Contacts of the strand formed by residues 31 - 37 (chain D) in PDB entry 1J8H
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
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Residue Dist Surf HB Arom Phob DC
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77B THR* 3.2 37.4 + - + +
309C VAL* 6.1 1.1 - - + -
29D PRO* 3.1 31.4 - - + +
30D PRO* 1.3 78.4 - - - +
32D LEU* 1.3 61.5 + - - +
33D PHE* 3.2 16.0 - - + -
49D TYR 3.5 15.5 - - - +
50D THR* 3.8 22.2 - - - -
51D SER* 5.0 0.9 - - - -
92D VAL* 3.4 1.8 - - - +
93D SER 2.9 38.2 + - - +
94D GLU 3.5 14.1 - - - -
95D SER 3.2 24.5 - - - +
96D PRO* 3.4 43.7 - - + +
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Residues in contact with LEU 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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3D VAL* 4.6 4.7 - - + -
22D CYS* 4.8 0.9 - - - -
24D TYR* 3.8 35.7 - - + -
30D PRO* 4.8 2.0 - - + -
31D TYR* 1.3 76.0 - - - +
33D PHE* 1.3 68.0 + - - +
48D LYS* 3.3 4.2 - - - +
49D TYR* 3.0 35.7 + - + +
66D PHE* 3.5 39.0 - - + -
73D PHE* 3.6 37.9 - - + -
90D CYS* 4.7 6.1 - - - -
91D ALA 3.2 12.8 - - - +
92D VAL* 4.1 11.2 - - + -
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Residues in contact with PHE 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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31D TYR* 3.2 30.5 - - + -
32D LEU* 1.3 78.4 - - - +
34D TRP* 1.3 63.2 + - - +
35D TYR* 3.7 32.8 - + + -
45D LEU* 4.6 7.2 - - + -
47D LEU 3.8 6.5 - - - +
48D LYS* 4.0 26.0 - - + -
49D TYR 6.0 0.2 - - - -
89D PHE 3.7 0.3 - - - +
90D CYS* 3.3 7.5 - - - -
91D ALA* 2.7 49.9 + - + +
93D SER* 3.7 17.0 - - - -
96D PRO 5.4 1.8 - - - -
97D PHE* 4.3 5.4 - - - -
98D GLY* 3.3 36.3 - - - -
104D LEU* 3.8 11.0 - - + -
105E GLY* 6.1 0.9 - - - -
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Residues in contact with TRP 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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5D GLN* 3.6 29.2 - - - -
20D LEU* 3.5 30.1 - - + -
21D ARG 3.9 5.6 - - - -
22D CYS* 3.4 20.6 - - + -
33D PHE* 1.3 73.9 - - - +
35D TYR* 1.3 56.4 + - - +
45D LEU* 3.7 2.4 - - - +
46D LEU* 2.7 42.5 + - + +
47D LEU* 3.0 27.7 + - + +
64D ALA* 4.2 1.8 - - + +
73D PHE* 2.8 49.8 + + - -
74D HIS 4.2 0.2 - - - -
75D LEU* 3.5 33.9 - - + +
88D TYR* 3.9 15.5 - - + -
89D PHE 3.4 20.4 - - - -
90D CYS* 3.8 13.9 - - + -
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Residues in contact with TYR 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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33D PHE* 3.7 29.1 - - + -
34D TRP* 1.3 78.8 - - - +
36D VAL* 1.3 59.7 + - - +
43D LEU* 4.1 29.8 - - + -
44D GLN* 3.1 20.6 - - - -
45D LEU* 3.6 27.7 - - + +
46D LEU* 5.0 0.9 - - - -
88D TYR* 3.4 7.2 - - - +
89D PHE* 2.6 44.7 + - + +
91D ALA* 4.7 2.0 - - + -
98D GLY 5.6 0.2 + - - -
104D LEU* 4.0 24.5 - - + +
106D PHE* 3.9 16.6 - + - -
105E GLY* 5.8 0.3 - - - -
106E TYR* 4.2 17.8 + - - +
108E PHE* 4.0 19.1 - + - -
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Residues in contact with VAL 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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35D TYR* 1.3 75.2 - - - +
37D GLN* 1.3 65.1 + - - +
38D TYR* 3.9 30.8 + - + +
42D GLY 3.9 1.6 - - - +
43D LEU* 3.5 2.9 - - - -
44D GLN* 2.8 56.7 + - + +
46D LEU* 4.0 18.8 - - + -
60D ASN* 5.0 0.2 - - - +
86D ALA* 3.8 14.4 - - + -
87D GLU 3.5 4.0 - - - +
88D TYR* 3.6 35.9 - - + -
89D PHE* 5.4 0.4 - - - -
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Residues in contact with GLN 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 VAL* 1.3 75.5 - - - +
38D TYR* 1.3 66.9 + - - +
39D PRO* 3.7 1.2 - - - +
41D GLN 3.0 27.6 + - - +
42D GLY* 4.2 8.7 - - - -
43D LEU* 3.7 24.4 - - + +
86D ALA* 3.4 4.0 - - - +
87D GLU* 2.8 39.9 + - + +
89D PHE* 3.9 12.5 - - + -
37E GLN* 3.0 31.2 + - - -
91E LEU* 5.8 0.6 - - - +
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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