Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 4HJ5
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 PHE 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR* 3.9 18.6 - - - -
27A TRP 3.8 10.1 - - - -
28A TYR* 3.9 20.0 - + + -
32A ASN* 1.3 75.8 - - - +
34A THR* 1.3 63.5 + - - +
35A LEU* 3.1 33.0 - - + -
69A CYS 3.9 0.3 - - - +
71A LEU* 2.9 38.3 + - + +
76A ASP* 3.4 26.6 - - - +
79A CYS* 3.6 33.4 - - + -
80A ARG* 3.5 31.0 - - - -
83A ILE* 3.8 19.5 - - + -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.4 4.5 - - - -
27A TRP* 2.9 46.7 + - - -
32A ASN* 3.6 11.8 + - - -
33A PHE* 1.3 77.3 - - - +
35A LEU* 1.3 70.1 + - - +
36A TYR* 3.7 21.5 - - + +
68A ARG* 3.6 33.6 - - + -
69A CYS 3.5 5.2 - - - +
70A ILE* 3.4 15.2 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.8 3.8 - - + -
25A LYS 3.5 4.7 - - - +
26A THR* 3.9 12.1 - - + -
33A PHE* 3.1 38.6 - - + -
34A THR* 1.3 78.2 - - - +
36A TYR* 1.3 64.2 + - - +
37A VAL* 3.8 22.0 - - + -
67A ILE 3.7 0.7 - - - +
68A ARG* 3.5 2.9 - - - -
69A CYS* 2.9 39.1 + - + +
71A LEU* 4.2 19.1 - - + -
83A ILE* 4.4 16.2 - - + -
89A VAL* 5.4 0.7 - - + -
91A MET* 4.9 2.7 - - - -
120A ILE* 3.6 31.2 - - + -
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 0.7 - - - -
24A ILE* 2.8 25.4 + - - -
25A LYS* 2.9 47.5 + - + +
27A TRP* 5.3 2.9 - - + -
34A THR* 3.7 18.0 - - + +
35A LEU* 1.3 74.7 - - - +
37A VAL* 1.3 64.0 + - - +
58A TRP* 3.7 32.3 - + + -
66A SER* 5.1 3.8 - - - -
67A ILE 3.5 5.4 - - - +
68A ARG* 3.4 47.8 + - + -
5B T 3.2 30.2 + + - -
6B C 3.6 20.8 + + - -
7B G 4.0 5.1 + - - -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.5 1.1 - - + -
19A PHE* 4.1 11.7 - - + -
21A ALA* 3.6 21.5 - - + -
22A GLN 3.1 11.9 - - - +
23A VAL* 3.9 19.1 - - + -
24A ILE* 4.3 1.3 - - - +
35A LEU* 3.8 26.9 - - + -
36A TYR* 1.3 81.4 - - - +
38A THR* 1.3 61.1 + - - +
66A SER* 3.4 4.4 - - - -
67A ILE* 3.0 48.7 + - + +
69A CYS* 4.3 7.4 - - - -
89A VAL* 4.6 6.1 - - + -
91A MET* 5.0 0.9 - - - -
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Residues in contact with THR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.0 7.0 - - - -
21A ALA* 3.5 1.4 - - - -
22A GLN* 2.7 36.7 + - + +
24A ILE* 3.6 24.9 - - + -
37A VAL* 1.3 73.4 - - - +
39A ASP* 1.3 58.2 + - - +
40A TYR* 2.9 50.4 + - + -
61A PRO* 3.9 6.9 - - + +
65A PHE 2.5 27.5 + - - -
66A SER* 3.6 7.6 - - - -
133A ILE* 4.7 0.3 - - - +
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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