Contacts of the helix formed by residues 91 - 107 (chain A) in PDB entry 2OU7
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 LEU 3.1 1.9 - - - -
90A LEU* 1.3 84.2 - - + +
92A PRO* 1.3 74.1 - - + +
93A HIS* 4.4 4.9 - - + +
94A GLN* 3.1 43.8 + - + +
95A ARG* 3.2 13.2 + - - +
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Residues in contact with PRO 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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90A LEU 3.8 6.5 - - - +
91A LYS* 1.3 88.3 - - + +
93A HIS* 1.3 56.7 + - - +
95A ARG* 3.2 14.2 + - + +
96A GLU* 2.9 39.5 + - - +
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Residues in contact with HIS 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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91A LYS* 3.2 6.3 - - + +
92A PRO* 1.3 75.5 - - - +
94A GLN* 1.3 62.4 + - + +
96A GLU* 3.4 20.0 + - + +
97A LYS* 3.0 47.9 + - + +
212A CYS* 3.8 3.2 - - + -
501A ZN 2.2 36.9 - - - -
502A ACT 3.3 18.4 - - + -
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Residues in contact with GLN 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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64A PHE* 4.4 17.4 - - + -
88A LEU 3.1 23.1 + - - +
89A LEU* 3.6 18.8 - - + +
90A LEU* 3.6 1.7 + - - +
91A LYS* 3.1 45.8 + - + +
93A HIS* 1.3 78.5 - - + +
95A ARG* 1.3 60.7 + - - +
97A LYS* 3.7 18.4 + - - +
98A MET* 3.3 21.8 + - - +
502A ACT 6.0 1.3 - - + +
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Residues in contact with ARG 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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86A LYS* 4.1 39.0 + - - +
89A LEU* 3.1 37.8 + - + +
90A LEU* 5.5 1.1 - - - +
91A LYS 3.2 7.1 + - - +
92A PRO* 3.2 14.7 + - + +
94A GLN* 1.3 76.1 - - - +
96A GLU* 1.3 59.9 + - + +
98A MET* 3.3 8.3 + - - +
99A SER* 2.9 31.3 + - - +
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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 PRO* 2.9 26.3 + - - +
93A HIS* 3.4 22.7 + - + +
95A ARG* 1.3 72.3 - - + +
97A LYS* 1.3 64.8 + - - +
99A SER* 3.3 7.3 + - - -
100A MET* 3.0 24.6 + - - +
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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 HIS* 3.0 41.8 + - + +
94A GLN* 3.9 18.5 - - - +
95A ARG 3.3 0.2 - - - -
96A GLU* 1.3 75.4 - - - +
98A MET* 1.3 57.2 + - - +
100A MET* 3.6 6.8 + - - +
101A GLU* 3.2 27.0 + - - +
196A GLY* 5.0 13.9 - - - +
197A LEU* 6.3 0.2 - - + -
212A CYS* 3.7 39.3 + - + +
502A ACT 3.7 15.3 + - - -
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Residues in contact with MET 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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82A LYS* 4.6 13.7 - - + +
84A VAL* 3.9 33.9 - - + -
89A LEU* 4.8 15.0 - - + -
94A GLN 3.3 15.5 + - - +
95A ARG* 3.3 7.8 + - - +
96A GLU 3.2 0.4 - - - -
97A LYS* 1.3 76.8 - - - +
99A SER* 1.3 65.9 + - - +
101A GLU* 3.7 24.6 - - - +
102A ILE* 3.3 38.1 + - + +
126A VAL* 4.4 16.8 - - + -
128A VAL* 5.6 6.3 - - + -
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Residues in contact with SER 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 ARG 2.9 18.0 + - - -
96A GLU* 3.3 9.4 + - - -
98A MET* 1.3 76.8 - - - +
100A MET* 1.3 58.4 + - - +
102A ILE* 3.4 7.1 + - - +
103A SER* 3.0 30.4 + - - -
