3.0 5.2 - - - -
96A ARG* 4.9 1.3 - - - -
97A GLY* 3.2 22.3 + - - -
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Residues in contact with ILE 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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31A LEU* 3.8 9.3 - - + +
34A LEU* 3.1 44.4 - - + +
35A LYS* 3.5 39.3 - - + -
90A LYS* 3.5 19.3 - - + +
91A LYS* 2.7 10.8 + - - +
93A MSE 1.3 76.9 - - - +
95A GLU* 1.3 59.4 + - + +
97A GLY 4.1 1.3 - - - -
98A GLU* 2.8 26.8 + - - +
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Residues in contact with GLU 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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91A LYS* 3.0 21.9 + - + +
92A ILE* 2.7 40.8 + - + +
93A MSE 3.0 0.2 - - - -
94A ILE* 1.3 80.3 - - + +
96A ARG* 1.3 60.5 + - + +
97A GLY 3.0 1.1 - - - -
98A GLU* 2.9 12.8 + - - +
99A LEU* 2.9 27.6 + - - +
102A ARG* 5.3 0.7 + - - -
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Residues in contact with ARG 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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75A PHE* 3.3 63.0 + - + +
76A ILE* 4.7 4.7 - - - -
77A SER* 3.9 25.5 + - - +
92A ILE* 3.0 39.1 + - + +
93A MSE 4.5 2.2 - - - +
95A GLU* 1.3 75.2 - - + +
97A GLY* 1.3 57.8 + - - +
99A LEU* 3.3 10.0 + - - +
100A PHE 2.9 21.5 + - - -
307A ALA* 3.8 35.7 - - - +
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Residues in contact with GLY 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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31A LEU* 4.0 7.5 - - - +
72A PHE* 3.4 33.1 - - - -
75A PHE* 5.1 0.4 - - - -
76A ILE* 4.8 3.5 - - - +
93A MSE 3.2 15.7 + - - -
95A GLU 3.0 0.6 - - - -
96A ARG* 1.3 80.0 - - - +
98A GLU* 1.3 58.2 + - - +
100A PHE* 3.3 4.2 + - - +
101A LEU* 3.0 26.5 + - - +
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Residues in contact with GLU 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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31A LEU* 3.7 21.3 - - + -
35A LYS* 2.8 31.4 + - - -
94A ILE* 2.8 26.2 + - - +
95A GLU* 2.9 13.2 + - - +
97A GLY* 1.3 76.5 - - - +
99A LEU* 1.3 58.9 + - - +
100A PHE 3.0 0.2 - - - -
101A LEU* 3.8 2.3 - - - +
102A ARG* 2.9 42.0 + - - +
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Residues in contact with LEU 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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75A PHE* 3.8 26.9 - - + -
95A GLU 2.9 12.2 + - - +
96A ARG* 3.5 11.0 - - - +
98A GLU* 1.3 78.4 - - - +
100A PHE* 1.3 58.3 + - - +
102A ARG* 3.9 32.2 - - - +
103A ARG* 3.4 21.2 + - + +
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Residues in contact with PHE 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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27A ILE* 3.4 32.8 - - + -
71A LEU* 3.9 28.0 - - + -
72A PHE* 3.5 36.8 - + + -
75A PHE* 3.7 33.9 - + + -
96A ARG 2.9 15.3 + - - +
97A GLY* 3.5 8.1 - - - +
98A GLU 3.0 0.2 - - - -
99A LEU* 1.3 78.6 - - - +
101A LEU* 1.3 66.4 + - - +
103A ARG* 2.9 12.1 + - + +
104A ILE* 2.9 40.2 + - + +
233A PHE* 5.3 2.9 - - + -
303A LEU* 5.6 6.7 - - + -
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Residues in contact with LEU 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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24A VAL* 4.2 14.4 - - + -
27A ILE* 4.2 14.8 - - + -
28A ARG* 3.3 56.8 - - + +
31A LEU* 3.6 24.7 - - + -
97A GLY 3.0 16.9 + - - +
98A GLU* 3.3 4.0 + - - +
100A PHE* 1.3 78.8 - - - +
102A ARG* 1.3 56.1 + - - +
103A ARG 3.0 1.0 + - - -
104A ILE* 3.1 19.4 - - + +
105A SER* 2.7 28.1 + - - +
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Residues in contact with ARG 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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95A GLU 5.3 0.4 + - - -
98A GLU* 2.9 20.5 + - - +
99A LEU* 3.9 42.8 - - - +
101A LEU* 1.3 77.4 - - - +
103A ARG* 1.3 62.5 + - - +
105A SER* 3.3 13.4 + - - -
106A LEU* 4.0 20.6 + - + +
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Residues in contact with ARG 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 LEU* 3.4 20.9 + - + +
100A PHE* 2.9 13.5 + - - +
102A ARG* 1.3 78.0 - - - +
104A ILE* 1.3 72.7 + - - +
105A SER 3.0 2.8 + - - -
106A LEU* 3.1 24.0 + - + +
107A SER* 3.9 3.7 + - - -
110A LYS* 5.2 11.7 + - - +
232A SER* 3.6 12.9 + - - -
287A ASP* 2.4 41.5 + - - +
288A LEU* 3.7 19.8 - - - +
303A LEU* 5.4 7.7 - - - +
510F SO4 5.8 4.0 - - - +
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Residues in contact with ILE 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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24A VAL* 4.3 20.7 - - + +
27A ILE* 3.5 33.4 - - + -
100A PHE* 2.9 44.4 + - + +
101A LEU* 3.1 33.0 - - + +
103A ARG* 1.3 81.7 - - - +
105A SER* 1.3 56.9 + - - +
106A LEU 3.1 2.9 + - - -
107A SER* 3.0 25.6 + - - +
108A ARG 5.0 0.3 + - - -
231A GLU* 5.2 0.2 - - - +
232A SER* 5.6 2.5 - - - +
233A PHE* 3.9 30.8 - - + -
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Residues in contact with SER 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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24A VAL* 5.3 7.4 - - - -
28A ARG* 5.0 6.6 + - - -
101A LEU* 2.7 29.7 + - - +
102A ARG* 3.3 12.7 + - - -
103A ARG 3.0 0.4 - - - -
104A ILE* 1.3 75.8 - - - +
106A LEU* 1.3 67.9 + - - +
107A SER 3.5 0.7 - - - -
108A ARG* 5.2 2.4 - - - +
109A ASN* 5.2 2.9 + - - -
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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