Contacts of the strand formed by residues 58 - 67 (chain D) in PDB entry 5JCZ
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 LYS 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ASP* 3.5 33.8 + - + +
10D TYR* 4.1 16.6 + - + -
54D GLN* 3.3 9.3 - - - -
55D VAL 2.9 33.9 + - - +
56D ASP 3.9 3.8 - - - +
57D GLY* 1.3 85.8 - - - +
59D THR* 1.3 60.7 + - - +
60D ILE* 3.5 2.8 + - + +
173D TYR* 3.5 35.0 - - + +
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Residues in contact with THR 59 (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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7D GLU 3.5 21.6 + - - +
8D TYR* 3.7 14.3 - - + +
9D ASP* 2.7 44.9 + - - +
10D TYR 3.2 5.7 + - - -
52D SER* 4.1 20.9 - - - -
53D ILE 3.6 3.6 - - - +
54D GLN* 2.8 25.3 + - - +
57D GLY 4.3 0.6 + - - -
58D LYS* 1.3 69.8 - - - +
60D ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 60 (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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10D TYR* 3.7 19.7 - - + +
12D PHE* 3.5 44.9 - - + -
51D ARG 3.8 0.3 - - - +
52D SER* 3.2 3.3 - - - -
53D ILE* 2.8 50.2 + - + +
55D VAL* 3.6 33.0 - - + -
58D LYS 4.3 4.3 - - - +
59D THR* 1.3 75.0 - - - +
61D LYS* 1.3 67.0 + - - +
62D ALA 3.6 1.4 + - - +
169D LEU* 4.1 13.5 - - + +
173D TYR* 3.7 21.1 - - + -
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Residues in contact with LYS 61 (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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1719C TYR* 5.0 5.1 + - - -
1723C GLN* 4.3 17.8 - - - +
6D ASP* 6.3 0.4 - - - +
8D TYR* 3.6 40.5 + - + -
10D TYR 2.8 16.8 + - - +
11D LEU* 3.4 20.5 - - + +
12D PHE 3.0 26.0 + - - -
50D THR* 4.0 29.8 - - - -
51D ARG 3.8 4.0 - - - +
52D SER* 3.7 17.7 - - - +
59D THR 4.0 1.0 + - - -
60D ILE* 1.3 72.1 - - - +
62D ALA* 1.3 66.1 + - - +
63D GLN* 6.1 0.7 - - - +
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Residues in contact with ALA 62 (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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12D PHE 3.7 6.1 - - - +
14D VAL* 5.3 1.8 - - + -
31D PHE* 4.5 3.8 - - + -
49D ALA 3.8 0.2 - - - +
50D THR* 3.1 9.7 - - - -
51D ARG 2.8 38.3 + - - +
60D ILE* 3.6 2.4 + - - +
61D LYS* 1.3 69.7 - - - +
63D GLN* 1.3 60.7 + - - +
64D ILE* 3.7 21.1 + - + +
165D PHE* 5.8 0.2 - - + -
169D LEU* 3.7 36.6 - - + -
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Residues in contact with GLN 63 (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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1632C THR 5.8 1.2 + - - -
1633C ILE* 5.0 6.2 - - - +
1719C TYR* 3.6 34.0 + - + -
11D LEU* 4.0 33.5 - - + +
12D PHE 2.9 13.2 + - - +
13D LYS* 3.3 15.7 - - - +
14D VAL 2.9 23.2 + - - +
48D PHE* 5.6 2.2 - - + -
49D ALA 4.0 2.0 - - - -
50D THR* 4.2 15.3 - - + -
61D LYS* 3.5 2.4 + - - +
62D ALA* 1.3 69.9 - - - +
64D ILE* 1.3 61.9 + - - +
65D TRP* 2.8 36.0 + - + +
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Residues in contact with ILE 64 (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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14D VAL* 3.2 16.4 - - + +
16D LEU* 3.9 26.2 - - + -
28D LEU* 3.8 22.4 - - + +
31D PHE* 3.5 26.9 - - + -
32D THR* 3.9 15.0 - - + -
48D PHE* 3.5 6.1 - - - +
49D ALA 2.9 35.2 + - - +
51D ARG 5.5 0.2 - - - +
62D ALA* 4.1 15.0 - - + +
63D GLN* 1.3 74.7 - - - +
65D TRP* 1.3 64.6 + - - +
165D PHE* 3.5 28.9 - - + -
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Residues in contact with TRP 65 (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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1633C ILE* 3.9 39.7 - - + -
1715C MET* 3.6 24.2 - - + -
13D LYS* 3.4 42.5 - - + +
14D VAL 2.7 12.7 + - - +
15D VAL* 3.9 6.5 - - + -
16D LEU* 3.1 32.6 + - - +
46D VAL* 3.9 10.1 - - + -
47D GLU 3.6 4.0 - - - +
48D PHE* 3.6 29.2 - + - -
63D GLN* 2.8 39.9 + - + +
64D ILE* 1.3 79.3 - - - +
66D ASP* 1.3 61.7 + - - +
79D ALA* 3.7 11.2 - - + -
80D TYR* 3.5 23.3 - + + -
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Residues in contact with ASP 66 (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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16D LEU* 3.9 12.0 - - + +
24D LYS* 3.8 17.0 - - - +
25D SER* 2.6 35.5 + - - -
28D LEU* 3.7 21.9 - - + +
43D THR* 3.6 9.7 + - - +
45D GLY 4.0 0.2 - - - +
46D VAL* 3.3 2.4 - - - +
47D GLU* 2.7 49.1 + - + +
65D TRP* 1.3 76.8 - - - +
67D THR* 1.3 78.9 + - - +
80D TYR* 3.4 5.3 - - - -
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Residues in contact with THR 67 (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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16D LEU 4.6 2.3 + - - +
24D LYS* 3.2 22.2 - - - -
43D THR* 4.0 10.2 + - - -
45D GLY* 2.7 24.1 + - - -
46D VAL* 4.0 5.5 - - - +
66D ASP* 1.3 80.0 + - - +
68D ALA* 1.3 67.8 + - - +
70D GLN* 5.3 2.9 + - - -
72D ARG* 3.6 32.7 + - - +
80D TYR* 3.4 38.0 + - + +
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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