Contacts of the strand formed by residues 42 - 46 (chain D) in PDB entry 2JG3
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 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D GLY 4.7 3.6 - - - +
41D GLY* 1.3 74.1 - - - -
43D VAL* 1.3 59.4 + - - +
66D ARG* 3.7 39.7 - - + +
95D PRO* 4.9 3.6 + - - +
97D GLU* 2.8 61.4 + - - +
98D ALA 2.9 16.4 + - - -
99D PHE* 3.7 33.4 - - + -
100D ASP* 2.8 36.0 + - - +
101D LEU 3.1 10.2 + - - +
155D LYS* 3.7 13.2 - - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ALA* 4.1 20.9 - - + -
41D GLY 4.0 2.2 - - - +
42D ARG* 1.3 76.1 - - - +
44D LEU* 1.3 56.2 + - - +
54D LEU* 4.1 10.7 - - + +
57D PHE* 4.2 13.5 - - + -
65D TYR* 3.9 25.8 - - + -
66D ARG 2.8 14.2 + - - +
67D PHE* 3.6 10.9 - - + -
68D VAL* 2.8 33.4 + - - +
99D PHE* 4.2 2.2 - - - -
101D LEU* 3.3 15.9 - - + +
103D LEU* 3.7 26.2 - - + -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 1.3 73.4 - - - +
45D GLU* 1.3 66.2 + - - +
46D PRO* 3.6 8.2 - - + +
54D LEU* 4.3 0.2 - - - -
68D VAL* 3.2 24.9 - - + +
70D VAL* 3.7 28.5 - - + -
90D PHE* 3.8 17.7 - - + -
93D TRP* 3.8 22.4 - - + -
99D PHE* 3.7 25.3 - - + -
101D LEU 2.8 12.3 + - - +
102D ILE* 3.3 23.4 - - + -
103D LEU* 2.9 31.6 + - - +
153D LEU* 4.2 1.6 - - + -
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 1.3 74.1 - - - +
46D PRO* 1.3 73.5 - - - +
47D ALA 4.5 2.1 - - - +
48D CYS* 3.3 25.6 - - + +
51D GLY* 3.2 13.0 - - - -
52D PRO* 3.4 19.1 - - - +
53D PHE* 3.0 42.5 + - + -
54D LEU* 3.2 25.3 + - + +
68D VAL 2.8 9.9 + - - -
69D GLY* 3.4 0.3 - - - -
70D VAL 3.1 22.3 + - - -
103D LEU* 3.4 12.8 - - + +
104D GLY* 4.6 1.5 - - - -
105D ASN 5.5 0.3 + - - -
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Residues in contact with PRO 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.6 9.0 - - + +
45D GLU* 1.3 90.2 - - - +
47D ALA* 1.3 73.4 + - - +
48D CYS 3.4 0.2 + - - -
70D VAL* 4.0 5.2 - - + +
90D PHE* 3.7 46.2 - - + -
102D ILE* 3.4 25.1 - - + -
103D LEU 3.4 13.9 - - - +
104D GLY* 4.8 0.4 - - - -
105D ASN 4.7 9.2 + - - +
106D PRO* 5.7 0.2 - - - +
146D PHE* 4.1 8.1 - - + -
162D PHE* 3.9 13.9 - - + -
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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