Contacts of the strand formed by residues 56 - 62 (chain K) in PDB entry 5IYB
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 56 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A ARG* 4.8 8.9 + - - +
77H PRO* 5.7 3.1 - - - +
50K LEU* 3.2 38.4 - - + +
51K LEU* 5.0 5.4 - - + -
53K ASP* 3.5 22.0 + - + +
54K PRO 3.4 5.3 - - - +
55K GLN* 1.3 77.4 - - - +
57K LEU* 1.3 63.7 + - - +
58K PHE 3.3 32.8 - - - +
59K ALA* 3.8 9.2 - - + -
75K VAL* 4.3 2.9 - - + -
76K GLN 3.8 1.6 - - - +
77K THR* 3.6 17.0 - - + -
86K ALA* 4.2 10.1 - - + -
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Residues in contact with LEU 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG* 5.1 0.9 + - - -
561A MET* 3.7 8.1 - - - +
574A VAL* 6.0 0.5 - - - +
74H GLU* 4.4 22.0 - - - +
75H TYR* 3.6 19.8 + - - -
76H ASN* 5.1 0.2 - - - +
77H PRO* 4.8 13.5 - - + +
78H THR* 3.9 20.0 - - + +
55K GLN 3.6 0.6 + - - -
56K VAL* 1.3 75.2 - - - +
58K PHE* 1.3 59.5 + - + +
76K GLN* 2.5 33.9 + - + +
77K THR 3.3 30.3 - - - +
78K THR* 3.7 24.5 - - + +
79K PRO* 5.1 4.0 - - + -
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Residues in contact with PHE 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A MET* 3.4 60.8 - - + -
564A LEU* 4.2 20.2 - - + -
565A MET* 4.5 10.5 - - - -
570A TRP* 4.7 4.9 - + + -
574A VAL* 4.2 19.3 - - + -
56K VAL* 3.3 7.0 - - - +
57K LEU* 1.3 78.3 - - + +
59K ALA* 1.3 61.3 + - - +
60K GLY 4.2 6.5 - - - -
74K ARG* 3.0 56.1 - - + +
75K VAL* 3.2 2.1 - - - -
76K GLN* 2.7 46.0 + - + +
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Residues in contact with ALA 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A MET* 3.9 16.6 - - - +
47K LYS* 3.9 11.8 - - + +
50K LEU* 3.8 38.6 - - + -
51K LEU* 3.7 21.9 - - + +
56K VAL* 3.8 9.4 - - + +
58K PHE* 1.3 83.2 - - - +
60K GLY* 1.3 58.4 + - - +
74K ARG 3.2 7.0 - - - +
75K VAL* 4.4 1.6 - - + -
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Residues in contact with GLY 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A MET* 5.0 4.0 - - - -
562A ASN* 5.8 0.9 - - - -
565A MET* 3.2 17.4 - - - +
47K LYS* 3.8 14.5 - - - +
58K PHE* 4.2 4.6 - - - -
59K ALA* 1.3 75.3 - - - +
61K TYR* 1.3 60.4 + - - -
73K ILE* 3.1 6.9 - - - +
74K ARG 2.6 39.4 + - - -
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Residues in contact with TYR 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A ASN* 4.0 18.2 - - - +
565A MET* 3.4 12.5 - - - +
566A PHE* 4.9 0.2 - - - -
1032B PHE* 4.5 0.5 + - - +
1033B THR* 4.4 10.7 - - + +
40K HIS* 3.3 35.2 + + - -
43K GLY* 3.9 19.3 - - - +
44K ASN* 3.5 42.5 + - - +
47K LYS* 3.7 29.2 - - + -
60K GLY* 1.3 75.3 - - - +
62K LYS* 1.3 74.7 + - - +
63K VAL 5.0 0.2 - - - -
71K ILE* 4.9 9.4 - - + -
72K ILE 2.9 14.8 - - - +
73K ILE* 3.7 16.4 - - + -
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Residues in contact with LYS 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A MET* 3.2 24.4 + - + +
566A PHE* 3.2 62.8 + - + +
567A LEU 4.8 2.4 + - - -
568A SER* 5.9 0.6 - - - +
674A THR* 6.0 0.2 - - - +
40K HIS* 6.1 0.4 - - - -
61K TYR* 1.3 87.9 - - - +
63K VAL* 1.3 63.2 + - - +
64K PRO* 4.0 14.1 - - + +
71K ILE* 3.6 2.6 - - - +
72K ILE* 3.1 55.4 + - + +
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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