Contacts of the helix formed by residues 95 - 109 (chain A) in PDB entry 4OQZ
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 THR 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ASP* 1.3 90.6 + - - +
96A PRO* 1.4 74.4 - - + +
97A GLU* 3.8 7.5 + - - +
98A LYS* 3.2 27.9 + - + +
99A ALA* 3.1 19.8 + - - +
166A ALA* 3.9 1.1 - - - -
170A GLN* 4.3 8.1 - - + +
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Residues in contact with PRO 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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95A THR* 1.4 86.6 - - - +
97A GLU* 1.3 55.7 + - - +
99A ALA* 3.4 0.7 + - + -
100A ARG* 3.1 49.0 + - - +
163A GLY* 3.4 21.3 - - - +
166A ALA* 3.7 13.6 - - + -
167A LEU* 3.7 34.5 - - + +
170A GLN* 4.5 11.2 - - + -
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Residues in contact with GLU 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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95A THR* 3.2 7.9 + - - +
96A PRO* 1.3 79.1 - - - +
98A LYS* 1.3 57.9 + - + +
100A ARG* 2.9 40.5 + - - +
101A ALA* 3.0 27.3 + - - +
104A ARG* 5.1 0.7 + - - -
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Residues in contact with LYS 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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69A TYR* 3.6 26.0 - - + +
70A ASP* 3.5 26.9 - - - +
73A TYR* 4.3 1.7 + - + -
94A ASP* 3.4 25.6 - - - +
95A THR* 3.2 16.4 + - - +
97A GLU* 1.3 77.7 - - + +
99A ALA* 1.4 57.4 + - - +
101A ALA* 3.5 8.5 + - + +
102A ALA* 3.0 27.7 + - - +
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Residues in contact with ALA 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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69A TYR* 3.6 34.4 - - + +
95A THR 3.1 9.5 + - - +
96A PRO 3.6 9.6 - - - +
97A GLU 3.3 0.2 - - - -
98A LYS* 1.4 73.0 - - - +
100A ARG* 1.4 60.7 + - - +
102A ALA* 3.3 2.4 + - - +
103A ALA* 3.0 29.3 + - - +
113A HIS* 3.8 3.3 + - - -
115A THR* 4.0 7.0 - - + +
162A PRO* 3.7 23.1 - - - +
166A ALA* 4.2 4.7 - - + -
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Residues in contact with ARG 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 PRO* 3.1 39.1 + - - +
97A GLU* 2.9 49.1 + - - +
99A ALA* 1.4 74.7 - - - +
101A ALA* 1.4 60.8 + - - +
103A ALA* 3.7 1.7 + - - +
104A ARG* 3.3 37.9 + - - +
161A ASP* 3.0 35.5 + - - +
162A PRO* 3.8 13.7 - - + +
163A GLY* 3.7 15.4 - - - +
167A LEU* 5.9 4.9 - - - +
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Residues in contact with ALA 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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73A TYR* 3.2 15.6 + - - +
97A GLU 3.0 15.8 + - - +
98A LYS* 3.9 8.7 - - + +
99A ALA 3.3 0.4 - - - -
100A ARG* 1.4 72.7 - - - +
102A ALA* 1.3 62.6 + - - +
104A ARG* 3.5 28.6 + - - +
105A ARG* 3.4 19.6 + - - +
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Residues in contact with ALA 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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69A TYR* 3.7 25.6 - - + -
72A MET* 5.0 9.9 - - - +
73A TYR* 3.2 16.1 + - + +
98A LYS 3.0 17.1 + - - +
99A ALA 3.3 5.8 + - - +
101A ALA* 1.3 74.3 - - - +
103A ALA* 1.4 63.4 + - - +
105A ARG* 3.4 4.5 + - - +
106A VAL* 3.2 27.0 + - - +
113A HIS* 3.9 12.3 - - + +
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Residues in contact with ALA 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 ALA 3.0 13.4 + - - +
100A ARG 3.9 2.0 - - - +
101A ALA 3.5 0.2 - - - -
102A ALA* 1.4 74.3 - - - +
104A ARG* 1.3 57.0 + - - +
106A VAL* 3.4 3.3 + - - +
107A ALA* 3.1 30.8 + - - +
113A HIS* 3.5 38.1 + - + +
162A PRO* 3.6 26.2 - - + -
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Residues in contact with ARG 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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97A GLU* 5.1 0.6 + - - -
100A ARG* 3.3 36.5 + - - +
101A ALA* 3.5 27.9 + - - +
103A ALA* 1.3 79.4 - - - +
105A ARG* 1.3 59.5 + - - +
107A ALA* 3.6 5.7 + - - +
108A GLU* 3.2 24.0 + - - +
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Residues in contact with ARG 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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72A MET* 6.5 0.4 - - - -
73A TYR* 4.1 26.6 - - + -
76A LEU* 5.3 7.0 - - + -
80A GLU* 3.1 26.3 + - - -
101A ALA 3.4 10.6 + - - +
102A ALA 3.4 8.6 + - - +
103A ALA 3.4 0.2 - - - -
104A ARG* 1.3 76.5 - - - +
106A VAL* 1.3 63.2 + - + +
108A GLU* 3.3 46.2 + - - +
109A LEU* 3.2 53.9 + - + +
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Residues in contact with VAL 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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72A MET* 3.7 28.9 - - + -
76A LEU* 4.6 7.4 - - + -
83A VAL* 4.0 12.5 - - + +
88A LEU* 4.5 12.1 - - + -
102A ALA 3.2 19.3 + - - +
103A ALA 3.4 4.7 + - - +
105A ARG* 1.3 73.6 - - + +
107A ALA* 1.4 62.8 + - - +
109A LEU* 3.1 17.0 + - - +
110A GLY 3.3 0.3 + - - -
111A GLY 3.0 40.4 + - - +
112A THR 3.9 17.0 - - - +
113A HIS* 3.9 11.4 - - + +
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Residues in contact with ALA 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 ALA 3.1 16.8 + - - +
104A ARG* 3.8 6.3 - - - +
106A VAL* 1.4 71.0 - - - +
108A GLU* 1.4 61.6 + - - +
110A GLY* 3.0 19.2 + - - -
111A GLY 3.3 13.9 + - - +
113A HIS 5.7 0.4 - - - +
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Residues in contact with GLU 108 (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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104A ARG 3.2 10.9 + - - +
105A ARG* 3.3 44.9 + - - +
107A ALA* 1.4 76.3 - - - +
109A LEU* 1.4 57.8 + - - +
110A GLY 3.4 3.5 + - - -
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Residues in contact with LEU 109 (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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76A LEU* 4.1 17.5 - - + -
80A GLU* 3.6 34.9 - - + +
83A VAL* 3.8 30.9 - - + +
84A ALA* 3.4 22.5 + - - +
105A ARG* 3.2 50.3 + - + +
106A VAL 3.1 10.3 + - - +
108A GLU* 1.4 74.2 - - - +
110A GLY* 1.3 59.2 + - - +
111A GLY 3.4 1.3 - - - -
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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