Contacts of the strand formed by residues 59 - 64 (chain A) in PDB entry 4JRI
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 ILE 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.7 29.6 - - + -
25A TYR 3.7 7.9 - - - +
26A LEU* 4.3 0.9 - - + +
27A VAL* 4.0 2.2 - - - -
44A ILE* 3.8 29.2 - - + -
54A VAL* 3.8 18.8 - - + -
55A TYR 3.5 10.3 - - - +
56A LYS* 3.0 20.1 + - - +
58A ALA* 1.3 81.6 - - - +
60A SER* 1.3 63.8 + - - +
61A THR 3.6 13.7 - - - +
62A VAL* 4.0 8.5 - - + -
55B TYR* 3.6 22.3 - - + +
57B HIS* 2.9 25.8 + - - -
58B ALA* 3.8 0.5 - - - +
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Residues in contact with SER 60 (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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25A TYR* 2.8 30.1 + - - +
26A LEU 3.7 12.5 + - - -
27A VAL* 4.0 5.3 - - - +
58A ALA 3.9 1.8 + - - -
59A ILE* 1.3 75.5 - - - +
61A THR* 1.3 64.7 + - - +
26B LEU* 3.9 24.9 - - - +
28B ASN* 4.3 4.4 + - - -
54B VAL* 3.4 7.6 - - - +
55B TYR* 2.9 26.2 + - - +
58B ALA* 3.4 19.7 - - - +
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Residues in contact with THR 61 (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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23A SER 3.8 1.0 - - - +
24A ILE* 3.6 2.4 - - - -
25A TYR* 3.0 41.1 + - + +
59A ILE* 3.6 2.9 - - - +
60A SER* 1.3 90.7 + - - +
62A VAL* 1.3 65.9 + - - +
63A VAL* 3.8 8.2 - - + +
26B LEU* 5.1 2.0 - - + -
32B LEU* 4.5 13.9 - - + -
52B GLN* 2.8 41.6 + - - +
53B MET 3.2 13.3 + - - -
54B VAL* 3.9 7.6 - - - +
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Residues in contact with VAL 62 (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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11A PHE* 3.7 22.2 - - + -
12A LEU* 4.6 7.2 - - + -
15A LEU* 4.3 12.1 - - + -
22A VAL* 4.4 11.4 - - + -
23A SER 3.7 2.9 - - - -
24A ILE* 4.2 21.3 - - + +
36A ILE* 4.7 2.0 - - + -
44A ILE* 4.4 10.5 - - + -
59A ILE* 4.0 17.3 - - + -
61A THR* 1.3 75.4 - - - +
63A VAL* 1.3 63.1 + - - +
64A PRO* 3.7 3.3 - - - +
52B GLN* 3.4 3.3 - - - -
53B MET* 2.9 47.9 + - + +
55B TYR* 4.3 3.8 - - + -
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Residues in contact with VAL 63 (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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22A VAL* 3.5 2.6 - - - -
23A SER* 2.9 39.8 + - - +
25A TYR* 3.9 27.8 - - + +
61A THR* 3.8 8.3 - - + +
62A VAL* 1.3 76.2 - - - +
64A PRO* 1.3 76.3 - - - +
65A SER* 4.6 0.2 - - - -
50B VAL* 4.1 15.3 - - + -
52B GLN* 3.5 31.2 - - + +
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Residues in contact with PRO 64 (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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11A PHE* 4.1 9.0 - - + -
15A LEU* 3.9 26.0 - - + -
20A VAL* 4.6 0.9 - - + -
21A PRO 4.1 6.1 - - - +
22A VAL* 4.3 4.9 - - + -
62A VAL 3.7 6.3 - - - +
63A VAL* 1.3 99.3 - - + +
65A SER* 1.3 63.8 + - - +
66A ARG 3.5 18.5 + - - +
68A VAL* 4.1 8.5 - - + -
50B VAL* 3.6 20.5 - - + +
51B SER 3.3 28.3 - - - +
52B GLN* 4.2 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