Contacts of the helix formed by residues 93 - 103 (chain A) in PDB entry 5M72
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 ARG 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LYS* 3.6 29.5 - - - +
65A LEU* 3.4 27.9 - - - +
69A ASN* 5.9 0.2 - - - +
88A GLU* 2.9 25.3 + - + +
89A TYR 4.4 0.2 + - - -
91A LEU* 3.6 25.0 + - - +
92A ASN* 1.3 77.3 - - - +
94A ILE* 1.3 64.7 + - - +
95A GLU* 3.3 7.6 - - - -
96A ASN* 3.2 32.7 + - + +
97A ALA* 3.0 18.7 + - - +
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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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89A TYR* 3.8 20.4 + - + +
92A ASN* 3.6 6.4 + - - +
93A ARG* 1.3 75.3 - - - +
95A GLU* 1.3 81.4 + - - +
97A ALA* 3.3 5.1 + - + +
98A LEU* 2.9 27.4 + - - +
118A VAL* 3.6 39.0 - - + -
121A ARG* 4.0 27.1 - - + -
122A LEU* 3.7 32.5 - - + +
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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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92A ASN 5.2 1.2 - - - +
93A ARG* 4.3 4.0 - - - -
94A ILE* 1.3 96.7 + - + +
96A ASN* 1.3 68.1 + - - +
98A LEU* 3.4 10.1 + - - +
99A LYS* 3.1 22.5 + - - +
122A LEU* 5.3 7.3 - - + +
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Residues in contact with ASN 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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88A GLU* 3.4 22.7 + - + +
93A ARG* 3.2 41.8 + - - +
95A GLU* 1.3 78.1 - - - +
97A ALA* 1.3 58.9 + - - +
99A LYS* 3.1 8.1 + - - +
100A THR* 2.9 32.2 + - - -
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Residues in contact with ALA 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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85A ALA* 3.5 25.2 - - + +
88A GLU* 3.5 10.5 + - - -
89A TYR* 3.8 16.2 - - + +
93A ARG 3.0 13.1 + - - +
94A ILE* 3.5 10.8 - - - +
95A GLU 3.3 0.2 - - - -
96A ASN* 1.3 75.6 - - - +
98A LEU* 1.3 63.1 + - - +
100A THR* 3.3 2.9 + - - -
101A ILE* 3.0 30.3 + - - +
118A VAL* 4.4 11.4 - - + -
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Residues in contact with LEU 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 ILE 2.9 16.9 + - - +
95A GLU* 3.7 8.5 - - - +
96A ASN 3.3 0.2 - - - -
97A ALA* 1.3 75.7 - - - +
99A LYS* 1.3 63.1 + - - +
101A ILE* 3.2 5.1 + - - +
102A GLU* 3.0 54.0 + - - +
115A TYR* 3.8 25.4 - - + +
118A VAL* 4.1 19.4 - - + +
119A LEU* 4.9 1.3 - - + -
122A LEU* 3.8 14.6 - - + -
124A ARG* 3.5 28.0 - - - +
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Residues in contact with LYS 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 GLU 3.1 13.5 + - - +
96A ASN* 3.1 10.1 + - - +
98A LEU* 1.3 76.9 - - - +
100A THR* 1.3 61.1 + - - +
102A GLU* 3.4 10.0 + - + +
103A SER* 2.7 45.0 + - - +
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Residues in contact with THR 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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81A SER* 3.4 35.0 + - - +
84A LYS* 2.9 32.2 + - + +
85A ALA* 3.7 11.4 - - + +
88A GLU* 2.8 24.7 + - - -
96A ASN 2.9 8.2 + - - -
97A ALA 3.7 4.0 - - - -
99A LYS* 1.3 78.1 - - - +
101A ILE* 1.3 61.4 + - - +
103A SER* 3.3 6.2 + - - -
104A ALA* 3.3 20.3 + - - +
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Residues in contact with ILE 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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85A ALA* 3.7 13.9 - - + -
97A ALA 3.0 15.1 + - - +
98A LEU* 3.2 8.0 + - - +
100A THR* 1.3 75.2 - - - +
102A GLU* 1.3 63.9 + - - +
104A ALA* 3.2 9.2 + - - +
107A GLN* 3.2 21.4 + - - +
111A LEU* 4.2 24.2 - - + +
114A LEU* 3.9 29.2 - - + -
115A TYR* 3.8 43.5 - - + +
118A VAL* 4.0 11.4 - - + -
205A GOL 3.9 18.6 - - - -
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Residues in contact with GLU 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 LEU* 3.0 49.2 + - + +
99A LYS* 4.0 8.5 - - + +
101A ILE* 1.3 74.7 - - - +
103A SER* 1.3 60.6 + - - +
104A ALA 3.6 2.8 + - - +
107A GLN* 4.6 3.3 + - - -
115A TYR* 4.6 8.3 + - + +
124A ARG* 4.8 7.4 + - - -
205A GOL 4.3 23.6 + - - +
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Residues in contact with SER 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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81A SER* 5.1 0.8 + - - -
99A LYS* 2.7 40.0 + - - +
100A THR* 3.8 6.5 - - - -
101A ILE 3.2 0.4 - - - -
102A GLU* 1.3 76.6 - - - +
104A ALA* 1.3 65.9 + - - +
105A ASN* 3.4 10.7 + - - -
202A SO4 4.8 0.3 + - - -
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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