Contacts of the helix formed by residues 98 - 111 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D THR* 2.9 15.3 + - - +
97D GLU* 1.3 81.0 - - + +
99D ARG* 1.3 60.1 + - - +
100D GLU* 3.5 12.2 + - - +
101D GLN* 3.1 45.0 + - - +
102D ILE* 3.0 29.1 + - - +
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ALA 5.1 1.6 + - - -
73D PHE 2.9 24.4 + - - -
74D ILE* 3.2 34.5 + - + +
75D SER 3.0 22.2 + - - -
76D PRO* 3.5 7.0 - - - +
78D LEU* 2.8 27.9 + - - +
80D MET* 3.5 16.0 - - - +
97D GLU* 2.8 34.1 + - - +
98D ASP* 1.3 71.7 + - - +
100D GLU* 1.3 61.8 + - - +
102D ILE* 3.6 22.5 - - + +
103D ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASP* 3.3 11.4 + - - +
99D ARG* 1.3 75.0 - - - +
101D GLN* 1.3 61.3 + - - +
103D ARG* 2.9 47.9 + - - +
104D GLN* 3.0 41.0 + - - +
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Residues in contact with GLN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D MET* 3.4 14.5 - - + +
94D LYS 5.0 1.9 - - - +
96D THR* 3.5 26.5 + - + +
98D ASP* 3.1 40.7 + - - +
100D GLU* 1.3 76.3 - - - +
102D ILE* 1.3 57.4 + - - +
104D GLN* 3.3 14.6 + - - +
105D GLY* 2.8 25.1 + - - -
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ALA* 4.3 7.2 - - + +
71D HIS* 5.6 2.9 - - + -
80D MET* 3.9 30.7 - - + -
82D PHE* 3.8 4.1 - - + -
93D MET* 3.7 23.8 - - + -
96D THR* 3.9 13.5 - - + +
98D ASP 3.0 18.8 + - - +
99D ARG* 3.6 50.9 - - + +
100D GLU 3.3 0.2 - - - -
101D GLN* 1.3 73.7 - - - +
103D ARG* 1.3 58.1 + - - +
105D GLY* 3.3 1.2 + - - -
106D LEU* 3.0 44.4 + - + +
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D HIS* 5.3 11.0 - - + -
99D ARG 2.9 17.4 + - - +
100D GLU* 2.9 40.9 + - - +
101D GLN 3.3 0.2 - - - -
102D ILE* 1.3 77.4 - - - +
104D GLN* 1.3 85.3 + - - +
106D LEU* 3.2 11.0 + - - +
107D GLU* 2.9 59.1 + - + +
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 3.0 32.3 + - - +
101D GLN* 3.6 13.0 - - - +
103D ARG* 1.3 97.1 - - - +
105D GLY* 1.3 57.1 + - - +
107D GLU* 3.3 10.8 + - - +
108D GLU* 3.0 43.1 + - - +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PHE* 3.8 19.5 - - - -
92D LEU* 3.5 11.5 - - - +
93D MET* 4.2 6.1 - - - -
101D GLN 2.8 16.5 + - - -
102D ILE 3.7 2.0 - - - -
103D ARG 3.3 0.2 - - - -
104D GLN* 1.3 77.4 - - - +
106D LEU* 1.3 56.3 + - - +
108D GLU* 3.2 10.6 + - - +
109D LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 106 (chain D).
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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63D TYR* 3.3 24.6 - - + +
66D VAL* 3.9 12.8 - - + -
67D GLU* 3.9 22.4 - - + +
70D ALA* 3.8 17.3 - - + -
71D HIS* 3.3 38.4 - - + +
82D PHE* 3.7 21.3 - - + -
102D ILE* 3.0 24.8 + - + +
103D ARG* 3.2 4.7 + - - +
105D GLY* 1.3 75.5 - - - +
107D GLU* 1.3 62.4 + - + +
109D LEU* 3.1 9.4 + - + -
110D GLN* 3.0 21.7 + - - +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 2.9 55.6 + - + +
104D GLN* 3.7 11.1 - - - +
105D GLY 3.3 0.2 - - - -
106D LEU* 1.3 76.8 - - + +
108D GLU* 1.3 61.6 + - - +
110D GLN* 3.3 38.3 + - - +
111D LYS* 3.5 17.8 + - - +
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Residues in contact with GLU 108 (chain D).
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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92D LEU* 3.5 39.6 - - + +
104D GLN* 3.0 30.4 + - - +
105D GLY* 3.2 9.1 + - - +
107D GLU* 1.3 77.6 - - + +
109D LEU* 1.3 62.2 + - - +
111D LYS* 3.1 38.5 + - - +
112D VAL* 3.6 8.7 + - - +
222D ACT 4.3 8.3 - - + +
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Residues in contact with LEU 109 (chain D).
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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49D LEU* 3.9 22.4 - - + -
59D TRP* 3.0 35.5 + - + -
63D TYR* 3.7 15.9 - - + -
66D VAL* 4.2 7.4 - - + -
82D PHE* 3.8 30.5 - - + -
84D VAL* 3.8 29.8 - - + -
92D LEU* 3.8 15.3 - - + -
105D GLY 3.0 14.3 + - - +
106D LEU* 3.1 22.8 + - + +
108D GLU* 1.3 76.0 - - - +
110D GLN* 1.3 60.5 + - - +
111D LYS 3.2 0.7 + - - -
112D VAL* 3.3 9.7 + - + +
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Residues in contact with GLN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TRP* 4.9 4.6 + - - +
63D TYR* 2.8 39.3 + - + +
67D GLU* 4.4 3.8 + - - -
106D LEU* 3.0 16.0 + - - +
107D GLU* 3.4 32.6 - - - +
108D GLU 3.2 0.4 - - - -
109D LEU* 1.3 76.5 - - - +
111D LYS* 1.3 61.2 + - + +
112D VAL 3.7 3.5 + - - +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 3.5 21.8 - - - +
108D GLU* 3.1 28.7 + - - +
109D LEU 3.1 0.8 - - - -
110D GLN* 1.3 79.8 - - + +
112D VAL* 1.3 64.6 + - - +
113D LEU* 3.4 7.4 + - - +
222D ACT 5.7 1.1 - - - -
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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