Contacts of the strand formed by residues 499 - 507 (chain A) in PDB entry 5FO9
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 ARG 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PRO* 5.1 1.3 - - - -
35A ARG* 4.5 8.3 - - - +
39A GLU 4.6 13.5 - - - +
40A GLU* 4.2 15.0 - - - +
41A THR* 6.1 0.4 - - - +
154A HIS* 5.7 2.9 - - - -
155A LYS* 3.6 41.1 - - - +
495A MET* 3.3 13.8 - - - +
496A ASN* 3.0 43.0 + - - +
497A LYS* 3.2 25.0 - - - +
498A GLY* 1.3 79.3 - - - +
500A LEU* 1.3 73.0 + - - +
501A LEU* 3.7 33.4 + - - +
524A ASP* 4.6 9.9 + - - +
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Residues in contact with LEU 500 (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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29A ILE 4.4 7.9 - - - +
31A PRO* 4.5 10.8 - - + -
40A GLU* 4.8 2.8 + - - -
41A THR* 3.3 57.7 + - + +
43A VAL* 3.9 24.7 - - + -
493A LEU* 4.1 21.5 - - + -
494A ILE 4.5 5.4 - - - +
495A MET* 3.6 29.2 - - + -
499A ARG* 1.3 85.0 + - - +
501A LEU* 1.3 64.2 + - - +
502A LYS* 3.5 6.3 - - - +
503A ALA* 5.8 0.9 - - + -
644A LEU* 4.2 5.6 - - + -
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Residues in contact with LEU 501 (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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494A ILE* 2.8 18.1 + - + +
496A ASN* 3.9 19.7 - - + +
499A ARG* 3.6 35.0 + - - +
500A LEU* 1.3 74.4 - - - +
502A LYS* 1.3 65.5 + - + +
524A ASP* 3.5 34.8 - - + +
525A PHE* 3.7 42.0 - - + -
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Residues in contact with LYS 502 (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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492A TYR* 4.4 19.8 + - + +
493A LEU* 3.5 3.8 - - - +
494A ILE* 2.9 50.4 + - + +
500A LEU* 3.5 6.8 - - - +
501A LEU* 1.3 81.9 - - + +
503A ALA* 1.3 82.2 + - - +
504A GLY* 5.7 0.2 - - - -
519A LEU* 5.5 9.1 - - + +
525A PHE* 6.2 3.1 - - + -
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Residues in contact with ALA 503 (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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43A VAL* 3.7 35.2 - - + -
83A MET* 3.9 14.3 - - + +
85A ASN* 5.8 4.3 - - - +
491A THR* 6.2 0.7 - - + -
492A TYR* 3.5 9.6 - - - +
493A LEU* 4.5 5.2 - - + -
500A LEU* 5.8 0.9 - - + -
502A LYS* 1.3 89.8 - - - +
504A GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 504 (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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83A MET* 3.6 12.2 - - - +
491A THR* 3.6 7.8 - - - +
492A TYR* 2.9 54.2 + - - +
502A LYS* 5.7 0.4 - - - -
503A ALA* 1.3 75.0 - - - +
505A ARG* 1.3 64.6 + - - +
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Residues in contact with ARG 505 (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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45A GLU* 2.6 33.1 + - - +
46A ALA 4.8 3.2 + - - -
47A HIS* 3.6 15.6 + - - -
80A THR 5.6 0.2 - - - +
81A ASN* 3.0 47.7 + - + +
82A HIS 4.1 2.6 + - - -
83A MET* 3.7 24.0 - - + +
489A TYR* 3.4 46.4 + - + -
490A TYR 3.5 3.8 - - - -
491A THR* 2.7 25.3 + - - +
492A TYR* 3.4 6.7 + - - -
504A GLY* 1.3 70.9 - - - -
506A GLN* 1.3 61.8 + - - +
507A VAL* 3.8 9.9 + - + +
517A LEU* 5.8 0.7 - - - +
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Residues in contact with GLN 506 (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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475A PHE* 4.5 7.6 - - + -
489A TYR* 3.4 1.9 - - - -
490A TYR* 2.9 49.0 + - + +
492A TYR* 4.0 13.9 - - + -
505A ARG* 1.3 71.6 - - - +
507A VAL* 1.3 99.0 + - - +
515A VAL* 4.1 25.9 - - + +
516A VAL 4.2 12.8 + - - +
517A LEU* 3.5 31.8 - - + +
518A PRO* 5.4 0.7 - - - +
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Residues in contact with VAL 507 (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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81A ASN* 5.3 12.1 - - - +
488A ARG 3.7 7.6 - - - +
489A TYR* 4.3 4.3 - - + +
505A ARG* 3.8 10.2 + - + +
506A GLN* 1.3 108.3 + - - +
508A ARG* 1.3 62.1 + - - +
509A GLU* 5.8 2.7 - - + +
512A GLN* 4.6 1.0 - - - +
515A VAL* 4.6 4.9 - - - +
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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