Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 1PJS
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 ARG 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU 4.2 0.8 + - - -
12A ASP* 4.3 28.5 - - - +
13A ARG 3.2 16.2 + - - +
14A ASP* 2.8 37.9 + - - +
15A CYS 3.0 23.2 + - - -
35A GLY 3.9 1.0 + - - -
36A ALA* 1.3 70.7 - - - +
38A LEU* 1.3 58.8 + - - +
39A THR* 5.1 1.7 + - - -
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Residues in contact with LEU 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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15A CYS* 3.5 13.7 - - + +
17A ILE* 3.7 23.3 - - + +
28A ALA* 3.9 30.1 - - + +
31A LEU* 4.3 15.9 - - + -
32A LEU* 4.0 17.9 - - + -
36A ALA* 3.2 5.7 + - + +
37A ARG* 1.3 74.3 - - - +
39A THR* 1.3 95.7 + - - +
40A VAL* 4.0 6.3 - - + -
57A MET 5.0 3.2 + - - -
58A LEU* 3.8 32.3 - - + +
59A THR* 3.2 24.2 + - - -
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Residues in contact with THR 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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14A ASP* 5.5 3.3 + - - +
15A CYS 3.1 9.7 + - - -
16A LEU* 3.2 19.7 - - + +
17A ILE 3.0 24.3 + - - -
37A ARG* 5.1 1.9 + - - -
38A LEU* 1.3 80.6 + - - +
40A VAL* 1.3 66.8 + - - +
59A THR* 3.4 17.8 - - + +
61A VAL* 3.8 27.8 - - + -
69A LEU* 4.8 11.9 - - + +
73A CYS* 6.0 1.8 - - - -
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Residues in contact with VAL 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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17A ILE* 3.2 11.4 - - + +
19A GLY 3.2 28.0 - - - +
38A LEU* 4.0 22.7 - - + -
39A THR* 1.3 79.0 - - - +
41A ASN* 1.3 59.5 + - - +
45A PHE* 3.4 23.9 - - + -
49A PHE* 3.9 28.9 - - + -
58A LEU* 4.5 4.9 - - + -
59A THR 2.9 7.9 + - - +
60A LEU* 3.5 15.9 - - + -
61A VAL 2.8 26.1 + - - -
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Residues in contact with ASN 41 (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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16A LEU* 4.3 8.0 - - + +
17A ILE 3.0 9.3 + - - +
18A VAL* 3.2 11.3 - - + +
19A GLY 2.6 31.4 + - - -
39A THR 4.2 0.8 - - - -
40A VAL* 1.3 71.4 - - - +
42A ALA* 1.3 55.8 + - - +
61A VAL* 3.1 21.7 + - + +
63A GLY 3.0 26.5 + - - -
64A PRO 3.3 6.3 + - - +
65A PHE* 3.0 36.1 - - - -
66A ASP 3.3 5.7 + - - -
69A LEU* 3.9 22.3 - - + +
502A NAD 4.5 0.9 - - - -
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Residues in contact with ALA 42 (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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19A GLY 3.4 2.5 - - - -
20A GLY 3.4 17.9 - - - +
41A ASN* 1.3 77.9 - - - +
43A LEU* 1.3 65.5 + - - +
44A THR 3.3 19.0 + - - +
45A PHE* 3.5 19.8 - - + -
61A VAL 3.1 6.9 + - - -
62A GLU* 3.5 8.0 - - - -
63A GLY 3.1 19.7 + - - -
502A NAD 3.1 15.3 - - - +
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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