Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 4WK0
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 ALA 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY* 3.7 0.5 - - - -
39A ALA 2.7 39.4 + - - -
42A ALA* 3.9 16.8 - - + -
43A ASN 5.2 1.3 - - - +
44A THR* 4.4 9.0 - - + -
53A GLY* 1.3 75.5 - - - +
55A VAL* 1.3 66.2 + - - +
56A TYR* 4.0 17.5 - - + +
69A PRO* 4.7 9.9 - - + -
70A ILE 5.7 2.0 - - - +
101A PHE* 3.2 11.1 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.5 2.7 - - + -
37A VAL 3.4 9.0 - - - +
54A ALA* 1.3 79.8 - - - +
56A TYR* 1.3 71.2 + - - +
69A PRO* 3.4 2.1 - - - +
70A ILE* 2.8 46.9 + - + +
72A PHE* 3.8 13.7 - - + -
101A PHE* 3.9 9.1 - - + -
102A GLY* 3.8 8.1 - - - -
105A VAL* 3.5 43.1 - - + -
112A ILE* 5.3 0.2 - - + -
114A ALA* 3.7 20.6 - - + -
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY* 5.9 0.2 - - - -
14A PRO* 3.3 31.1 - - + +
19A PHE* 3.8 27.4 - + + -
35A VAL 3.7 0.7 - - - +
36A LEU* 3.3 9.7 - - - +
37A VAL* 2.7 43.0 + - + +
39A ALA* 3.7 23.6 - - + -
42A ALA* 4.2 7.5 - - + +
43A ASN 5.1 3.1 + - - -
54A ALA* 4.0 13.5 - - + +
55A VAL* 1.3 78.7 - - - +
57A LEU* 1.3 59.7 + - - +
58A CYS* 4.0 3.3 - - - -
67A CYS* 4.2 17.9 - - + -
68A THR 3.4 9.2 - - - -
69A PRO* 3.6 36.6 - - + +
70A ILE* 4.5 0.4 - - - -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.9 13.0 - - + -
34A SER* 3.5 29.8 - - - +
35A VAL 3.8 0.4 - - - -
36A LEU* 3.4 22.4 - - + -
55A VAL 4.1 0.6 + - - -
56A TYR* 1.3 73.6 - - - +
58A CYS* 1.3 59.8 + - - +
59A PRO* 3.5 16.1 - - + +
67A CYS* 3.4 0.9 - - - -
68A THR* 2.7 44.5 + - - +
70A ILE* 3.8 15.9 - - + +
142A PHE* 4.2 23.1 - - + -
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Residues in contact with CYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.1 18.2 - - + -
34A SER* 3.8 2.5 - - - -
35A VAL* 2.8 48.0 + - + +
37A VAL* 4.2 13.2 - - - -
56A TYR* 4.2 6.3 - - - -
57A LEU* 1.3 76.8 - - - +
59A PRO* 1.3 68.6 - - - +
60A TRP* 3.3 3.3 + - + -
66A GLN* 3.4 4.7 - - + +
67A CYS* 2.0 47.1 - - - -
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Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLY* 6.2 0.9 - - - -
33A VAL 4.7 1.1 - - - +
34A SER* 3.5 16.4 - - - +
57A LEU* 3.5 17.9 - - + +
58A CYS* 1.3 84.6 - - - +
60A TRP* 1.3 63.3 + - - +
61A GLY 3.6 3.2 + - - -
62A ALA 4.9 2.9 + - - -
66A GLN* 3.1 30.4 - - - +
68A THR* 5.4 2.9 - - + +
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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