Contacts of the strand formed by residues 55 - 59 (chain A) in PDB entry 6P59
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 ILE 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 5.2 4.5 - - + -
44A PHE* 4.5 7.4 - - + -
47A ALA* 3.5 34.5 - - + +
48A CYS* 3.9 15.7 - - - +
54A GLU* 1.3 79.9 - - - +
56A ALA* 1.3 59.9 + - - +
57A PHE* 3.6 31.2 - - + -
67A GLN* 3.2 2.5 + - - -
68A PHE* 2.9 41.5 + - + +
86A VAL* 3.8 36.1 - - + -
95A VAL* 5.7 0.2 - - + -
97A LEU* 4.4 0.7 - - + -
6B TRP* 3.9 8.0 - - + -
77B THR* 4.9 0.7 - - - -
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Residues in contact with ALA 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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28A LYS 4.1 2.1 - - - +
29A TYR* 3.9 19.0 - - - -
30A THR* 4.6 7.3 + - - +
55A ILE* 1.3 75.8 - - - +
57A PHE* 1.3 70.8 + - - +
58A VAL* 4.3 1.6 - - + -
65A SER* 4.6 5.4 - - - +
66A LEU 3.3 10.8 - - - +
67A GLN* 3.7 22.9 - - - +
13B ARG* 3.8 21.3 - - - +
77B THR* 4.9 10.4 + - - +
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Residues in contact with PHE 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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27A ILE* 4.2 18.6 - - + +
28A LYS 3.3 20.0 - - - +
29A TYR* 4.4 6.1 - + + -
44A PHE* 3.7 33.2 - + - -
55A ILE* 3.6 30.7 - - + -
56A ALA* 1.3 80.5 - - - +
58A VAL* 1.3 63.0 + - - +
59A ALA 4.0 0.5 + - - -
65A SER* 3.2 1.4 - - - -
66A LEU* 2.8 41.1 + - + +
68A PHE* 4.0 17.0 - + - -
97A LEU* 3.4 29.6 - - + -
110A TRP* 6.1 1.3 - + + -
114A ILE* 3.3 36.1 - - + -
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Residues in contact with VAL 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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27A ILE* 3.5 3.5 - - - -
28A LYS* 3.3 27.4 + - + +
30A THR* 3.5 36.1 - - + +
56A ALA* 4.4 1.5 + - + -
57A PHE* 1.3 71.8 - - - +
59A ALA* 1.3 69.1 + - - +
60A THR* 3.2 6.6 + - + +
62A THR 4.6 7.0 - - - +
63A ASN* 5.1 4.0 - - - +
64A LEU 3.3 8.7 - - - +
65A SER* 3.5 12.3 - - - -
13B ARG* 3.4 34.1 - - - +
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Residues in contact with ALA 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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20A LYS 4.9 3.6 - - - +
21A LEU* 4.7 10.8 - - + -
25A CYS* 4.4 24.9 - - + -
26A GLU 3.6 6.3 - - - -
27A ILE* 4.3 6.3 - - + +
57A PHE 4.0 1.8 + - - -
58A VAL* 1.3 70.2 - - - +
60A THR* 1.3 69.2 + - - +
62A THR* 2.8 43.4 + - + +
64A LEU* 3.2 12.3 + - + +
65A SER* 4.9 0.2 - - - +
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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