Contacts of the strand formed by residues 35 - 45 (chain D) in PDB entry 1XS2
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 HIS 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ARG* 3.6 45.2 + - + +
20D LEU 3.5 7.2 - - - +
21D PRO* 3.8 27.6 - - + +
22D LEU* 3.5 12.8 - - - +
34D THR* 1.3 121.0 + - + +
36D LYS* 1.3 62.3 + - - +
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Residues in contact with LYS 36 (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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18D ALA 3.7 0.3 - - - +
19D ARG* 3.5 2.2 - - - -
20D LEU* 2.9 32.6 + - - +
22D LEU* 4.5 3.8 - - + -
35D HIS* 1.3 79.0 - - - +
37D VAL* 1.3 88.2 + - - +
38D VAL* 3.7 16.3 + - + +
53D GLU* 4.3 8.8 + - - -
54D GLY 5.2 6.7 + - - -
55D THR* 5.4 7.6 + - - +
56D MET 5.6 3.8 - - - -
298D MET* 3.0 28.9 + - - +
299D LEU* 3.1 35.5 + - + +
300D GLU* 4.6 0.8 - - - +
330D TRP* 3.9 22.9 - - + -
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Residues in contact with VAL 37 (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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17D VAL* 3.4 31.9 - - + -
18D ALA 3.2 5.6 - - - +
19D ARG* 3.4 39.3 - - - +
36D LYS* 1.3 92.9 - - - +
38D VAL* 1.3 60.2 + - - +
39D PRO* 3.6 6.4 - - + +
56D MET 5.1 1.9 - - - +
58D ALA* 5.6 8.3 - - + +
67D ILE* 3.8 31.0 - - + +
368D GLU* 4.3 6.1 - - - +
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Residues in contact with VAL 38 (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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16D VAL 3.7 1.2 - - - +
17D VAL* 3.6 2.6 - - - -
18D ALA* 2.7 41.7 + - + +
20D LEU* 4.4 23.3 - - + -
36D LYS* 3.8 24.0 - - + +
37D VAL* 1.3 79.2 - - - +
39D PRO* 1.3 60.9 - - - +
40D LEU* 3.6 18.9 + - + +
53D GLU* 3.6 35.4 - - + +
301D SER* 4.1 9.9 - - - +
334D LEU* 4.2 5.8 - - + -
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Residues in contact with PRO 39 (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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15D ILE* 5.8 0.4 - - + -
16D VAL 3.9 3.4 - - - +
17D VAL* 4.3 14.3 - - + -
36D LYS* 5.7 0.2 - - - -
37D VAL* 3.6 9.2 - - + +
38D VAL* 1.3 86.3 - - - +
40D LEU* 1.3 59.7 + - - +
53D GLU* 3.4 4.5 - - - +
54D GLY* 2.7 46.4 + - - +
56D MET* 4.1 19.3 - - - +
67D ILE* 4.1 25.8 - - + -
71D LEU* 4.5 15.3 - - + -
109D MET* 4.2 13.0 - - + -
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Residues in contact with LEU 40 (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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15D ILE* 3.5 9.2 - - - +
16D VAL* 2.9 44.9 + - + +
38D VAL* 3.8 25.1 - - + +
39D PRO* 1.3 75.9 - - - +
41D LEU* 1.3 61.9 + - - +
42D ILE* 4.2 3.4 - - + -
51D VAL* 4.5 6.7 - - + -
52D ALA 3.2 11.7 - - - +
53D GLU* 4.1 9.9 - - + -
109D MET* 4.2 3.8 - - - +
301D SER* 4.7 1.6 - - - +
303D ILE* 4.4 17.9 - - + -
334D LEU* 4.3 5.8 - - + -
358D LEU* 4.1 24.0 - - + -
363D LEU* 4.0 32.5 - - + -
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Residues in contact with LEU 41 (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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13D ALA* 4.3 11.0 - - + -
14D GLU 3.4 13.7 - - - +
15D ILE* 4.1 17.0 - - + -
40D LEU* 1.3 74.7 - - - +
42D ILE* 1.3 61.6 - - - +
43D LEU* 4.3 16.2 - - + -
50D GLY 3.7 0.9 - - - +
51D VAL* 3.3 4.9 - - - +
52D ALA 2.8 35.1 + - - +
74D LEU* 4.5 5.4 - - + -
79D LEU* 4.1 18.4 - - + -
109D MET* 3.4 44.8 - - + +
110D VAL* 3.5 26.7 - - + +
113D ALA* 4.1 3.2 - - + +
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Residues in contact with ILE 42 (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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12D ALA 4.0 0.2 - - - +
13D ALA* 3.2 7.6 - - - +
14D GLU* 2.9 48.6 + - + +
16D VAL* 4.4 13.2 - - + -
40D LEU* 4.9 4.5 - - + -
41D LEU* 1.3 77.5 - - - +
43D LEU* 1.3 61.6 + - - +
44D HIS* 3.7 27.5 + - + +
49D GLN* 4.0 20.0 - - + +
50D GLY 3.2 7.6 - - - +
51D VAL* 4.1 15.0 - - + -
358D LEU* 4.0 15.7 - - + -
360D ARG* 3.6 28.5 - - - +
363D LEU* 5.5 0.7 - - + -
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Residues in contact with LEU 43 (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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10D ILE* 4.1 31.9 - - + -
12D ALA 3.7 0.9 - - - -
13D ALA* 3.7 24.5 - - + -
41D LEU* 4.1 15.5 - - + -
42D ILE* 1.3 74.0 - - - +
44D HIS* 1.3 61.2 + - - +
49D GLN* 3.1 7.6 - - - +
50D GLY 2.7 38.8 + - - +
79D LEU* 4.5 0.9 - - + -
82D ILE* 4.3 14.6 - - + -
110D VAL* 3.9 8.7 - - + +
113D ALA* 3.7 26.0 - - + +
114D ALA* 3.7 18.2 - - + +
117D LEU* 4.1 14.2 - - + +
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Residues in contact with HIS 44 (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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10D ILE* 3.6 5.4 - - - -
11D GLU* 2.9 26.5 + - + -
12D ALA* 3.0 38.6 + - + +
14D GLU* 2.7 33.6 + - + -
42D ILE* 3.7 11.5 - - + +
43D LEU* 1.3 75.2 - - - +
45D GLY* 1.3 58.8 + - - +
48D VAL 3.6 5.4 + - - +
49D GLN* 3.0 36.0 + - - +
117D LEU* 4.5 3.4 - - - -
360D ARG* 4.6 0.7 - - - -
372D GLU* 4.8 3.8 + - - -
374D ARG* 6.1 0.9 - - - -
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Residues in contact with GLY 45 (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 LYS 3.2 18.6 - - - -
11D GLU* 3.9 6.1 - - - -
44D HIS* 1.3 74.7 - - - +
46D GLU* 1.3 74.4 + - - +
47D GLY 3.1 2.7 - - - +
48D VAL* 3.0 26.4 + - - +
117D LEU* 3.5 11.8 - - - +
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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