Contacts of the strand formed by residues 30 - 36 (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 ALA 30 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23K LYS* 3.7 7.8 - - - +
24K ASP* 3.5 24.9 + - + +
27K VAL* 3.9 33.9 + - + +
28K PRO 3.2 0.4 - - - -
29K ASN* 1.3 78.9 - - - +
31K CYS* 1.3 71.9 + - - +
74K ARG* 4.3 7.2 - - - +
75K VAL 3.7 5.6 - - - +
76K GLN* 3.9 17.3 - - + -
83K PRO* 4.5 1.3 - - - -
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Residues in contact with CYS 31 (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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273C THR* 5.1 3.6 - - - -
21K ILE* 5.0 3.1 - - + -
22K ASN 4.1 4.7 - - - +
23K LYS* 4.4 23.1 - - - -
24K ASP* 4.4 4.0 - - - +
29K ASN 5.7 0.2 - - - -
30K ALA* 1.3 85.0 - - - +
32K LEU* 1.3 62.0 - - - +
33K PHE* 4.0 17.3 - - + -
74K ARG* 3.7 6.3 - - - +
75K VAL* 3.0 35.8 + - - +
83K PRO* 3.8 15.2 - - + +
84K GLN* 3.2 31.2 - - - +
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Residues in contact with LEU 32 (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* 4.7 3.8 - - + -
20K THR 4.1 1.0 - - - +
21K ILE* 4.1 1.7 - - - +
22K ASN* 3.1 41.9 + - + +
23K LYS 5.6 0.2 - - - -
24K ASP* 5.5 6.1 - - + +
31K CYS* 1.3 77.1 - - - +
33K PHE* 1.3 64.8 + - - +
34K THR* 4.0 6.0 + - - +
72K ILE* 4.5 19.1 - - + -
73K ILE 3.5 14.6 - - - +
74K ARG* 3.5 33.0 - - + +
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Residues in contact with PHE 33 (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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263C LEU* 4.4 4.5 - - + -
19K ILE* 4.1 16.4 - - + -
20K THR 4.0 1.3 - - - -
21K ILE* 3.3 37.0 - - + -
31K CYS* 4.0 13.5 - - + -
32K LEU* 1.3 77.3 - - - +
34K THR* 1.3 63.7 + - - +
35K ILE* 4.1 1.9 + - + -
71K ILE 3.9 0.2 - - - +
72K ILE* 3.1 4.7 - - - +
73K ILE* 2.5 56.8 + - + +
75K VAL* 3.6 31.6 - - + -
83K PRO 4.2 4.7 - - - -
84K GLN* 4.1 34.8 - - + -
87K PHE* 4.2 33.9 - + + -
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Residues in contact with THR 34 (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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19K ILE* 3.2 7.0 - - - +
20K THR* 3.0 44.9 + - - +
32K LEU* 4.8 6.1 + - - +
33K PHE* 1.3 74.5 - - - +
35K ILE* 1.3 66.2 + - - +
36K ASN* 4.2 3.5 + - + +
70K LYS* 3.6 34.8 - - + -
71K ILE 3.5 9.2 - - - +
72K ILE* 3.5 14.8 - - + +
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Residues in contact with ILE 35 (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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259C LEU* 4.2 24.9 - - + -
18K LYS* 3.8 13.5 - - - +
19K ILE* 4.4 12.3 - - + -
33K PHE* 5.0 1.3 - - + +
34K THR* 1.3 80.6 - - - +
36K ASN* 1.3 62.9 + - - +
38K GLU* 3.4 29.1 - - + +
42K LEU* 3.9 22.2 - - + -
70K LYS* 3.6 2.6 - - - +
71K ILE* 2.9 46.9 + - + +
73K ILE* 3.7 30.7 - - + -
87K PHE* 4.6 5.6 - - + -
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Residues in contact with ASN 36 (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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12K LEU* 4.2 5.2 - - + +
16K GLU* 2.7 45.2 + - - +
17K LYS 3.8 17.1 + - - +
18K LYS* 3.2 28.8 + - - +
19K ILE* 5.0 0.4 - - - +
34K THR* 4.1 4.6 + - + -
35K ILE* 1.3 74.0 - - - +
37K LYS* 1.3 85.0 + - - +
38K GLU* 3.5 1.7 + - - +
69K HIS 3.3 11.9 - - - +
70K LYS* 4.3 12.9 - - + +
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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