Contacts of the strand formed by residues 52 - 60 (chain K) in PDB entry 1YI2
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 52 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 5.0 11.6 - - + +
34K VAL* 4.1 0.9 - - - +
35K HIS* 2.8 79.1 + - + +
50K GLY 4.0 1.2 + - - -
51K ASP* 1.3 71.4 - - - +
53K ILE* 1.3 59.8 + - - +
70K GLU* 3.9 32.2 + - + +
71K ALA 3.4 14.8 - - - +
72K VAL* 4.6 5.8 - - + +
98K VAL* 5.4 4.3 - - + -
100K GLU 5.6 2.8 + - - -
102K GLU* 3.2 34.1 + - + +
121K PHE* 4.5 14.3 - - + -
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Residues in contact with ILE 53 (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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18K ILE* 4.2 11.7 - - + -
31K VAL* 3.7 24.9 - - + -
33K SER 3.2 13.9 - - - +
34K VAL* 4.4 2.7 - - + -
35K HIS* 5.1 0.4 - - - -
47K ALA* 3.8 28.5 - - + -
51K ASP* 3.7 5.6 + - + -
52K LYS* 1.3 77.3 - - - +
54K THR* 1.3 60.7 + - - +
55K VAL* 3.3 25.8 - - + -
70K GLU* 3.7 5.7 - - - +
71K ALA 3.0 37.9 + - - +
73K VAL* 3.9 26.2 - - + -
95K ALA* 4.7 4.5 - - + -
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Residues in contact with THR 54 (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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25960 A 3.7 32.3 - - - +
25970 U 3.3 25.6 + - - +
31K VAL* 3.9 1.0 - - - -
32K ILE* 3.0 26.3 + - + -
33K SER* 2.8 16.8 + - - +
35K HIS* 5.2 3.1 + - - +
53K ILE* 1.3 71.7 - - - +
55K VAL* 1.3 73.6 + - - +
68K VAL* 3.8 21.5 - - + -
69K LEU 3.8 6.5 - - - +
70K GLU* 4.5 9.8 + - + +
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Residues in contact with VAL 55 (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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29K LEU* 3.3 35.4 - - + -
30K LYS 3.0 17.7 - - - +
31K VAL* 4.4 1.3 - - - +
32K ILE* 4.1 6.1 - - - -
53K ILE* 3.3 34.8 - - + +
54K THR* 1.3 84.0 - - - +
56K SER* 1.3 84.1 + - - +
57K VAL* 5.9 0.7 - - - -
68K VAL* 3.1 7.6 - - - +
69K LEU* 2.7 44.2 + - + +
71K ALA* 4.2 11.9 - - + -
97K ILE* 6.5 0.2 - - + -
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Residues in contact with SER 56 (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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19930 C 2.8 40.5 + - - -
29K LEU* 3.7 0.3 - - - -
30K LYS* 3.0 42.0 + - - +
32K ILE* 3.5 17.5 - - - +
55K VAL* 1.3 82.0 - - - +
57K VAL* 1.3 61.5 + - - +
58K THR* 3.5 1.0 + - - -
66K ARG 5.1 0.7 - - - -
67K GLN 3.1 9.4 - - - -
68K VAL* 4.5 1.8 - - - -
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Residues in contact with VAL 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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19930 C 5.1 3.5 + - - -
26K ALA* 4.0 19.1 - - + -
28K GLU 3.9 4.3 - - - +
29K LEU* 3.6 18.4 - - + -
55K VAL 5.8 0.4 - - - +
56K SER* 1.3 74.3 + - - +
58K THR* 1.3 60.1 + - - +
59K LYS 3.4 25.4 - - - +
64K MET* 3.3 31.6 - - + +
65K ARG* 3.7 10.9 - - - +
66K ARG* 3.1 20.8 + - - +
67K GLN 3.1 13.0 + - - +
69K LEU* 4.2 18.8 - - + -
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Residues in contact with THR 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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19930 C 5.0 1.6 + - - -
17K LEU* 3.9 9.8 - - + +
28K GLU* 2.9 40.3 + - - +
30K LYS* 3.5 33.9 + - - +
56K SER* 3.5 1.3 + - - -
57K VAL* 1.3 74.4 - - - +
59K LYS* 1.3 66.0 + - + +
65K ARG* 4.0 12.7 - - - +
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Residues in contact with LYS 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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27K ARG* 2.8 31.7 + - + -
28K GLU* 3.3 49.8 + - + +
57K VAL* 3.4 13.2 - - - +
58K THR* 1.3 87.4 - - + +
60K GLY* 1.3 60.2 + - - +
65K ARG* 4.3 3.6 - - - +
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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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25K GLY 3.1 12.8 - - - -
26K ALA* 4.4 0.7 - - - -
27K ARG* 4.0 20.2 - - - +
57K VAL* 5.0 1.3 - - - -
59K LYS* 1.3 75.7 - - - +
61K THR* 1.3 66.3 + - - -
62K PRO* 3.6 1.9 - - - +
65K ARG* 3.3 19.0 + - - +
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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