Contacts of the strand formed by residues 43 - 52 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A VAL* 3.9 25.4 - - + -
228A ILE* 4.5 0.4 - - + -
238A TYR* 3.6 22.5 - - + -
241A ALA* 4.9 2.0 - - + -
243A MET* 4.2 8.5 - - - -
37C TYR* 3.2 26.8 + - - +
38C ILE* 4.0 4.5 - - - +
41C ILE* 3.7 21.9 - - + +
42C GLY* 1.3 80.5 - - - +
44C ASP* 1.3 64.4 + - - +
62C TRP* 3.8 26.9 - - + -
63C ASP 3.3 15.5 - - - +
64C THR* 4.0 7.9 - - + -
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TYR* 3.4 15.0 + - - -
25C LEU* 4.4 8.1 - - + +
36C SER* 3.3 19.8 + - - +
37C TYR* 2.8 26.8 + - - +
38C ILE* 3.8 12.1 - - + +
43C VAL* 1.3 76.5 - - - +
45C PHE* 1.3 60.6 + - - +
46C LYS* 2.6 39.4 + - - +
61C ILE 3.8 0.3 - - - +
62C TRP* 3.4 3.5 - - - +
63C ASP* 2.9 36.6 + - + +
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Residues in contact with PHE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ASP* 3.8 20.2 - - + -
238A TYR* 3.1 46.9 + + - -
402A SO4 3.2 34.8 - - - -
25C LEU* 5.1 0.7 - - - -
31C ASN* 4.4 11.2 + - - -
44C ASP* 1.3 75.2 - - - +
46C LYS* 1.3 80.5 + - - +
47C ILE* 3.7 31.6 - - + -
60C GLN* 5.3 0.4 - - + -
61C ILE 3.1 11.4 - - - +
62C TRP* 3.5 38.8 - + + +
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 4.0 19.0 - - + +
26C LEU* 5.0 5.8 - - - -
28C PHE* 4.1 6.1 - - + -
29C ALA* 3.7 22.4 - - + -
31C ASN* 3.4 21.5 - - + +
33C PHE 4.3 6.3 - - - -
34C SER* 3.7 19.7 - - - +
35C GLY 3.1 25.6 + - - -
36C SER* 4.2 1.4 - - - +
37C TYR* 5.7 0.2 - - - -
44C ASP* 2.6 37.4 + - - +
45C PHE* 1.3 81.5 + - - +
47C ILE* 1.3 68.9 + - - +
59C LEU 3.8 0.3 - - - +
60C GLN* 3.6 0.2 - - - -
61C ILE* 2.9 43.1 + - + +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A SO4 3.8 9.2 - - - +
28C PHE* 3.9 2.2 - - - -
29C ALA 3.5 1.7 - - - -
30C ASP* 2.6 39.6 + - + +
31C ASN* 2.7 20.1 + - - +
45C PHE* 3.7 24.2 - - + -
46C LYS* 1.3 85.2 - - - +
48C ARG* 1.3 61.8 + - - +
49C THR* 4.6 3.6 - - - +
58C LYS* 3.8 31.4 - - + +
59C LEU 3.3 5.6 - - - +
60C GLN* 3.5 30.7 - - + -
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Residues in contact with ARG 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ARG 3.4 24.4 + - - -
28C PHE* 2.9 60.9 + - + +
30C ASP* 3.4 10.3 - - - +
47C ILE* 1.3 74.4 - - - +
49C THR* 1.3 74.9 + - - +
50C VAL* 4.7 14.1 - - + +
58C LYS* 3.5 2.3 - - - +
59C LEU* 2.8 45.7 + - + +
158C GLU* 2.9 33.2 + - - -
161C PHE* 3.9 23.3 - - - +
162C ASN* 4.3 9.7 + - - -
165C THR* 5.6 3.2 + - - -
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Residues in contact with THR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP* 4.8 16.9 + - - +
5C TYR* 5.1 1.6 - - + -
30C ASP* 2.7 21.9 + - - +
47C ILE* 4.6 4.2 - - - +
48C ARG* 1.3 79.5 + - - +
50C VAL* 1.3 69.3 + - - +
56C LYS* 5.1 8.5 - - + -
57C VAL 3.3 17.3 - - - +
58C LYS* 3.8 19.2 - - + +
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ARG* 4.7 15.7 - - - +
49C THR* 1.3 78.3 - - - +
51C GLU* 1.3 63.4 + - - +
52C ILE* 3.8 31.6 + - + -
55C GLU 3.5 1.0 - - - +
56C LYS* 4.7 0.7 - - - -
57C VAL* 2.7 45.4 + - + +
59C LEU* 4.2 14.6 - - + -
162C ASN* 5.5 7.0 - - - +
165C THR* 4.4 2.9 - - + -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 1.3 78.8 - - - +
52C ILE* 1.3 63.4 + - - +
53C ASN 4.1 1.9 + - - -
54C GLY* 4.7 6.3 - - - +
55C GLU 3.3 13.9 - - - +
56C LYS* 4.4 4.9 - - + +
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Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.8 23.1 - - + +
51C GLU* 1.3 76.8 - - - +
53C ASN* 1.3 87.7 + - - +
54C GLY 3.1 0.2 - - - -
55C GLU* 2.9 29.7 + - - +
57C VAL* 4.6 7.6 - - + -
162C ASN* 5.8 5.2 - - - +
165C THR* 3.6 32.1 - - + -
166C GLU* 4.7 24.7 - - + +
169C LEU* 4.6 19.7 - - + +
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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