Contacts of the helix formed by residues 90 - 104 (chain D) in PDB entry 1I3R
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 GLN 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ASN* 2.6 44.0 + - - +
87D TRP* 3.6 17.0 - - - +
88D ASN 3.1 4.2 - - - -
89D SER* 1.3 82.4 - - - +
91D PRO* 1.3 67.8 - - - +
92D GLU* 3.1 2.9 - - + -
93D PHE* 2.8 21.0 + - + +
94D LEU* 3.0 11.3 + - - +
38E LYS 5.8 0.4 - - - +
39E SER* 3.1 29.7 + - - +
56E ALA* 5.9 0.2 - - - +
57E GLN* 2.7 35.1 + - - +
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Residues in contact with PRO 91 (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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88D ASN 4.6 1.3 - - - +
89D SER 3.1 14.8 - - - +
90D GLN* 1.3 82.4 - - - +
92D GLU* 1.3 70.3 + - + +
94D LEU* 3.8 9.7 - - + +
95D GLU* 3.0 27.7 + - - +
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Residues in contact with GLU 92 (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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90D GLN* 3.0 2.3 + - + -
91D PRO* 1.3 81.9 - - + +
93D PHE* 1.3 62.9 + - - +
95D GLU* 3.5 5.7 + - - +
96D GLN* 3.2 20.7 + - - +
41E THR* 4.7 3.1 + - - -
53E SER* 4.2 21.3 + - - -
54E PHE 3.5 21.3 + - - +
55E GLU* 3.9 24.9 - - + +
56E ALA* 4.2 5.6 + - - +
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Residues in contact with PHE 93 (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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9D ASN* 4.4 12.8 - - - -
11D GLY* 3.6 29.6 - - - -
56D TYR* 5.9 0.4 - - - -
73D PHE* 3.9 27.6 - + - -
87D TRP* 3.9 34.1 - + + -
90D GLN* 2.8 29.2 + - + +
92D GLU* 1.3 77.0 - - - +
94D LEU* 1.3 66.9 + - - +
96D GLN* 2.9 28.6 + - - +
97D LYS* 2.9 34.7 + - + +
57E GLN* 3.6 28.0 - - + -
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Residues in contact with LEU 94 (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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66D PHE* 4.3 4.3 - - + -
71D GLY 4.1 15.5 - - - +
72D GLU* 4.2 9.9 - - + +
73D PHE* 4.0 22.2 - - + -
87D TRP 3.7 11.0 - - - +
88D ASN* 3.2 47.3 - - - +
90D GLN 3.0 8.3 + - - +
91D PRO* 3.8 11.0 - - + +
93D PHE* 1.3 75.6 - - - +
95D GLU* 1.3 59.0 + - - +
97D LYS* 2.9 6.5 + - - +
98D ARG* 2.8 59.7 + - - +
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Residues in contact with GLU 95 (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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91D PRO 3.0 15.9 + - - +
92D GLU* 3.6 6.3 - - - +
94D LEU* 1.3 78.0 - - - +
96D GLN* 1.3 63.1 + - - +
98D ARG* 3.3 29.4 + - - +
99D ALA* 3.1 23.8 + - + +
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Residues in contact with GLN 96 (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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9D ASN* 3.4 41.3 + - - +
92D GLU 3.2 9.6 + - - +
93D PHE* 2.9 27.5 + - + +
95D GLU* 1.3 78.6 - - - +
97D LYS* 1.3 62.0 + - - +
99D ALA* 3.3 12.3 + - - +
100D GLU* 3.1 29.0 + - + +
103D THR* 5.0 0.5 + - - -
55E GLU* 4.7 21.3 - - - +
57E GLN* 5.6 2.9 - - - +
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Residues in contact with LYS 97 (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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8D PHE* 4.3 8.7 - - - +
9D ASN 3.0 28.2 + - - +
10D GLU* 4.4 8.5 + - - -
11D GLY 5.7 0.2 - - - +
39D SER* 5.5 0.2 + - - -
