Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 3NJ8
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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9A GLY 5.4 3.4 + - - +
10A GLN 3.0 8.9 + - - +
11A THR* 2.7 33.3 + - + +
12A ALA* 2.8 27.4 + - - +
35A GLY 3.6 2.0 + - - -
36A ALA* 1.3 71.8 - - - +
38A VAL* 1.3 58.9 + - - +
74A ALA* 3.4 28.9 - - + +
118A LEU* 3.8 32.0 + - - +
120A ASN 5.6 0.8 + - - -
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Residues in contact with VAL 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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11A THR* 5.8 0.2 - - - -
12A ALA* 3.6 5.2 - - + +
14A VAL* 3.8 21.3 - - + -
28A ALA* 3.9 22.4 - - + +
31A LEU* 4.0 16.8 - - + -
32A ALA* 3.8 20.6 - - + -
36A ALA* 3.6 15.0 + - + +
37A ARG* 1.3 81.3 - - - +
39A ALA* 1.3 68.7 + - - +
40A LEU* 4.6 0.4 - - + -
72A GLU 4.9 6.7 + - - +
73A PHE* 3.4 18.5 - - + +
74A ALA* 2.7 33.4 + - - +
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Residues in contact with ALA 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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12A ALA 2.8 15.1 + - - +
13A PHE* 4.0 16.6 - - + -
14A VAL* 2.8 27.8 + - - +
38A VAL* 1.3 75.6 - - - +
40A LEU* 1.3 66.2 + - - +
74A ALA* 4.6 0.2 - - + -
75A GLY 3.5 15.5 - - - +
77A TYR* 4.4 4.9 - - + -
114A VAL* 6.0 0.2 - - + -
118A LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 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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13A PHE* 4.1 5.6 - - - -
14A VAL* 3.6 22.7 - - + +
17A VAL* 3.6 38.6 - - + -
28A ALA* 4.1 14.6 - - + -
38A VAL* 4.6 0.2 - - + -
39A ALA* 1.3 82.7 - - - +
41A GLY* 1.3 56.1 + - - +
42A THR* 4.1 0.9 - - - +
50A PHE* 3.9 11.9 - - + -
73A PHE* 3.6 45.8 - - + -
75A GLY 2.8 11.0 + - - +
76A VAL* 4.5 11.2 - - + -
77A TYR* 2.6 38.2 + - - +
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Residues in contact with GLY 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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13A PHE* 3.9 6.9 - - - -
14A VAL 3.1 11.2 + - - -
16A GLY* 2.9 25.1 + - - -
17A VAL 3.1 9.2 + - - -
40A LEU* 1.3 73.6 - - - +
42A THR* 1.3 61.4 + - - -
43A TRP 4.2 0.2 + - - -
77A TYR 3.1 7.6 - - - -
79A LEU* 3.6 25.4 - - - -
316A NAD 5.5 0.4 + - - -
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Residues in contact with THR 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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17A VAL* 2.5 27.2 + - - +
18A ALA* 3.9 18.2 - - + -
40A LEU* 4.1 2.0 - - - +
41A GLY* 1.3 73.3 - - - -
43A TRP* 1.3 77.7 + - - +
44A PRO* 3.0 4.9 - - - +
46A VAL 4.1 4.0 - - - +
47A LEU* 3.6 33.0 - - + +
50A PHE* 3.4 17.8 - - + -
76A VAL* 3.9 6.1 - - - +
77A TYR 2.7 10.3 + - - -
78A PRO* 3.6 5.9 - - - +
79A LEU* 3.1 17.5 + - - +
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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