Contacts of the helix formed by residues 104 - 113 (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 VAL 104 (chain D).
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Specific contacts
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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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Residues in contact with CYS 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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7C ILE* 4.8 0.6 - - - +
8D PHE* 4.0 2.2 - - - -
41D CYS* 2.0 53.4 - - + -
43D PHE* 3.5 8.1 - - + -
50D VAL* 3.9 14.6 - - + -
52D LEU* 3.8 22.4 - - - -
100D GLU 3.0 9.2 + - - -
101D VAL* 3.2 22.7 - - - +
104D VAL* 1.3 74.7 - - - +
106D ARG* 1.3 58.9 + - - +
108D ASN* 3.8 2.3 - - - +
109D TYR* 2.8 29.3 + - - +
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Residues in contact with ARG 106 (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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43D PHE* 4.5 0.7 - - - -
47D THR* 2.9 48.2 + - + -
48D GLN 3.4 12.7 + - - -
49D ARG* 4.4 0.4 - - - +
50D VAL* 4.0 24.3 + - + +
101D VAL* 3.2 27.0 + - - +
102D ASP* 2.8 42.9 + - - +
105D CYS* 1.3 79.2 - - - +
107D HIS* 1.3 66.2 + - - +
109D TYR* 3.3 7.3 + - - +
110D GLU* 3.1 35.5 + - - +
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Residues in contact with HIS 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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3D LYS* 6.2 0.2 - - - -
4D VAL 2.8 25.8 + - - -
6D THR* 3.5 23.4 - - + +
102D ASP 3.2 9.7 + - - +
103D THR* 3.3 21.8 - - - +
104D VAL 3.7 1.6 - - - +
105D CYS 3.2 0.8 - - - -
106D ARG* 1.3 80.6 - - - +
108D ASN* 1.3 80.2 + - - +
110D GLU* 3.2 16.6 + - - +
111D ILE* 3.4 26.0 + - + +
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Residues in contact with ASN 108 (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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7C ILE* 4.7 5.7 - - + +
24C PHE* 4.0 9.6 - - + -
5D ILE* 2.9 31.9 - - - +
6D THR* 2.9 35.0 + - - -
41D CYS* 6.1 0.4 - - - -
104D VAL* 2.8 36.8 + - - +
105D CYS* 4.0 2.4 - - - +
107D HIS* 1.3 77.7 - - - +
109D TYR* 1.3 61.9 + - - +
111D ILE* 3.1 7.5 + - - +
112D PHE* 2.9 46.1 + - + -
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Residues in contact with TYR 109 (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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3C GLU* 4.2 5.7 - - - +
5C HIS* 3.9 22.9 - + + -
7C ILE* 4.2 11.4 - - + +
26C PHE* 5.2 1.6 - + - -
43D PHE* 3.7 45.3 - + + -
46D GLY* 3.2 33.6 + - - -
47D THR* 3.4 18.2 - - + -
105D CYS 2.8 19.4 + - - +
106D ARG* 3.5 7.0 - - - +
108D ASN* 1.3 78.3 - - - +
110D GLU* 1.3 54.4 + - + +
112D PHE* 3.4 2.0 + - + -
113D ASP* 2.7 62.1 + - + +
117D VAL* 4.1 22.1 - - + +
308D NAG 6.4 0.2 - - + -
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Residues in contact with GLU 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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3D LYS* 4.3 2.3 + - - -
47D THR* 4.7 12.6 + - + +
106D ARG* 3.1 28.3 + - - +
107D HIS* 3.2 9.4 + - - +
109D TYR* 1.3 76.0 - - + +
111D ILE* 1.3 67.0 + - + +
113D ASP* 3.6 12.8 + - - +
114D ASN* 3.2 18.2 + - - -
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Residues in contact with ILE 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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51C PHE 3.9 6.2 - - - +
52C ALA* 3.5 29.4 - - + -
3D LYS* 3.9 18.7 - - + +
4D VAL 3.5 42.8 - - - +
5D ILE* 3.8 11.2 - - + +
107D HIS* 3.4 27.3 + - + +
108D ASN* 3.1 8.9 + - - +
110D GLU* 1.3 81.3 - - + +
112D PHE* 1.3 67.6 + - + +
113D ASP 3.5 0.2 + - - -
114D ASN* 3.5 14.5 + - - +
115D PHE* 3.2 16.2 - - + -
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Residues in contact with PHE 112 (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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7C ILE* 3.4 28.5 - - + -
24C PHE* 4.1 15.9 - + - -
26C PHE* 4.8 6.3 - + + -
31C ILE* 3.5 36.6 - - + -
5D ILE* 3.6 40.4 - - + -
108D ASN* 2.9 30.5 + - + +
109D TYR* 4.0 3.6 - - + +
111D ILE* 1.3 75.9 - - + +
113D ASP* 1.3 55.3 + - - +
114D ASN 2.9 11.4 + - - -
115D PHE* 3.7 17.7 - + - -
116D LEU* 2.9 49.4 + - + -
117D VAL* 3.4 7.0 + - + -
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Residues in contact with ASP 113 (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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109D TYR* 2.7 49.6 + - + +
110D GLU* 3.8 13.0 - - + +
111D ILE 3.3 1.0 - - - -
112D PHE* 1.3 72.5 - - - +
114D ASN* 1.3 60.2 + - - +
117D VAL* 3.8 21.8 - - - +
118D PRO* 3.4 16.4 - - - +
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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