Contacts of the strand formed by residues 31 - 40 (chain A) in PDB entry 1JAT
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 ASN 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A HIS* 3.0 13.7 + - + +
29A ASP 3.4 0.4 - - - -
30A ASP* 1.3 87.1 + - - +
32A LEU* 1.3 57.8 + - - +
33A ARG* 3.0 33.1 + - - +
34A TYR* 3.0 36.4 + - + +
57A TYR* 4.7 0.8 - - - -
2B SER 5.4 2.8 - - - +
3B LYS* 3.1 33.5 + - - +
5B PRO* 4.0 11.3 - - - +
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Residues in contact with LEU 32 (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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4A LEU* 3.8 33.9 - - + +
8A ILE* 4.5 4.3 - - - +
12A THR* 4.9 0.9 + - - -
27A PRO* 3.8 25.6 - - + +
28A HIS 3.7 15.9 - - - +
29A ASP* 4.6 12.3 - - - +
31A ASN* 1.3 72.8 - - - +
33A ARG* 1.3 59.3 + - - +
34A TYR 3.4 0.4 - - - -
35A PHE* 3.6 16.6 - - - -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.8 19.8 - - + +
5A PRO* 3.6 31.3 - - - +
8A ILE* 3.5 19.7 - - + +
31A ASN* 3.0 11.7 + - - +
32A LEU* 1.3 80.7 - - - +
34A TYR* 1.3 57.8 + - - +
35A PHE* 3.6 12.4 - - - -
57A TYR* 3.3 15.2 - - + -
58A LEU* 2.9 51.7 + - + +
59A PRO 3.0 27.4 + - - -
60A ASP* 3.9 25.5 + - - +
62A TYR* 4.7 2.0 + - - +
2B SER* 3.9 22.5 + - - +
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Residues in contact with TYR 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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27A PRO* 3.2 2.4 - - - +
28A HIS* 2.9 58.4 + + - +
30A ASP* 5.9 0.2 - - - -
31A ASN* 3.0 26.8 + - + +
33A ARG* 1.3 78.3 - - - +
35A PHE* 1.3 62.7 + - - +
55A GLU* 2.6 37.9 + - + -
56A LEU 3.5 10.8 - - - -
57A TYR* 4.4 1.8 - - + -
5B PRO* 3.5 37.6 - - + +
7B ASN* 3.8 10.2 + - - -
8B PHE* 3.9 17.3 - + - -
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Residues in contact with PHE 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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12A THR* 3.4 26.9 - - + -
15A LEU* 4.6 14.1 - - + -
25A ALA* 4.3 8.3 - - + -
26A GLU* 3.4 12.6 - - - +
27A PRO* 3.5 32.1 - - + -
28A HIS* 4.2 4.6 - - - -
32A LEU 3.6 22.9 - - - -
33A ARG 3.6 8.3 - - - -
34A TYR* 1.3 80.4 - - - +
36A GLN* 1.3 60.9 + - - +
37A VAL* 3.9 15.2 + - + -
55A GLU* 3.4 9.4 - - - +
56A LEU* 2.7 52.5 + - + +
58A LEU* 3.8 25.1 - - + -
101A ILE* 4.9 5.8 - - + -
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Residues in contact with GLN 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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24A THR* 3.9 1.0 + - - +
25A ALA* 3.4 2.6 + - - -
26A GLU* 2.9 50.2 + - + +
28A HIS* 4.1 21.0 + - + +
35A PHE* 1.3 72.1 - - - +
37A VAL* 1.3 60.0 + - - +
38A THR* 5.2 3.1 - - + -
53A GLU* 2.9 32.5 + - - +
54A LEU 4.0 3.1 - - - -
55A GLU* 5.0 0.7 - - - +
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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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23A ILE* 4.4 2.9 - - + -
24A THR* 3.2 10.5 - - - +
25A ALA* 4.0 15.3 - - + -
35A PHE* 4.2 15.5 - - + +
36A GLN* 1.3 79.2 - - - +
38A THR* 1.3 75.4 + - - +
39A ILE* 4.2 10.3 - - + -
53A GLU* 3.1 7.6 - - - +
54A LEU* 2.8 48.9 + - + +
56A LEU* 4.2 18.2 - - + +
69A VAL* 6.1 0.7 - - + -
105A LEU* 4.0 26.5 - - + -
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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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22A GLY 3.9 0.7 + - - +
23A ILE* 3.3 5.4 - - - +
24A THR* 2.4 65.1 + - - +
36A GLN* 5.2 5.2 - - + -
37A VAL* 1.3 73.0 - - - +
39A ILE* 1.3 65.7 + - - +
51A ILE* 3.8 17.5 - - + +
52A PHE 3.1 9.4 - - - +
53A GLU* 3.0 27.8 - - - +
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Residues in contact with ILE 39 (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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22A GLY 3.5 3.1 - - - +
23A ILE* 4.0 17.3 - - + -
37A VAL* 4.2 6.7 - - + -
38A THR* 1.3 80.8 - - - +
40A GLU* 1.3 76.0 + - - +
41A GLY 3.6 0.3 + - - -
51A ILE* 4.2 2.5 - - - -
52A PHE* 2.8 39.5 + - + -
54A LEU* 4.1 21.8 - - + -
105A LEU* 4.0 17.0 - - + +
108A ILE* 3.7 34.8 - - + -
109A GLN* 4.2 19.7 - - + +
112A LEU* 4.0 17.5 - - + -
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Residues in contact with GLU 40 (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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22A GLY* 2.9 39.4 + - - +
38A THR 4.3 0.2 - - - -
39A ILE* 1.3 85.4 - - - +
41A GLY* 1.3 67.0 + - - +
42A PRO* 3.4 7.6 - - - +
50A GLY 3.9 4.9 - - - -
51A ILE* 4.1 24.5 - - + +
109A GLN* 4.9 4.4 - - - +
151A LYS* 3.9 19.9 + - - +
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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