Contacts of the strand formed by residues 57 - 61 (chain C) in PDB entry 3BSU
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 ARG 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ASN* 5.8 1.6 + - - -
47A ARG* 6.4 0.2 - - - +
31C VAL 3.6 0.5 - - - -
32C ARG* 2.9 62.3 + - + +
33C ARG* 3.0 41.3 + - + +
55C ALA 3.5 3.7 + - - +
56C ALA* 1.3 75.8 - - - +
58C PHE* 1.3 62.3 + - - +
70C PHE* 3.9 27.8 - - + -
9E 5IU 6.4 2.0 - - - +
10E G 6.2 2.4 - - - -
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Residues in contact with PHE 58 (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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30C ALA 2.9 14.4 - - - +
31C VAL* 4.0 7.4 - - + -
43C TRP* 3.7 21.3 - + - -
46C CYS* 4.2 6.5 - - - -
50C VAL* 3.4 47.1 - - + -
51C ASP* 5.4 1.8 - - - -
56C ALA* 4.0 15.9 - - + -
57C ARG* 1.3 79.0 + - - +
59C LYS* 1.3 68.4 + - - +
70C PHE* 3.9 7.2 - - - -
4D A 5.4 4.7 - + - -
10E G 3.4 58.4 - - + +
11E T 3.3 28.5 - - - -
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Residues in contact with LYS 59 (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 TYR* 4.8 1.6 - - - -
30C ALA* 2.7 31.7 + - - +
58C PHE* 1.3 79.8 - - - +
60C LYS* 1.3 68.0 + - - +
61C PHE* 3.2 44.3 - - + -
70C PHE* 3.8 21.0 - - + -
10E G 3.8 30.9 + - - +
11E T 3.7 12.1 - - - +
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Residues in contact with LYS 60 (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 MET* 3.5 40.2 - - + -
28C PHE 3.3 7.0 - - - +
29C TYR* 4.0 21.8 - - + +
59C LYS* 1.3 82.0 - - - +
61C PHE* 1.3 68.2 + - - +
11E T 2.9 32.0 + - - +
12E C 2.5 38.8 + - - +
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Residues in contact with PHE 61 (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 MET* 3.3 10.2 - - - -
28C PHE* 2.5 43.6 + - - +
30C ALA* 3.9 0.9 - - + -
59C LYS* 3.2 52.9 - - + -
60C LYS* 1.3 75.6 - - - +
62C ALA* 1.3 60.8 + - - +
63C THR 3.4 16.6 - - - +
66C GLU* 3.3 38.6 - - + -
67C ALA* 3.7 14.1 - - - +
70C PHE* 3.6 40.2 - + + -
73C LYS* 5.7 2.0 - - - -
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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