Contacts of the strand formed by residues 19 - 26 (chain D) in PDB entry 4K2S
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 PHE 19 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE 3.8 1.1 - - - +
12D VAL* 3.5 4.3 - - - +
13D THR* 2.8 41.7 + - + +
15D PRO* 4.0 24.5 - - + -
17D ARG* 3.5 49.1 - - + -
18D ASN* 1.3 75.5 - - - +
20D VAL* 1.3 67.7 + - - +
21D THR* 4.9 5.8 - - - +
35D ASP* 5.1 4.3 - - - +
37D THR* 3.3 19.3 - - + +
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR* 4.2 22.2 - - + -
11D ILE 3.4 7.9 - - - +
12D VAL* 4.0 22.4 - - + -
18D ASN* 5.9 0.2 - - + -
19D PHE* 1.3 77.5 - - - +
21D THR* 1.3 64.7 + - - +
35D ASP* 3.2 8.1 - - - +
36D ALA* 2.8 50.3 + - + +
37D THR* 2.9 8.0 + - - -
42D GLU* 4.0 36.6 - - + +
43D MET* 5.5 0.2 - - - -
46D ALA* 4.5 11.0 - - + +
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Residues in contact with THR 21 (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 TYR 3.8 0.3 - - - +
10D THR* 3.2 5.6 - - - -
11D ILE* 2.8 51.9 + - + +
13D THR* 5.7 3.3 - - - +
19D PHE* 4.9 7.4 - - - +
20D VAL* 1.3 81.7 + - - +
22D LEU* 1.3 63.4 + - - +
23D LYS 4.0 0.3 + - - -
33D ILE* 3.9 34.5 - - + -
34D GLY 3.5 13.5 - - - +
35D ASP* 4.8 2.8 + - - +
36D ALA* 4.9 0.4 - - - -
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Residues in contact with LEU 22 (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 ALA* 4.3 2.2 - - + -
9D TYR 3.5 30.7 - - - +
10D THR* 4.3 8.1 - - + +
21D THR* 1.3 74.3 - - - +
23D LYS* 1.3 64.1 + - - +
24D ILE* 4.0 26.3 - - + +
33D ILE* 3.1 6.6 - - - +
34D GLY* 2.8 41.8 + - - +
36D ALA* 4.7 3.0 - - + +
49D LEU* 4.3 29.6 - - + -
54D VAL* 4.1 17.7 - - + -
57D LEU* 4.8 7.9 - - + -
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Residues in contact with LYS 23 (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 ALA* 3.1 6.6 - - - +
9D TYR* 2.9 74.6 + - + +
11D ILE* 4.3 14.6 - - + -
21D THR 4.0 0.8 + - - -
22D LEU* 1.3 73.0 - - - +
24D ILE* 1.3 63.4 + - - +
25D VAL* 3.8 21.4 + - + +
31D HIS* 4.3 21.9 - - + -
32D GLY 3.5 9.2 - - - +
33D ILE* 4.0 14.6 - - + -
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Residues in contact with ILE 24 (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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5D ILE* 3.8 38.6 - - + -
7D ASP 3.7 2.0 - - - -
8D ALA* 3.9 11.4 - - + -
22D LEU* 4.0 23.1 - - + -
23D LYS* 1.3 78.3 - - - +
25D VAL* 1.3 65.9 + - - +
26D THR* 4.3 2.9 + - + +
30D THR 4.0 0.2 - - - +
31D HIS* 3.1 6.4 - - - +
32D GLY* 2.9 36.7 + - - +
57D LEU* 4.3 15.5 - - + -
62D ALA* 5.5 5.4 - - + -
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Residues in contact with VAL 25 (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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5D ILE* 3.7 2.1 - - - -
6D ARG* 2.7 48.7 + - - +
7D ASP* 2.8 29.9 + - + +
9D TYR* 4.8 8.5 - - + -
23D LYS* 3.8 33.2 - - + +
24D ILE* 1.3 80.9 - - - +
26D THR* 1.3 66.2 + - - +
29D GLY* 4.0 9.9 - - - +
30D THR 3.4 9.4 - - - +
31D HIS* 4.2 3.6 - - + -
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Residues in contact with THR 26 (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 LEU* 4.0 13.5 - - + +
4D LYS 3.3 11.7 - - - -
5D ILE* 4.2 1.3 - - - +
6D ARG* 3.6 7.6 - - - +
24D ILE* 5.4 4.0 - - + +
25D VAL* 1.3 83.2 - - - +
27D GLU* 1.3 59.8 + - - +
28D SER* 3.0 16.4 + - - -
29D GLY* 3.0 15.8 + - - -
30D THR* 2.5 44.7 + - - +
31D HIS* 5.5 0.4 - - - -
62D ALA* 4.2 25.4 - - + -
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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