Contacts of the strand formed by residues 51 - 58 (chain B) in PDB entry 1J3R
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 VAL 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.9 11.7 - - + -
26B ARG 3.8 6.5 - - - +
27B ARG* 3.5 34.8 - - + +
50B PRO* 1.3 74.3 - - - +
52B VAL* 1.3 64.6 + - - +
53B TYR 3.8 11.2 - - - +
54B GLU* 3.8 34.8 - - + +
75B TYR* 3.8 24.1 - - + +
84B PHE* 3.9 7.1 - - - -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG 2.8 10.0 + - - +
27B ARG 3.7 4.3 - - - -
28B LEU* 3.7 43.7 - - + +
31B MET* 3.9 11.4 - - - -
35B PHE* 5.1 1.1 - - + -
50B PRO 4.0 1.6 - - - +
51B VAL* 1.3 74.8 - - - +
53B TYR* 1.3 69.9 + - + +
74B LEU* 3.6 7.0 - - + +
75B TYR* 2.8 31.0 + - - +
84B PHE* 3.9 22.2 - - + -
85B MET 3.5 30.3 - - - +
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Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.9 0.2 - - - -
26B ARG* 3.0 68.7 + - + +
31B MET* 4.2 11.7 - - - -
51B VAL* 3.7 0.9 - - - +
52B VAL* 1.3 92.8 - - + +
54B GLU* 1.3 68.1 + - - +
55B VAL* 4.0 17.7 - - + -
72B THR* 4.2 5.2 - - + -
73B VAL 3.2 13.9 - - - +
74B LEU* 3.7 13.7 - - + -
75B TYR* 4.2 2.2 - - - -
85B MET 3.8 7.6 - - - -
86B THR* 3.6 28.9 - - + -
87B LYS* 3.5 12.1 + - - +
601B 6PG 3.2 38.1 + - - -
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS* 3.9 17.0 + - - -
24B SER 3.3 10.1 - - - +
25B VAL* 3.8 19.0 - - + +
51B VAL* 3.8 15.6 - - + +
53B TYR* 1.3 80.3 - - - +
55B VAL* 1.3 64.2 + - - +
56B TYR* 3.6 28.0 + - + +
71B THR 4.0 0.2 - - - +
72B THR* 3.4 3.5 - - - +
73B VAL* 2.8 35.7 + - + +
75B TYR* 2.9 36.0 + - + -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS 3.4 1.1 - - - +
23B LYS* 3.2 6.2 - - - +
24B SER* 2.8 49.4 + - - +
26B ARG* 6.2 0.7 - - + -
53B TYR* 4.0 12.6 - - + -
54B GLU* 1.3 79.2 - - - +
56B TYR* 1.3 69.1 + - - +
57B ALA* 3.9 8.3 - - + -
70B ALA* 3.9 11.7 - - + -
71B THR 3.4 9.6 - - - +
72B THR* 3.9 13.5 - - - +
601B 6PG 3.9 40.2 - - - +
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY 4.0 4.7 - - - -
17B ILE* 3.6 44.2 - - + +
18B ILE* 3.7 18.2 - - + +
21B ALA* 3.8 17.7 - - + -
22B LYS 3.6 3.6 - - - -
23B LYS* 3.8 42.6 + - + -
54B GLU* 3.6 28.2 + - + -
55B VAL* 1.3 72.3 - - - +
57B ALA* 1.3 59.2 + - - +
70B ALA* 3.1 5.0 - - - -
71B THR* 2.9 49.9 + - - +
73B VAL* 4.1 20.8 - - + +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA* 3.8 0.6 - - - +
22B LYS* 2.7 48.1 + - + +
55B VAL* 4.2 8.7 - - + -
56B TYR* 1.3 75.1 - - - +
58B ILE* 1.3 64.7 + - - +
59B GLU* 4.0 22.6 + - + +
69B PHE 4.1 0.9 - - - +
70B ALA* 3.5 19.1 - - + -
153B TYR* 4.5 2.0 - - - +
601B 6PG 5.2 1.1 - - - +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.7 26.5 - - + -
9B VAL* 3.9 14.4 - - + -
18B ILE* 3.9 21.1 - - + -
19B GLU 3.9 11.9 - - - +
20B ASN* 4.3 5.8 - - + +
21B ALA* 3.8 13.5 - - + -
57B ALA* 1.3 78.1 - - - +
59B GLU* 1.3 61.9 + - - +
60B GLN* 4.3 8.9 + - - +
68B ASN* 3.7 2.6 - - - -
69B PHE* 3.1 60.8 + - + -
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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