Contacts of the strand formed by residues 517 - 524 (chain F) in PDB entry 4R8A
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 517 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481F CYS* 4.3 8.6 + - - -
483F PRO* 3.3 32.9 - - - +
486F HIS* 4.5 5.5 - - - -
511F PHE* 3.7 0.7 - - - -
512F TRP* 2.8 35.4 + - + -
515F GLN* 3.3 12.2 - - + +
516F ARG* 1.3 82.4 + - - +
518F TYR* 1.3 91.2 + - - +
519F ARG* 3.6 36.1 - - - +
545F GLU 6.0 0.2 + - - -
547F PRO* 4.4 13.6 - - - +
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Residues in contact with TYR 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F CYS* 4.3 4.4 - - + +
482F LEU* 3.8 18.8 - - + -
483F PRO* 3.5 17.9 - - + -
486F HIS* 2.8 24.2 + - - -
490F TRP* 3.4 18.1 - + - -
509F ILE* 4.5 4.0 - - + -
510F GLN 3.4 6.5 - - - +
511F PHE* 3.8 26.2 - - + -
517F ARG* 1.3 106.5 + - - +
519F ARG* 1.3 77.7 + - - +
520F MET* 3.5 28.0 - - + -
546F MET* 3.7 4.6 - - + +
547F PRO* 3.2 41.7 - - + +
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Residues in contact with ARG 519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F GLN* 2.9 52.4 + - - +
512F TRP* 3.2 46.5 - - - +
515F GLN* 3.6 22.0 - - - +
517F ARG* 3.6 24.4 - - - +
518F TYR* 1.3 78.2 - - - +
520F MET* 1.3 60.3 + - - +
521F VAL* 4.9 1.8 - - + -
547F PRO* 3.5 21.5 - - + +
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Residues in contact with MET 520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390F ILE* 4.4 8.3 - - + -
482F LEU* 4.9 1.8 - - + -
490F TRP* 3.7 24.7 - - + -
505F LEU* 4.8 7.4 - - - -
506F PRO* 3.5 28.1 - - + +
508F LEU 3.4 2.9 - - - +
509F ILE* 3.4 37.5 - - + -
518F TYR* 3.5 26.7 - - + -
519F ARG* 1.3 74.9 - - - +
521F VAL* 1.3 62.6 + - - +
541F CYS* 5.2 3.8 - - - -
547F PRO 2.9 11.9 + - - +
548F VAL* 3.2 26.3 - - + +
549F ALA 3.1 23.6 + - - -
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Residues in contact with VAL 521 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F LEU* 5.4 5.8 - - + -
375F LEU* 4.7 12.1 - - + -
506F PRO* 3.6 5.2 - - - -
507F ASP* 3.4 1.4 + - - +
508F LEU* 2.7 54.3 + - + +
510F GLN* 4.3 21.1 - - + +
519F ARG* 4.8 2.5 - - + +
520F MET* 1.3 81.9 - - - +
522F GLU* 1.3 62.1 + - - +
523F VAL* 4.2 6.1 - - + -
549F ALA* 3.2 23.6 - - + +
551F CYS* 3.5 32.3 - - + +
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Residues in contact with GLU 522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F LEU 4.0 0.9 - - - +
506F PRO* 3.3 20.7 - - + +
507F ASP* 2.8 50.9 + - - +
521F VAL* 1.3 74.2 - - - +
523F VAL* 1.3 63.0 + - - +
524F LYS* 3.1 28.8 + - - -
530F LEU* 4.0 14.8 - - + -
534F GLN* 3.8 18.1 + - + +
538F LEU* 5.3 7.6 - - + -
549F ALA 3.2 6.9 + - - +
550F VAL* 3.4 10.0 - - + +
551F CYS 2.9 19.4 + - - -
5G A 2.9 15.4 + - - -
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Residues in contact with VAL 523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F VAL* 4.0 7.4 - - + -
368F GLU* 3.5 44.5 - - + +
371F VAL* 3.7 39.5 - - + -
507F ASP* 3.0 18.5 + - - +
508F LEU* 3.8 21.8 - - + -
521F VAL* 4.2 3.8 - - + -
522F GLU* 1.3 85.5 - - - +
524F LYS* 1.3 66.2 + - - +
551F CYS* 3.2 17.7 - - + +
553F VAL* 5.3 0.7 - - + -
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Residues in contact with LYS 524 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F VAL* 4.4 3.6 - - - -
368F GLU* 5.2 0.7 - - - +
522F GLU* 3.1 14.8 + - - -
523F VAL* 1.3 80.2 - - - +
525F GLY* 1.3 64.8 + - - +
528F ASP* 2.9 48.4 + - - +
529F ARG 3.2 25.0 + - - +
530F LEU* 3.6 17.9 - - - +
531F GLN* 4.4 0.4 - - - +
534F GLN* 2.9 21.0 + - - -
550F VAL* 4.4 9.6 - - + -
551F CYS 2.8 11.6 + - - +
552F TYR* 3.8 25.6 - - + +
553F VAL* 3.0 26.2 + - - +
5G A 3.0 13.1 + - - -
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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