Contacts of the strand formed by residues 41 - 47 (chain K) in PDB entry 3IT8
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 HIS 41 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35K TYR* 3.5 11.2 - - - -
36K ASN* 2.9 23.4 + - - +
39K THR* 3.1 33.2 + - + +
40K ARG* 1.3 79.2 - - - +
42K GLY* 1.3 72.6 + - - +
43K ASN* 3.3 17.6 + - - -
67K ASN* 3.6 22.4 + - - +
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Residues in contact with GLY 42 (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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33K ILE* 4.2 3.6 - - - -
34K SER 3.3 10.8 - - - -
41K HIS* 1.3 84.3 + - - +
43K ASN* 1.3 67.9 + - - +
63K ASP* 5.1 8.3 - - - +
66K PHE* 3.7 24.7 - - - -
67K ASN* 3.0 14.9 + - - -
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Residues in contact with ASN 43 (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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33K ILE* 3.2 7.7 - - - +
34K SER 2.9 30.6 + - - +
36K ASN* 2.9 45.0 - - - +
39K THR* 5.3 0.2 + - - -
41K HIS* 3.3 14.6 + - - -
42K GLY* 1.3 81.2 - - - +
44K VAL* 1.3 65.9 + - - +
45K ASN* 3.3 12.2 + - - +
63K ASP* 6.2 0.9 - - - -
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Residues in contact with VAL 44 (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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31K THR* 4.5 6.1 - - + -
32K LYS 3.5 6.7 - - - +
33K ILE* 3.9 15.3 - - + -
43K ASN* 1.3 73.8 - - - +
45K ASN* 1.3 60.7 + - - +
46K PHE 3.3 28.7 - - - +
47K ARG* 4.5 23.1 - - + +
63K ASP* 3.6 26.0 - - - +
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Residues in contact with ASN 45 (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 LYS* 2.8 39.5 + - + +
34K SER* 2.4 44.1 + - - +
43K ASN* 3.5 14.5 - - - +
44K VAL* 1.3 75.4 - - - +
46K PHE* 1.3 61.5 + - + +
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Residues in contact with PHE 46 (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* 3.6 46.7 - - + -
30K VAL 4.0 3.1 - - - -
31K THR* 3.3 4.4 - - - +
32K LYS* 3.1 37.8 + - + -
44K VAL* 3.3 12.6 - - - +
45K ASN* 1.3 84.4 - - + +
47K ARG* 1.3 77.8 + - - +
48K ALA* 3.4 27.4 - - + -
49K ASP* 5.9 1.3 - - - -
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Residues in contact with ARG 47 (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 VAL 3.3 5.8 - - - -
31K THR* 2.3 50.1 + - - +
44K VAL* 4.5 23.6 - - + +
46K PHE* 1.3 86.5 - - - +
48K ALA* 1.3 75.9 + - - +
49K ASP* 3.3 2.6 + - - -
51K PHE* 4.3 20.3 + - - +
53K ILE* 3.3 37.6 - - - +
63K ASP* 4.9 5.5 + - - +
64K TYR* 3.5 13.5 + - - -
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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