Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 4JZJ
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 MET 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.8 20.6 - - + -
22A CYS* 4.3 10.5 - - - +
24A GLY 5.3 1.6 - - - +
27A TYR* 3.3 25.6 - - - +
29A PHE* 4.2 27.8 - - + +
32A TYR* 4.2 0.8 + - - +
33A TYR* 1.3 79.4 - - - +
35A LYS* 1.3 63.4 + - - +
36A TRP* 5.2 2.0 - - - +
50A ASP* 3.2 4.7 - - - +
51A ILE* 2.7 55.0 + - + +
53A PRO* 4.2 10.3 - - + +
79A THR* 3.6 24.9 - - + +
96A CYS* 4.6 3.4 - - + -
97A ALA 3.6 15.9 - - - +
98A ARG* 3.9 7.9 - - - -
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Residues in contact with LYS 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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33A TYR* 4.5 2.5 - - + +
34A MET* 1.3 78.7 - - - +
36A TRP* 1.3 70.0 + - - +
47A TRP* 4.2 5.5 - - - +
49A GLY 3.4 5.2 - - - -
50A ASP* 3.2 26.7 + - - +
96A CYS* 3.2 8.0 - - - +
97A ALA* 2.8 34.4 + - + +
98A ARG 4.3 1.8 - - - -
99A SER* 4.2 11.0 - - - +
104A ALA 2.6 28.8 + - - +
105A SER* 3.4 25.6 + - - +
106A TRP 3.4 19.3 - - - +
107A PHE* 3.8 36.8 - - + -
102B TYR* 6.2 0.8 - - - -
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Residues in contact with TRP 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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6A GLN* 3.4 26.2 - - - -
20A ILE* 3.8 29.4 - - + -
21A SER 4.5 3.1 - - - -
22A CYS* 3.9 9.4 - - + -
34A MET* 5.2 1.3 - - - +
35A LYS* 1.3 79.3 + - - +
37A ALA* 1.3 57.8 + - - +
47A TRP* 3.7 5.9 - - - -
48A MET* 2.7 43.0 + - + +
49A GLY 3.0 11.9 + - - +
70A ILE* 3.9 19.2 - - + +
79A THR* 3.7 45.9 + - + +
80A TYR 4.1 8.4 + - - -
81A LEU* 3.3 37.4 - - + +
94A TYR* 4.4 4.5 - - + -
95A TYR 3.3 22.7 - - - -
96A CYS* 3.8 20.0 - - + +
107A PHE* 4.5 2.2 - - - -
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Residues in contact with ALA 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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36A TRP* 1.3 76.4 - - - +
38A ARG* 1.3 63.1 + - - +
45A LEU* 5.2 3.6 - - + -
46A GLU 3.1 18.8 - - - +
48A MET* 4.0 5.8 - - - -
94A TYR* 3.6 3.6 - - - -
95A TYR* 2.8 33.5 + - - +
107A PHE* 3.6 26.2 - - + -
110A TRP* 4.6 13.7 - - + -
104B PHE* 5.2 2.7 - - + -
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Residues in contact with ARG 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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37A ALA* 1.3 74.1 - - - +
39A GLN* 1.3 61.4 + - - +
40A MET* 3.4 26.3 + - + +
44A GLY 4.0 0.7 - - - +
45A LEU* 3.4 8.5 - - - +
46A GLU* 3.0 62.6 + - + +
48A MET* 4.0 2.6 - - - -
63A LYS* 3.9 18.6 - - - +
64A PHE* 3.6 23.3 - - + -
89A SER* 3.5 22.8 + - - -
90A ASP* 4.2 6.7 + - - +
92A ALA* 3.9 9.6 - - + +
93A MET 3.2 6.1 - - - +
94A TYR* 3.4 46.9 + - + -
95A TYR* 5.2 0.4 - - - -
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Residues in contact with GLN 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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38A ARG* 1.3 74.3 - - - +
40A MET* 1.3 71.0 + - - +
41A PRO* 4.3 1.2 - - - +
43A LYS 4.5 1.4 + - - +
44A GLY 3.9 6.7 - - - +
45A LEU* 3.8 18.8 - - + +
92A ALA* 3.6 3.5 - - - +
93A MET* 2.8 39.2 + - + +
95A TYR* 3.6 17.9 + - + -
44B GLN* 2.9 41.8 + - - -
93B TYR* 2.9 24.9 + - - -
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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