Contacts of the strand formed by residues 55 - 58 (chain l) in PDB entry 5K0Y
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 55 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33U ILE* 4.3 12.6 - - + +
34U SER* 3.4 44.1 + - - +
36U GLN* 5.1 7.9 - - + +
143U PRO* 3.7 12.8 - - - +
146U ARG* 4.2 1.6 + - - -
11l LEU* 4.4 5.8 - - + -
12l ALA 3.6 17.5 - - - +
13l ARG* 4.2 13.0 - - + -
35l MET* 4.4 18.4 - - + -
53l GLY 4.3 5.4 - - - +
54l ASP* 1.4 83.8 - - - +
56l LEU* 1.4 74.6 + - - +
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Residues in contact with LEU 56 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U SER* 4.0 0.2 + - - -
140U ASP* 4.2 15.3 - - + -
141U VAL 3.5 29.8 - - - +
142U SER* 4.2 8.1 - - - +
143U PRO* 4.4 2.5 - - + -
146U ARG* 4.3 1.6 - - - +
11l LEU* 3.8 1.9 - - - -
12l ALA 2.9 34.8 + - - +
14l VAL* 4.5 10.3 - - + -
30l VAL* 4.8 0.7 - - + -
32l VAL* 3.9 24.2 - - + -
44l ARG* 5.0 6.1 - - + -
46l VAL* 3.7 28.9 - - + -
50l VAL* 6.1 1.3 - - + -
54l ASP* 4.2 1.8 + - - +
55l VAL* 1.4 84.8 - - - +
57l THR* 1.3 63.0 + - - +
58l LEU* 3.7 19.5 - - + -
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Residues in contact with THR 57 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U ASP* 4.8 0.9 + - - -
34U SER* 3.0 27.9 + - - -
122U ARG* 3.7 26.9 + - + +
140U ASP* 2.9 18.6 - - - +
146U ARG* 3.4 19.9 + - - +
9l ILE* 3.4 29.4 - - + -
10l LYS 4.0 1.8 - - - -
11l LEU* 4.1 10.8 - - + +
56l LEU* 1.3 70.2 - - - +
58l LEU* 1.4 56.8 + - - +
59l LEU* 3.5 12.2 + - + +
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Residues in contact with LEU 58 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140U ASP* 3.2 27.1 - - - +
9l ILE* 3.5 5.4 - - - +
10l LYS* 3.0 41.4 + - + +
12l ALA* 3.6 28.0 - - + -
32l VAL* 4.6 3.4 - - + -
34l PHE* 3.9 26.7 - - + -
42l ILE* 5.0 0.4 - - + -
44l ARG* 4.2 27.6 - - + +
56l LEU* 4.0 19.7 - - + -
57l THR* 1.4 71.2 - - - +
59l LEU* 1.3 58.5 + - - +
60l GLU 3.7 17.7 - - - +
61l SER* 5.7 0.9 - - - -
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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