Contacts of the strand formed by residues 50 - 57 (chain C) in PDB entry 4WLU
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 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 3.8 6.5 - - + +
27C VAL* 4.2 21.3 - - + -
44C LEU* 3.6 35.4 - - + +
47C SER* 3.5 17.6 + - - +
48C PRO 3.2 1.2 - - - -
49C LEU* 1.3 84.1 - - + +
51C SER* 1.3 60.9 + - - +
52C ARG 3.5 27.1 - - - +
53C LEU* 4.4 10.8 - - + -
74C LYS* 3.6 11.4 - - - +
75C ALA* 3.3 24.2 + - + +
259C VAL* 5.8 0.9 - - + -
260C PHE* 4.9 3.1 - - + -
263C VAL* 5.8 1.8 - - + -
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Residues in contact with SER 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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24C ASN* 2.8 41.8 + - - -
25C ALA 3.1 5.6 + - - -
49C LEU 4.1 1.0 + - - -
50C VAL* 1.3 73.1 - - - +
52C ARG* 1.3 62.8 + - - +
74C LYS* 4.0 16.9 - - - +
75C ALA* 3.4 8.0 - - - +
76C ALA* 2.9 22.5 + - - +
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Residues in contact with ARG 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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25C ALA 3.4 3.0 + - - +
26C LYS* 3.5 43.4 - - + +
27C VAL 2.9 27.0 + - - -
50C VAL* 3.5 7.2 - - - +
51C SER* 1.3 83.4 - - - +
53C LEU* 1.3 63.2 + - - +
54C THR* 3.9 9.1 - - - +
76C ALA* 3.6 28.6 + - + +
77C VAL 4.5 1.2 + - - -
78C LYS* 3.8 26.8 - - - +
80C TYR* 4.1 15.6 + - - -
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Residues in contact with LEU 53 (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 VAL* 3.5 19.1 - - + +
29C VAL* 4.2 2.2 - - + -
41C SER* 3.6 25.1 - - - +
44C LEU* 3.8 31.9 - - + -
45C LYS* 3.9 20.4 - - + +
50C VAL* 4.4 8.5 - - + -
52C ARG* 1.3 73.5 - - - +
54C THR* 1.3 61.2 + - - +
55C LEU* 3.7 25.4 - - + -
68C LEU* 4.8 1.8 - - + -
75C ALA* 4.7 3.6 - - + -
76C ALA 2.7 14.0 + - - +
77C VAL* 3.2 19.2 - - + +
78C LYS 2.9 25.5 + - - +
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Residues in contact with THR 54 (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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26C LYS* 3.9 13.1 - - - +
27C VAL 3.1 6.6 + - - +
28C ALA* 3.3 17.5 + - - +
29C VAL 3.0 25.6 + - - +
52C ARG* 3.9 25.5 - - - +
53C LEU* 1.3 76.4 - - - +
55C LEU* 1.3 64.2 + - - +
78C LYS* 3.4 3.4 - - + +
80C TYR* 3.8 21.1 - - + +
89C CYS* 3.1 34.9 + - - +
93C CYS* 4.1 2.4 - - - -
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Residues in contact with LEU 55 (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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29C VAL* 3.8 5.8 - - + -
32C ALA* 3.7 13.0 - - + -
41C SER* 3.3 24.7 - - - +
53C LEU* 3.7 26.0 - - + -
54C THR* 1.3 76.9 - - - +
56C TYR* 1.3 57.5 + - - +
61C THR* 3.6 8.7 - - + +
64C VAL* 4.0 12.3 - - + -
65C ALA* 4.0 15.0 - - + +
68C LEU* 3.7 26.5 - - + -
77C VAL* 3.8 18.4 - - + -
78C LYS 2.8 14.6 + - - +
79C GLY* 4.3 1.8 - - - -
80C TYR* 2.7 36.4 + - - +
89C CYS* 4.2 1.1 - - - -
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Residues in contact with TYR 56 (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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29C VAL 3.0 7.7 + - - -
30C LEU* 3.6 26.7 - - + -
31C GLY 2.7 30.1 + - - -
32C ALA* 3.0 7.2 + - - +
54C THR 4.2 0.2 - - - -
55C LEU* 1.3 75.4 - - - +
57C ASP* 1.3 64.3 + - - +
58C ILE* 4.6 4.2 - - - +
61C THR* 3.7 2.0 - - - -
80C TYR* 3.6 17.7 - - + -
81C LEU 4.4 0.4 - - - -
82C GLY* 3.1 29.9 - - - -
83C PRO* 3.0 30.8 - - - +
86C LEU* 3.7 38.1 - - + +
89C CYS* 3.7 9.6 - - + -
124C LEU* 3.8 12.9 - - + +
402C NAD 3.6 26.0 + + - -
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Residues in contact with ASP 57 (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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31C GLY* 3.2 10.7 - - - -
33C SER* 2.9 38.4 + - - +
56C TYR* 1.3 78.9 - - - +
58C ILE* 1.3 76.0 + - - +
59C ALA* 3.4 11.9 + - - +
61C THR* 3.5 6.5 - - + +
80C TYR 3.3 5.5 + - - -
81C LEU* 3.5 5.9 - - - -
82C GLY 3.2 21.0 + - - -
402C NAD 2.7 59.2 + - - -
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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