Contacts of the strand formed by residues 35 - 41 (chain D) in PDB entry 1K9A
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 35 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU* 4.3 30.1 - - + +
14D CYS 3.8 3.8 - - - +
15D ILE* 3.8 19.5 - - + -
33D GLY 4.5 4.3 - - - +
34D ASP* 1.3 75.4 - - - +
36D LEU* 1.3 73.5 + - - +
37D THR* 4.3 5.0 + - - +
51D LYS 4.2 0.2 - - - +
52D ASN* 4.0 15.9 - - - +
53D LYS* 4.2 10.9 + - + +
68D ARG* 4.4 13.0 - - - +
143E GLU* 6.0 2.5 - - - +
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Residues in contact with LEU 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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12D THR 3.7 0.3 - - - +
13D GLU* 3.5 4.7 - - - -
14D CYS* 2.9 37.8 + - + +
16D ALA* 3.9 12.1 - - + +
28D LEU* 3.9 25.4 - - + -
30D PHE* 3.6 48.9 - - + -
34D ASP* 4.1 6.1 - - + +
35D VAL* 1.3 79.4 - - - +
37D THR* 1.3 62.4 + - - +
38D ILE* 3.9 1.0 + - + +
50D ALA* 4.6 2.2 - - + -
51D LYS 3.6 6.5 - - - +
52D ASN* 4.8 4.3 - - + -
60D ILE* 4.1 21.1 - - + -
65D VAL* 3.7 23.6 - - + -
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Residues in contact with THR 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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11D GLY* 3.9 25.4 - - - +
12D THR 3.5 2.7 - - - -
13D GLU* 4.8 8.5 + - + +
35D VAL* 4.8 8.3 + - - +
36D LEU* 1.3 73.3 - - - +
38D ILE* 1.3 66.2 + - - +
39D VAL* 3.6 2.1 + - + +
50D ALA* 3.0 7.2 - - - +
51D LYS* 2.8 49.0 + - + +
52D ASN 5.4 2.4 + - - -
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Residues in contact with ILE 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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8D TRP* 3.8 30.7 - - + +
9D PRO 3.9 17.9 - - - +
10D SER* 3.6 0.6 + - - -
11D GLY* 2.7 30.0 + - - -
12D THR* 2.8 28.3 + - - +
14D CYS* 3.9 20.6 - - + -
36D LEU 4.9 1.3 - - - +
37D THR* 1.3 73.5 - - - +
39D VAL* 1.3 65.2 + - - +
40D ALA* 3.7 9.6 - - - +
48D TYR* 3.7 36.1 - - + -
49D LYS 4.1 1.3 - - - +
50D ALA* 4.4 1.8 - - + -
60D ILE* 4.2 17.7 - - + -
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Residues in contact with VAL 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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10D SER* 2.8 28.2 + - - +
37D THR* 4.2 2.0 - - + +
38D ILE* 1.3 77.0 - - - +
40D ALA* 1.3 66.9 + - + +
49D LYS* 2.8 41.8 + - + +
50D ALA* 3.7 19.5 - - - -
51D LYS* 4.0 15.9 - - + -
57D GLU* 3.6 20.0 - - - +
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Residues in contact with ALA 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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8D TRP 5.4 1.1 - - - -
10D SER* 5.1 2.9 - - - +
38D ILE* 3.7 6.1 - - - +
39D VAL* 1.3 91.4 - - + +
41D VAL* 1.3 65.6 + - + +
48D TYR* 3.9 5.2 - - - -
49D LYS* 2.7 43.6 + - - +
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Residues in contact with VAL 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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7D SER* 4.3 20.2 - - - +
8D TRP 4.9 2.7 + - - +
38D ILE* 4.9 0.2 - - - +
40D ALA* 1.3 83.3 - - + +
42D THR* 1.3 82.0 + - - +
44D ASP 4.0 5.6 - - - +
45D PRO* 4.1 11.9 - - + -
47D TRP 3.5 11.4 - - - +
48D TYR* 3.4 37.7 - - + +
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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