Contacts of the strand formed by residues 43 - 52 (chain D) in PDB entry 6EKK
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 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B VAL* 3.9 30.5 - - + -
228B ILE* 4.4 0.9 - - + -
238B TYR* 3.6 21.6 - - + -
241B ALA* 4.7 1.3 - - + -
243B MET* 4.4 3.6 - - + -
37D TYR* 3.1 26.0 - - - +
38D ILE* 3.8 5.4 - - - +
41D ILE* 3.6 23.1 - - + +
42D GLY* 1.3 80.3 - - - +
44D ASP* 1.3 64.0 + - - +
62D TRP* 3.9 26.0 - - + -
63D ASP 3.3 15.0 - - - +
64D THR* 4.1 8.7 - - + -
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Residues in contact with ASP 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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238B TYR* 3.4 14.4 + - - -
22D SER* 6.1 0.5 - - - -
25D LEU* 4.9 6.8 - - - +
35D GLY 3.9 0.9 - - - +
36D SER* 3.3 17.7 + - - +
37D TYR* 2.9 24.7 + - - +
38D ILE* 4.1 10.3 - - + +
43D VAL* 1.3 76.0 - - - +
45D PHE* 1.3 65.0 + - - +
46D LYS* 2.6 38.8 + - - +
61D ILE 3.8 0.3 - - - +
62D TRP* 3.4 5.2 - - - -
63D ASP* 2.9 37.4 + - + +
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Residues in contact with PHE 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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237B ASP* 3.9 32.5 - - + -
238B TYR* 3.1 48.0 + + - -
25D LEU* 5.6 0.2 - - - -
31D ASN* 4.2 10.6 + - - -
44D ASP* 1.3 75.9 - - - +
46D LYS* 1.3 80.8 + - - +
47D ILE* 3.6 37.7 - - + -
60D GLN* 5.1 1.8 - - + -
61D ILE 3.1 7.9 - - - +
62D TRP* 3.5 47.6 - + + +
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Residues in contact with LYS 46 (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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25D LEU* 4.2 17.3 - - + -
26D LEU* 4.9 7.9 - - + -
29D ALA* 3.7 21.3 - - + -
31D ASN* 3.3 23.6 - - + +
33D PHE 4.4 4.9 - - - -
34D SER* 3.8 18.6 - - - +
35D GLY 3.0 24.2 + - - -
36D SER* 4.1 1.8 - - - +
37D TYR* 5.8 0.4 - - - -
44D ASP* 2.6 43.2 + - - +
45D PHE* 1.3 79.0 + - - +
47D ILE* 1.3 65.0 + - - +
60D GLN* 3.5 3.6 - - - -
61D ILE* 2.8 47.4 + - + +
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Residues in contact with ILE 47 (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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29D ALA* 3.4 3.8 - - - -
30D ASP* 2.7 37.1 + - + +
31D ASN* 2.9 15.1 + - - +
45D PHE* 3.6 26.0 - - + -
46D LYS* 1.3 79.3 - - - +
48D ARG* 1.3 60.3 + - - +
49D THR* 4.3 7.6 - - + +
58D LYS* 3.9 21.1 - - + -
59D LEU 3.2 7.6 - - - +
60D GLN* 3.4 38.1 - - + +
61D ILE* 5.8 0.7 - - - -
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Residues in contact with ARG 48 (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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27D ARG 4.9 2.4 + - - -
28D PHE* 3.1 77.7 + - + +
30D ASP* 3.1 28.5 + - - -
47D ILE* 1.3 73.6 - - - +
49D THR* 1.3 76.0 + - - +
50D VAL* 3.7 30.2 - - + +
57D VAL 3.6 1.6 - - - +
58D LYS* 3.5 1.4 - - - -
59D LEU* 2.8 36.4 + - + +
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Residues in contact with THR 49 (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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30D ASP* 2.6 31.1 + - - +
47D ILE* 4.3 7.4 - - + -
48D ARG* 1.3 82.0 + - - +
50D VAL* 1.3 63.6 + - - +
57D VAL 3.3 5.6 - - - -
58D LYS* 3.8 25.4 - - + -
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Residues in contact with VAL 50 (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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28D PHE* 5.2 3.6 - - + -
48D ARG* 3.7 32.1 - - + +
49D THR* 1.3 76.5 - - - +
51D GLU* 1.3 76.9 - - - +
52D ILE* 3.5 26.9 + - + -
56D LYS* 4.7 0.7 - - - -
57D VAL* 2.9 33.5 + - + +
59D LEU* 4.0 22.7 - - + -
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Residues in contact with GLU 51 (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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6D ASP* 4.9 1.0 - - - +
50D VAL* 1.3 79.2 - - - +
52D ILE* 1.3 63.9 + - - +
54D GLY* 3.1 29.1 - - - +
55D GLU 3.2 20.1 - - - +
56D LYS* 3.4 18.9 + - - +
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Residues in contact with ILE 52 (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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50D VAL* 3.8 28.7 - - + +
51D GLU* 1.3 80.1 - - - +
53D ASN* 1.3 88.3 + - + +
54D GLY 3.1 0.9 - - - -
55D GLU* 2.7 28.2 + - - +
57D VAL* 4.2 12.5 - - + +
165D THR* 3.4 32.8 - - + -
169D LEU* 4.1 18.7 - - + +
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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