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Residues in contact with MET 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 3.0 16.0 + - - +
97A LYS* 3.8 7.6 - - - +
99A SER* 1.3 77.9 - - - +
101A GLU* 1.3 58.0 + - - +
103A SER* 3.6 17.7 - - - +
104A ILE* 2.9 64.0 + - + +
198A ALA 4.6 7.0 - - - +
199A THR* 5.8 1.3 - - - -
200A LYS* 5.7 6.1 - - + -
202A GLU* 6.1 1.1 - - - +
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Residues in contact with GLU 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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82A LYS* 3.6 14.1 + - - +
97A LYS 3.2 13.8 + - - +
98A MET* 3.7 28.0 - - - +
100A MET* 1.3 79.8 - - - +
102A ILE* 1.3 58.5 + - + +
104A ILE* 3.9 1.9 - - - +
105A HIS* 2.8 36.9 + - + +
194A ASP* 3.8 7.1 - - - +
195A PHE* 3.6 32.4 + - + +
196A GLY* 3.8 10.7 + - - -
505A MG 2.9 28.0 - - - -
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Residues in contact with ILE 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 MET* 3.3 39.1 + - + +
99A SER* 3.9 6.1 - - - +
100A MET 3.3 0.2 - - - -
101A GLU* 1.3 78.6 - - + +
103A SER* 1.3 61.1 + - - +
105A HIS* 4.4 3.8 - - - +
106A ARG* 2.8 41.5 + - - +
116A PHE* 3.9 27.4 - - + -
119A PHE* 3.9 44.2 - - + -
126A VAL* 4.8 9.9 - - + -
128A VAL* 4.8 11.2 - - + -
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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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99A SER 3.0 18.0 + - - -
100A MET* 3.6 21.1 - - - +
102A ILE* 1.3 78.8 - - - +
104A ILE* 1.3 61.6 + - - +
106A ARG* 3.8 15.3 - - - +
107A SER* 3.5 19.2 + - - -
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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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100A MET* 2.9 45.2 + - + +
101A GLU* 3.9 3.4 - - - +
103A SER* 1.3 74.2 - - - +
105A HIS* 1.3 66.1 + - - +
107A SER* 2.7 23.5 + - - -
108A LEU* 3.2 11.7 - - + +
172A VAL* 4.2 19.5 - - + -
195A PHE* 4.2 25.1 - - + +
198A ALA* 3.5 39.0 - - + +
199A THR* 3.8 15.3 - - - +
200A LYS* 4.3 13.0 - - + +
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Residues in contact with HIS 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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101A GLU* 2.8 28.0 + - + +
102A ILE* 4.2 0.7 - - - +
104A ILE* 1.3 76.0 - - - +
106A ARG* 1.3 59.5 + - - +
108A LEU* 3.3 26.1 + - + +
113A VAL* 4.5 1.3 - - + -
114A VAL* 2.9 34.7 + - + +
116A PHE* 3.2 24.3 - + + +
128A VAL* 5.5 0.4 - - - +
130A LEU* 3.4 30.7 - - + +
193A GLY* 5.2 0.2 - - - -
194A ASP 5.5 3.8 - - - -
195A PHE* 3.0 45.2 + + + -
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Residues in contact with ARG 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 ILE* 2.8 28.4 + - - +
103A SER* 3.8 16.6 - - - +
105A HIS* 1.3 68.4 - - - +
107A SER* 1.3 62.0 + - - +
108A LEU 3.0 13.3 + - - +
116A PHE* 3.5 35.5 - - + +
119A PHE* 3.7 32.4 - - - -
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Residues in contact with SER 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 SER 3.5 13.3 + - - -
104A ILE* 2.7 21.5 + - - +
106A ARG* 1.3 81.7 - - - +
108A LEU* 1.3 65.0 + - - +
109A ALA 4.3 0.2 + - - -
166A TYR* 3.9 4.9 + - - -
170A ASN* 5.4 2.8 - - - +
200A LYS* 4.8 16.1 - - - -
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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