Contacts of the helix formed by residues 98 - 111 (chain A) in PDB entry 3N2N
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 ASP 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A THR* 3.0 15.8 + - - +
97A GLU* 1.3 86.9 + - - +
99A ARG* 1.3 60.5 + - - +
100A GLU* 3.6 12.3 - - - +
101A GLN* 3.1 38.4 + - + +
102A ILE* 2.9 28.2 + - - +
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Residues in contact with ARG 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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70A ALA 5.3 1.0 + - - -
73A PHE 2.8 24.2 + - - -
74A ILE* 3.3 35.5 + - + +
75A SER 3.1 21.7 + - - -
76A PRO* 3.7 6.8 - - - +
78A LEU* 2.8 29.9 + - - +
80A MET* 3.5 17.0 - - - +
97A GLU* 2.9 26.2 + - - +
98A ASP* 1.3 70.1 + - - +
100A GLU* 1.3 61.6 + - + +
102A ILE* 3.6 22.9 - - + +
103A ARG* 2.8 28.4 + - - +
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Residues in contact with GLU 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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98A ASP* 3.2 12.2 + - - +
99A ARG* 1.3 77.5 - - + +
101A GLN* 1.3 64.9 + - + +
103A ARG* 2.9 47.9 + - - +
104A GLN* 3.1 35.6 + - - +
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Residues in contact with GLN 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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93A MET* 3.4 13.7 - - + +
96A THR* 4.1 17.0 - - + +
98A ASP* 3.1 32.4 + - + +
100A GLU* 1.3 75.1 - - - +
102A ILE* 1.3 53.7 + - - +
104A GLN* 3.3 26.8 + - - +
105A GLY 2.8 29.3 + - - -
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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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70A ALA* 4.4 5.8 - - + +
80A MET* 3.9 37.0 - - + -
82A PHE* 4.0 4.3 - - + -
93A MET* 3.6 15.5 - - + -
96A THR* 3.8 18.4 - - + +
98A ASP 2.9 18.8 + - - +
99A ARG* 3.6 50.5 - - + +
101A GLN* 1.3 74.0 - - - +
103A ARG* 1.3 58.0 + - - +
105A GLY* 3.3 0.9 + - - -
106A LEU* 2.9 45.1 + - + +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG 2.8 21.4 + - - +
100A GLU* 2.9 41.0 + - - +
101A GLN 3.3 0.2 - - - -
102A ILE* 1.3 76.0 - - - +
104A GLN* 1.3 80.3 + - - +
106A LEU* 3.4 9.8 + - - +
107A GLU* 2.8 72.6 + - + +
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Residues in contact with GLN 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 GLU* 3.1 25.8 + - - +
101A GLN* 3.7 28.1 + - - +
103A ARG* 1.3 96.5 + - - +
105A GLY* 1.3 65.0 + - - +
107A GLU* 3.3 15.9 + - - +
108A GLU* 3.1 38.4 + - - +
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Residues in contact with GLY 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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82A PHE* 3.8 18.4 - - - -
92A LEU* 3.5 17.9 - - - +
93A MET* 4.1 7.0 - - - -
101A GLN 2.8 17.2 + - - -
102A ILE 3.6 2.0 - - - -
104A GLN* 1.3 76.7 - - - +
106A LEU* 1.3 55.5 + - - +
108A GLU* 3.2 6.0 + - - -
109A LEU* 2.9 25.6 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.2 27.0 - - + +
66A VAL* 4.1 10.8 - - + -
67A GLU* 4.0 25.6 - - + +
70A ALA* 3.9 13.5 - - + -
71A HIS* 3.8 33.0 - - + +
82A PHE* 3.7 24.6 - - + -
102A ILE* 2.9 26.5 + - + +
103A ARG* 3.7 8.1 - - - +
105A GLY* 1.3 71.7 - - - +
107A GLU* 1.3 60.3 + - + +
109A LEU* 3.2 4.8 + - + -
110A GLN* 2.9 27.2 + - - +
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Residues in contact with GLU 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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63A TYR* 5.3 0.2 - - - -
103A ARG* 2.8 54.6 + - + +
104A GLN* 3.3 16.3 + - - +
106A LEU* 1.3 76.8 - - + +
108A GLU* 1.3 62.8 + - + +
110A GLN* 3.5 13.4 + - - +
111A LYS* 3.6 24.1 + - - +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.1 34.3 - - + +
104A GLN* 3.1 32.6 + - - +
105A GLY* 3.6 8.6 + - - +
106A LEU 3.2 0.2 - - - -
107A GLU* 1.3 75.1 - - + +
109A LEU* 1.3 64.8 + - - +
111A LYS* 3.3 30.8 + - - +
112A VAL* 3.5 12.6 + - - +
222A ACT 4.3 8.9 - - + +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.8 25.1 - - + -
59A TRP* 2.8 39.9 + - + -
63A TYR* 3.8 12.6 - - + -
66A VAL* 4.0 17.7 - - + -
82A PHE* 3.7 31.2 - - + -
84A VAL* 3.7 30.1 - - + -
92A LEU* 3.9 16.4 - - + +
105A GLY 2.9 14.0 + - - +
106A LEU* 3.2 12.3 + - + +
108A GLU* 1.3 74.4 - - - +
110A GLN* 1.3 57.6 + - - +
112A VAL* 3.3 9.0 + - + +
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Residues in contact with GLN 110 (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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59A TRP* 4.2 8.2 + - - +
60A ASN* 5.0 11.3 + - - +
63A TYR* 3.7 35.6 - - + +
106A LEU 2.9 15.7 + - - +
107A GLU* 3.6 8.9 - - - +
108A GLU 3.3 0.2 - - - -
109A LEU* 1.3 76.2 - - - +
111A LYS* 1.3 72.9 + - - +
112A VAL 3.3 2.8 + - - +
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Residues in contact with LYS 111 (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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107A GLU* 3.6 17.7 + - - +
108A GLU* 3.3 28.3 + - - +
109A LEU 3.2 0.8 - - - -
110A GLN* 1.3 86.4 - - - +
112A VAL* 1.3 65.6 + - - +
113A LEU* 3.4 17.8 + - - +
222A ACT 5.7 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