Contacts of the strand formed by residues 70 - 77 (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 LYS 70 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K THR* 3.6 26.0 - - + -
35K ILE 3.6 13.5 - - - +
36K ASN* 4.3 11.7 - - - +
37K LYS 4.4 1.3 - - - +
38K GLU 4.0 4.0 + - - -
63K VAL* 3.2 25.4 - - - +
64K PRO* 3.5 17.7 - - + +
68K GLU* 2.9 24.8 + - + +
69K HIS* 1.3 76.1 - - - +
71K ILE* 1.3 69.3 + - - +
72K ILE* 5.0 6.5 - - + -
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Residues in contact with ILE 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K THR* 3.5 3.1 - - - +
35K ILE* 2.9 63.8 + - + +
38K GLU* 3.8 31.2 - - + +
39K ASP 4.0 23.6 - - - +
42K LEU* 4.6 2.0 - - + -
43K GLY* 4.1 19.5 - - - +
61K TYR* 4.9 9.9 - - + -
62K LYS 3.6 9.2 - - - +
63K VAL* 4.1 15.5 - - + +
64K PRO* 4.7 1.1 - - - -
70K LYS* 1.3 80.4 - - - +
72K ILE* 1.3 65.7 + - - +
73K ILE* 5.1 2.9 - - + -
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Residues in contact with ILE 72 (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* 3.3 8.9 - - + +
32K LEU* 4.5 20.6 - - + -
33K PHE 3.1 4.0 - - - +
34K THR* 3.5 28.3 - - + +
61K TYR* 2.9 25.2 - - - +
62K LYS* 3.1 49.1 + - + +
64K PRO* 4.8 13.0 - - + -
70K LYS* 5.0 7.4 - - - -
71K ILE* 1.3 77.9 - - - +
73K ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 73 (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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32K LEU* 3.5 3.2 - - - -
33K PHE* 2.5 48.7 + - + +
35K ILE* 3.7 32.3 - - + -
43K GLY* 5.2 0.7 - - - +
46K ILE* 3.9 21.8 - - + -
47K LYS* 5.6 3.1 - - - -
50K LEU* 4.2 23.6 - - + -
60K GLY 3.1 12.3 - - - +
61K TYR* 3.7 15.0 - - + -
71K ILE* 5.1 6.3 - - + -
72K ILE* 1.3 77.2 - - - +
74K ARG* 1.3 67.2 + - - +
75K VAL* 3.9 3.6 + - + +
87K PHE* 3.9 21.5 - - + -
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Residues in contact with ARG 74 (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* 3.5 19.7 - - + +
570A TRP* 3.1 34.8 - - - -
572A GLY* 4.2 3.0 - - - -
24K ASP* 3.7 15.7 + - + +
26K LYS* 5.8 1.4 - - - +
27K VAL* 3.4 30.9 - - - +
30K ALA* 4.3 7.5 - - + +
31K CYS 3.7 10.3 - - - +
32K LEU* 3.5 21.8 - - + -
58K PHE* 3.0 37.1 - - + +
59K ALA* 3.2 3.3 - - - +
60K GLY 2.6 38.1 + - - -
73K ILE* 1.3 72.9 - - - +
75K VAL* 1.3 62.8 + - - +
76K GLN* 3.6 14.2 + - - +
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Residues in contact with VAL 75 (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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30K ALA* 3.7 1.6 - - - +
31K CYS 3.0 31.7 + - - +
33K PHE* 3.6 34.1 - - + -
50K LEU* 4.3 29.6 - - + -
56K VAL* 4.3 15.0 - - + -
58K PHE 3.2 11.0 - - - +
59K ALA* 4.4 0.4 - - + -
73K ILE* 4.9 2.0 - - + +
74K ARG* 1.3 77.0 - - - +
76K GLN* 1.3 65.7 + - - +
77K THR* 4.5 7.9 - - + -
83K PRO* 3.7 24.8 - - + +
86K ALA* 5.3 0.2 - - + -
87K PHE* 5.3 1.8 - - + -
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Residues in contact with GLN 76 (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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570A TRP* 5.1 0.9 - - - -
572A GLY 4.0 8.9 + - - +
27K VAL* 3.6 25.5 - - - +
28K PRO* 3.4 21.2 + - - +
29K ASN 3.7 12.8 - - - +
30K ALA* 3.9 5.4 - - + -
56K VAL* 3.5 1.0 - - - +
57K LEU* 2.5 47.1 + - + +
58K PHE* 2.7 32.6 + - + +
74K ARG* 3.6 21.6 + - - +
75K VAL* 1.3 75.7 - - - +
77K THR* 1.3 64.7 + - - +
83K PRO* 5.1 0.4 - - - -
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Residues in contact with THR 77 (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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28K PRO 5.0 0.3 - - - +
29K ASN* 3.2 18.3 + - - +
55K GLN 3.4 18.4 - - - +
56K VAL* 3.6 20.4 - - + -
57K LEU* 3.3 16.5 - - - +
75K VAL* 4.5 2.7 - - + -
76K GLN* 1.3 81.8 + - - +
78K THR* 1.3 66.4 + - - +
79K PRO* 3.7 1.2 - - - +
81K TYR* 2.7 36.6 + - + -
83K PRO* 3.3 24.3 - - + +
86K ALA* 4.3 9.0 - - + -
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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