Contacts of the strand formed by residues 513 - 519 (chain O) in PDB entry 5I2D
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 513 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15O PRO* 4.9 6.4 - - - +
98O PRO* 3.7 29.2 - - + -
99O ALA 3.6 5.2 - - - +
100O ALA* 4.0 15.3 - - + -
112O ILE* 3.8 18.2 - - + -
458O ALA* 4.0 15.3 - - + +
461O ILE* 3.9 11.2 - - + -
462O GLN* 3.8 27.3 + - + +
465O LEU* 3.6 27.8 - - + -
510O GLU 3.0 20.9 + - - +
511O TRP* 3.0 8.1 - - - +
512O MET* 1.3 85.5 - - - +
514O LEU* 1.3 63.1 + - - +
515O GLU 3.9 1.4 + - - -
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Residues in contact with LEU 514 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096N ALA* 3.7 27.4 - - + -
12O LEU* 6.4 0.2 - - + -
13O ALA 5.1 2.0 - - - +
15O PRO* 5.6 1.6 - - + -
18O ILE* 4.4 14.4 - - + -
95O LEU* 4.2 2.6 - - - +
98O PRO* 3.4 5.0 - - - +
99O ALA* 2.6 46.9 + - + +
101O HIS* 4.2 19.1 - - + -
511O TRP 4.1 15.3 - - - +
513O ILE* 1.3 73.2 - - - +
515O GLU* 1.3 60.0 + - - +
516O ALA 4.3 7.4 - - - +
517O VAL* 4.4 20.9 - - + -
518O PRO* 5.2 4.0 - - + -
578O VAL* 4.5 7.0 - - + -
582O LEU* 4.1 28.5 - - + -
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Residues in contact with GLU 515 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PRO* 4.2 21.8 - - + +
16O GLU* 5.5 1.0 - - - +
19O ARG* 3.4 23.3 + - - +
94O GLU* 4.0 4.9 - - - +
95O LEU* 3.1 40.0 + - - +
98O PRO* 4.4 15.2 - - + +
462O GLN* 2.6 35.5 + - - +
466O LYS* 4.3 8.8 + - - -
513O ILE 3.9 1.2 + - - +
514O LEU* 1.3 75.1 - - - +
516O ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 516 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PRO* 4.2 6.9 - - + +
18O ILE* 3.3 36.4 - - + +
19O ARG* 3.9 38.1 - - + +
92O HIS* 4.0 7.4 - - + -
93O ILE 3.4 4.9 - - - -
94O GLU* 3.9 6.9 + - - +
514O LEU* 4.3 4.0 - - - +
515O GLU* 1.3 82.7 + - - +
517O VAL* 1.3 61.5 + - - +
518O PRO* 3.7 0.7 - - - +
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Residues in contact with VAL 517 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N ALA 5.3 2.0 - - - +
18O ILE* 4.3 1.8 - - - -
92O HIS* 3.3 1.4 - - - -
93O ILE* 2.9 40.4 + - + +
95O LEU* 3.7 33.9 - - + -
514O LEU* 4.4 20.0 - - + -
516O ALA* 1.3 75.0 - - - +
518O PRO* 1.3 79.8 - - + +
519O VAL* 4.0 1.7 - - - +
544O TYR* 5.0 2.0 - - + -
547O LEU* 4.2 13.5 - - + -
578O VAL* 4.7 8.1 - - + -
581O LEU* 3.9 25.1 - - + -
582O LEU* 5.5 2.5 - - + -
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Residues in contact with PRO 518 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093N GLN 3.3 27.4 - - - +
1094N ALA* 3.9 12.8 - - - +
1096N ALA* 4.1 13.9 - - + +
18O ILE* 3.8 31.8 - - + -
21O TRP* 4.7 2.5 - - + -
90O MET* 3.7 14.1 - - + -
91O GLY 3.8 6.1 - - - +
514O LEU* 5.2 3.6 - - + -
516O ALA 3.7 7.2 - - - +
517O VAL* 1.3 102.7 - - + +
519O VAL* 1.3 60.7 + - - +
520O LEU 4.1 0.2 - - - -
544O TYR* 3.3 12.8 + - - -
582O LEU* 6.3 0.4 - - + -
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Residues in contact with VAL 519 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O VAL* 4.5 9.6 - - + -
44O LEU* 4.6 9.4 - - + -
50O PHE* 4.0 15.7 - - + -
90O MET* 3.5 10.9 - - - +
91O GLY* 2.9 42.5 + - - -
92O HIS* 3.8 11.2 - - - +
93O ILE* 3.7 35.7 - - + -
517O VAL 4.0 0.2 - - - +
518O PRO* 1.3 78.0 - - - +
520O LEU* 1.3 76.9 + - - +
525O ARG* 4.0 9.9 - - - +
544O TYR* 3.6 14.1 - - + -
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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