52D LEU* 4.1 10.0 - - + +
54D VAL* 4.3 21.9 - - - +
56D TYR* 4.8 6.0 + - - -
66D PHE* 3.9 34.9 - - + -
73D PHE* 4.1 21.3 - - + -
93D PHE* 2.9 25.3 + - + +
94D LEU* 3.3 10.5 - - - +
96D GLN* 1.3 77.9 - - - +
98D ARG* 1.3 61.7 + - - +
100D GLU* 2.6 50.7 + - - +
101D VAL* 4.5 0.2 - - - +
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Residues in contact with ARG 98 (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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66D PHE* 4.0 12.8 - - + -
68D SER* 6.0 2.0 - - - +
71D GLY* 2.7 39.5 + - - +
72D GLU* 3.6 23.4 + - - +
94D LEU* 2.8 39.6 + - - +
95D GLU* 3.5 28.5 + - - +
97D LYS* 1.3 70.7 - - - +
99D ALA* 1.3 57.0 + - - +
101D VAL* 3.3 21.4 - - - +
102D ASP* 5.2 1.7 - - - +
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Residues in contact with ALA 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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95D GLU 3.1 14.8 + - - +
96D GLN* 3.8 7.2 - - - +
97D LYS 3.1 1.0 - - - -
98D ARG* 1.3 74.1 - - - +
100D GLU* 1.3 52.9 + - - +
101D VAL 2.9 5.6 - - - -
102D ASP* 2.7 33.1 + - + +
103D THR* 2.8 25.1 + - + -
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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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7D ALA 4.7 0.7 - - - +
8D PHE* 3.7 15.0 - - + -
9D ASN* 3.1 29.8 + - - +
52D LEU* 4.0 11.7 - - + +
96D GLN* 3.1 24.4 + - + +
97D LYS* 2.6 51.9 + - - +
99D ALA* 1.3 77.3 - - - +
101D VAL* 1.3 58.3 + - - +
103D THR* 3.1 15.5 - - - +
104D VAL* 2.8 34.1 + - + +
105D CYS* 3.0 9.9 + - - +
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Residues in contact with VAL 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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50D VAL* 3.7 38.6 - - + +
52D LEU* 4.1 18.2 - - + +
68D SER* 3.8 24.5 - - - +
97D LYS 4.5 0.7 - - - +
98D ARG* 3.3 23.8 - - - +
99D ALA 2.9 0.2 - - - -
100D GLU* 1.3 78.5 - - - +
102D ASP* 1.3 61.8 + - - +
105D CYS* 3.2 11.3 - - - +
106D ARG* 3.2 35.7 + - - +
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Residues in contact with ASP 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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98D ARG 5.2 1.0 - - - +
99D ALA* 2.7 13.9 + - + +
101D VAL* 1.3 81.8 - - - +
103D THR* 1.3 66.6 + - + +
104D VAL 3.2 1.8 - - - -
106D ARG* 2.8 41.3 + - + +
107D HIS* 3.2 23.6 + - - +
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Residues in contact with THR 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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6D THR* 3.1 18.5 + - - +
96D GLN 5.0 0.3 + - - -
99D ALA* 2.8 26.8 + - + +
100D GLU* 3.1 23.7 + - - +
102D ASP* 1.3 74.3 - - + +
104D VAL* 1.3 63.5 + - - +
107D HIS* 3.3 14.1 - - - +
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Residues in contact with VAL 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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24C PHE* 5.3 0.2 - - + -
6D THR* 3.6 19.3 - - - +
7D ALA 3.9 15.7 - - - +
8D PHE* 3.5 39.7 - - + +
41D CYS* 5.0 0.7 - - - -
100D GLU* 2.8 29.5 + - + +
103D THR* 1.3 89.6 - - - +
105D CYS* 1.3 61.3 + - - +
106D ARG 3.6 0.4 - - - -
107D HIS 3.9 0.4 - - - -
108D ASN* 2.8 55.1 + - - +
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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