Contacts of the strand formed by residues 31 - 38 (chain D) in PDB entry 5J7C
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 TYR 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASN* 5.8 0.4 - - - -
48B ASP* 2.6 30.9 + - - -
50B SER* 3.1 17.5 + - - -
59B ASN* 3.3 15.8 + - - -
61B ARG* 3.6 22.1 - - - +
62B TRP* 3.8 10.8 - + - -
29D ALA* 4.0 2.7 - - - +
30D THR* 1.3 97.9 - - + +
32D TYR* 1.3 76.3 + - - +
48D PHE* 3.9 10.1 - + + -
49D THR* 3.2 31.4 - - - +
50D MET 4.2 5.8 - - - -
51D PRO* 3.8 14.6 - - + -
75D ALA* 3.8 1.2 - - - -
76D VAL* 2.9 45.0 + - + +
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Residues in contact with TYR 32 (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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23D TRP* 3.5 47.3 - + + +
24D ARG 4.7 2.0 - - - -
25D GLY* 3.2 7.2 - - - -
26D TYR* 2.8 35.8 + + - -
29D ALA* 3.4 28.2 - - + +
31D TYR* 1.3 82.6 - - - +
33D GLY* 1.3 61.9 + - - +
34D ILE* 5.3 0.7 - - + -
48D PHE* 3.2 10.1 - - - +
49D THR* 3.0 40.9 + - + +
53D ASP 4.9 8.3 - - - -
54D LEU* 6.2 1.8 - - + -
56D HIS* 3.7 17.7 - + - -
73D VAL* 4.3 8.3 - - + -
74D TYR 3.3 8.1 - - - +
75D ALA* 3.7 23.6 - - + -
76D VAL* 4.4 0.9 - - - +
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Residues in contact with GLY 33 (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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32D TYR* 1.3 73.2 - - - +
34D ILE* 1.3 61.2 + - - +
47D GLU 3.3 8.1 - - - -
48D PHE* 3.6 12.0 - - - -
72D THR 3.6 0.2 - - - +
73D VAL* 3.3 6.6 - - - +
74D TYR* 2.8 58.2 + - - -
76D VAL* 4.1 3.6 - - - +
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Residues in contact with ILE 34 (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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21D ILE* 3.7 22.4 - - + -
23D TRP* 4.2 7.4 - - + -
32D TYR 4.6 4.9 - - - +
33D GLY* 1.3 77.0 - - - +
35D ILE* 1.3 63.6 + - - +
36D TYR* 4.5 8.6 - - + -
45D VAL 3.5 1.9 - - - +
46D GLN* 3.2 3.5 - - - -
47D GLU* 2.8 50.9 + - + +
48D PHE 5.5 0.4 - - - -
49D THR* 4.0 17.3 - - + -
58D ALA* 3.5 31.4 - - + -
60D ILE* 4.2 17.9 - - + -
71D ILE* 4.5 3.4 - - + -
72D THR 3.3 8.5 - - - +
73D VAL* 4.3 8.7 - - + -
74D TYR* 4.6 0.2 - - - -
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Residues in contact with ILE 35 (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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44C LEU* 4.1 21.1 - - + -
34D ILE* 1.3 77.5 - - - +
36D TYR* 1.3 64.0 + - - +
44D LEU* 3.6 31.6 - - + -
45D VAL 3.2 7.9 - - - +
46D GLN* 3.6 30.7 - - + +
70D THR 3.6 1.7 - - - +
71D ILE* 3.5 1.4 - - - +
72D THR* 2.6 58.3 + - + +
74D TYR* 3.9 19.1 - - + -
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Residues in contact with TYR 36 (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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34D ILE* 4.5 8.7 - - + -
35D ILE* 1.3 77.6 - - - +
37D GLY* 1.3 61.6 + - - +
44D LEU* 4.4 5.4 - - - -
45D VAL* 2.9 66.1 + - + +
47D GLU* 3.1 32.9 + - + -
60D ILE* 3.5 45.0 - - + +
61D SER 4.0 12.4 + - - -
63D LEU* 3.9 17.0 - - + -
69D TYR* 5.0 3.4 - + - -
70D THR 3.2 5.6 - - - -
71D ILE* 3.6 24.0 - - + -
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Residues in contact with GLY 37 (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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36D TYR* 1.3 78.4 - - - +
38D GLU* 1.3 62.6 - - - -
43D SER 4.1 14.6 - - - -
44D LEU* 4.5 8.1 - - - +
69D TYR* 3.3 13.0 - - - -
70D THR* 2.7 34.7 + - - +
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Residues in contact with GLU 38 (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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68A ARG 5.4 1.4 - - - +
70A PRO* 3.4 37.3 - - + +
46C GLN* 4.7 2.8 + - - -
37D GLY* 1.3 71.2 - - - -
39D THR* 1.3 59.0 + - - +
40D GLY 3.1 0.9 + - - -
41D GLY* 2.7 33.1 + - - -
43D SER 4.5 5.2 + - - +
44D LEU* 6.0 0.9 - - - +
67D VAL* 3.3 29.6 - - + +
68D ASP* 3.3 15.8 + - + +
69D TYR* 3.5 10.4 - - + -
70D THR* 5.5 0.2 - - - -
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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