Contacts of the strand formed by residues 2 - 12 (chain B) in PDB entry 1IXR
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 ILE 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.3 8.5 - - + -
25A GLY 3.8 2.5 - - - -
26A PHE* 3.6 28.7 - - + -
1B MET* 1.3 91.7 + - + +
3B ARG* 1.3 56.8 + - - +
4B TYR 3.8 4.9 - - - +
5B LEU* 3.7 35.7 - - + -
26B PHE* 5.7 8.7 - - + -
48B THR* 2.6 28.9 + - - +
49B HIS* 4.0 0.5 - - - -
50B LEU* 3.7 34.2 + - + +
59B LEU* 4.9 11.4 - - + -
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Residues in contact with ARG 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 5.2 9.2 + - - -
18A VAL* 3.6 23.8 - - + -
25A GLY 2.9 12.0 + - - +
27A PHE* 3.7 45.2 - - + +
1B MET 3.3 0.4 + - - -
2B ILE* 1.3 75.2 - - - +
4B TYR* 1.3 60.2 + - + +
47B HIS* 3.2 6.3 - - + -
48B THR* 2.4 38.6 + - - +
65B GLU* 3.1 34.0 + - - +
68B LEU* 3.1 31.7 - - + +
69B ALA* 5.8 0.4 - - - +
72B GLU* 3.3 21.9 + - - -
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Residues in contact with TYR 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.6 20.4 - - + -
18A VAL* 4.9 6.5 - - + -
20A LEU* 4.0 26.9 - - + -
23A GLY 5.3 2.0 - - - -
25A GLY* 2.8 31.0 + - - -
2B ILE* 3.8 2.4 - - - +
3B ARG* 1.3 84.1 - - + +
5B LEU* 1.3 81.7 + - - +
6B ARG* 3.2 38.5 + - + +
45B GLY* 4.0 17.8 - - - -
46B VAL 3.3 16.8 - - - -
47B HIS* 4.3 22.9 - + + -
48B THR* 3.9 0.2 - - - -
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY 3.8 5.6 - - - +
24A VAL* 3.4 37.5 - - + -
2B ILE* 3.7 18.8 - - + -
4B TYR* 1.3 96.3 - - - +
6B ARG* 1.3 62.2 + - - +
19B LEU* 4.7 10.0 - - + +
21B ALA* 4.7 7.6 - - + -
26B PHE* 3.9 38.1 - - + -
28B LEU* 5.3 5.4 - - + -
44B VAL 3.5 1.0 - - - +
45B GLY* 3.3 4.9 - - - -
46B VAL* 2.9 32.8 + - + +
48B THR* 3.8 14.6 - - + -
59B LEU* 4.7 9.2 - - + -
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY* 3.5 17.9 + - - +
4B TYR* 3.2 27.5 + - + +
5B LEU* 1.3 72.5 - - - +
7B GLY* 1.3 57.3 + - - +
19B LEU* 3.5 4.3 - - - -
21B ALA* 2.9 21.0 - - - +
22B GLY 4.5 0.9 + - - -
43B GLU* 3.1 41.2 + - - +
44B VAL* 2.9 37.4 + - - +
45B GLY* 3.3 8.8 - - - +
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Residues in contact with GLY 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 1.3 76.0 - - - +
8B LEU* 1.3 64.8 + - - -
19B LEU* 3.0 21.5 - - - +
20B LEU 3.2 12.1 - - - -
21B ALA* 3.8 0.2 - - - -
43B GLU* 3.6 11.7 - - - +
44B VAL* 3.2 27.0 + - - +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLY* 1.3 72.4 - - - -
9B VAL* 1.3 60.5 + - - +
10B LEU* 3.0 23.8 + - + +
18B VAL 3.2 3.1 - - - +
19B LEU* 3.3 5.0 - - - -
20B LEU* 3.1 38.7 + - + +
41B GLY* 3.6 28.7 - - - +
42B LYS 3.9 2.0 - - - -
43B GLU* 4.1 23.1 - - + +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 1.3 73.4 - - - +
10B LEU* 1.3 49.2 + - - +
11B LYS* 2.3 25.3 + - - -
12B LYS* 4.1 16.6 - - + -
17B PHE* 3.9 17.3 - - + -
18B VAL 3.2 7.4 - - - -
38B LEU* 3.9 28.3 - - + -
39B GLU 3.6 13.0 - - - +
40B GLU* 3.7 23.1 - - - +
41B GLY 4.2 2.4 - - - +
42B LYS* 3.0 22.8 + - + +
44B VAL* 4.1 19.1 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.0 20.5 + - + +
9B VAL* 1.3 70.4 - - - +
11B LYS* 1.3 79.1 + - + +
18B VAL* 3.1 27.4 - - + +
20B LEU* 3.2 41.7 - - + -
25B GLY* 5.8 4.9 - - - -
40B GLU* 4.3 6.3 - - - +
41B GLY 4.6 3.2 - - - +
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Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL 2.3 18.1 + - - -
10B LEU* 1.3 93.2 - - + +
12B LYS* 1.3 68.0 + - - +
13B GLU* 5.8 2.2 - - - +
17B PHE* 3.4 2.0 - - - -
18B VAL* 2.8 39.3 + - + +
40B GLU* 2.5 36.0 + - - +
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.1 14.1 - - + -
11B LYS* 1.3 83.5 - - - +
13B GLU* 1.3 81.4 + - - +
16B GLY 3.5 5.4 - - - +
17B PHE* 4.0 4.9 - - + -
35B LEU* 2.9 39.2 + - - -
36B GLN* 3.4 17.2 + - - +
38B LEU* 2.8 28.2 + - + +
39B GLU* 4.4 0.4 - - - -
40B GLU* 3.4 32.0 + - + +
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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