Contacts of the strand formed by residues 46 - 53 (chain A) in PDB entry 4JGN
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 VAL 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A MET* 3.7 31.4 - - + -
41A TRP 4.0 0.7 - - - +
42A GLY* 3.3 2.4 - - - -
43A PHE* 2.8 35.8 + - - +
45A LYS* 1.3 88.3 - - + +
47A VAL* 1.3 61.9 + - - +
48A PHE* 3.6 27.3 - - + -
80A PHE* 3.5 29.6 - - + -
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Residues in contact with VAL 47 (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 MET* 5.4 2.4 - - - +
40A SER* 3.9 17.0 - - - +
41A TRP 3.4 12.6 - - - +
42A GLY* 4.2 8.5 - - - -
44A GLY 5.5 1.6 - - - +
45A LYS 3.8 9.9 + - - +
46A VAL* 1.3 82.9 - - - +
48A PHE* 1.3 75.3 + - - +
49A LYS* 4.0 27.2 + - + +
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Residues in contact with PHE 48 (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 MET* 4.0 28.3 - - + -
5A THR 3.7 22.4 - - - -
6A SER* 3.9 1.1 - - - -
7A PRO* 3.4 19.7 - - + -
8A PHE* 3.5 18.2 - - + -
40A SER* 3.1 4.9 - - - -
41A TRP 2.9 41.2 + - - +
43A PHE* 3.8 26.2 - + - -
46A VAL* 3.6 26.0 - - + -
47A VAL* 1.3 77.6 - - - +
49A LYS* 1.3 61.4 + - - +
76A ALA* 5.2 0.2 - - + -
80A PHE* 4.3 8.5 - + - -
301A SO4 3.5 35.0 - - - +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.9 1.1 - - - -
12A ASP* 4.1 5.1 - - - +
39A GLU 3.4 8.5 - - - +
40A SER* 4.0 11.9 - - - -
47A VAL* 4.0 24.7 + - + +
48A PHE* 1.3 79.7 - - - +
50A ARG* 1.3 86.5 + - - +
301A SO4 4.6 1.9 + - - -
505E C 4.6 21.4 + - - +
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Residues in contact with ARG 50 (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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6A SER* 3.5 10.5 + - - -
8A PHE* 3.5 38.2 + - + +
10A LEU 2.7 24.4 + - - +
11A PRO* 3.7 5.7 - - - +
12A ASP* 3.4 35.3 - - - +
38A LYS* 3.3 4.5 - - - +
39A GLU* 2.9 44.2 + - + +
49A LYS* 1.3 91.7 + - - +
51A TYR* 1.3 59.6 + - - +
52A LEU* 4.1 18.6 + - + -
67A SER* 5.8 0.4 - - - -
301A SO4 2.8 47.0 + - - -
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Residues in contact with TYR 51 (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 ASP* 2.8 6.5 + - - -
13A GLU* 2.8 34.6 + - - +
14A SER* 3.6 22.4 - - - +
15A PRO* 3.7 22.9 - - + -
35A LEU* 3.5 3.1 + - + +
36A GLY* 3.0 41.3 + - - -
37A PHE 3.4 5.8 - - - -
38A LYS* 3.4 34.8 - - + +
50A ARG* 1.3 73.7 - - - +
52A LEU* 1.3 67.0 + - - +
53A ARG* 4.0 11.2 - - - -
503E U 2.7 49.9 + - - -
504E G 3.4 13.2 - - - +
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Residues in contact with LEU 52 (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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10A LEU* 4.3 18.6 - - + -
11A PRO 3.6 21.8 - - - +
13A GLU* 3.5 13.5 - - - +
36A GLY* 3.1 0.9 - - - -
37A PHE* 2.9 59.1 + - + -
39A GLU* 3.4 14.4 - - - +
50A ARG* 4.1 13.4 - - + -
51A TYR* 1.3 87.8 - - - +
53A ARG* 1.3 63.0 + - - +
63A ARG* 4.8 0.2 - - - +
64A VAL* 4.1 9.9 - - + -
67A SER* 3.4 32.5 - - - +
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Residues in contact with ARG 53 (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 GLU* 2.7 57.1 + - + +
14A SER 4.0 1.6 + - - -
15A PRO* 3.5 18.0 - - - +
19A GLU* 2.7 45.8 + - - -
35A LEU* 3.4 28.5 - - - +
51A TYR* 4.0 10.9 - - - -
52A LEU* 1.3 72.8 - - - +
54A TYR* 1.3 60.9 + - - +
60A SER* 4.0 2.8 + - - -
63A ARG* 2.9 21.3 + - - +
64A VAL* 3.4 7.8 - - - +
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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