Contacts of the strand formed by residues 556 - 564 (chain A) in PDB entry 5FBQ
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 TRP 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A VAL* 4.3 6.3 - - + -
387A GLU* 3.1 44.3 + - + +
388A VAL 3.5 10.5 - - - -
389A LEU* 3.6 6.7 - - + -
541A VAL* 4.2 13.0 - - + -
544A ILE* 4.6 2.5 - - + -
545A ARG* 3.1 72.8 + - + -
548A SER* 3.9 3.9 + - - -
550A TYR* 3.6 36.8 - - + +
551A GLY* 4.3 6.1 - - - -
553A LEU 3.6 14.7 - - - +
554A PRO 3.1 6.1 - - - +
555A ASN* 1.3 75.1 - - - +
557A ARG* 1.3 74.5 + - - +
558A LEU* 3.8 32.3 - - + -
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Residues in contact with ARG 557 (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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359A PHE* 3.8 30.8 - - + -
387A GLU* 3.8 2.3 - - - -
388A VAL* 3.0 46.1 + - + +
390A GLU* 3.5 34.2 + - + +
545A ARG* 5.3 2.2 - - - +
554A PRO 5.6 1.3 - - - +
555A ASN 4.5 5.6 - - - +
556A TRP* 1.3 90.5 - - - +
558A LEU* 1.3 62.5 + - - +
559A LEU* 5.7 2.6 - - + +
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Residues in contact with LEU 558 (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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367A PRO* 4.5 4.5 - - + -
385A TYR* 4.6 6.7 - - + -
386A VAL 3.3 20.9 - - - +
387A GLU* 3.4 26.5 - - + -
537A TRP* 3.8 35.3 - - + -
540A LYS 5.1 0.2 - - - -
541A VAL* 4.4 19.2 - - + +
544A ILE* 3.6 38.8 - - + -
556A TRP* 3.8 18.1 - - + -
557A ARG* 1.3 75.1 - - - +
559A LEU* 1.3 73.2 + - - +
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Residues in contact with LEU 559 (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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354A LEU* 4.6 16.6 - - + -
356A THR* 6.0 2.0 - - + -
357A ALA* 3.8 28.3 - - + -
359A PHE* 4.2 20.0 - - + -
361A HIS* 3.9 12.8 - - + +
385A TYR* 3.5 6.1 - - - +
386A VAL* 2.7 39.9 + - + +
388A VAL* 3.8 28.7 - - + -
537A TRP* 4.7 2.7 - - - -
557A ARG* 5.7 2.9 - - + +
558A LEU* 1.3 82.9 - - - +
560A SER* 1.3 62.6 + - - +
561A VAL* 5.9 0.2 - - + -
611A GLU* 5.4 7.4 - - - +
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Residues in contact with SER 560 (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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354A LEU* 5.3 0.4 - - - -
356A THR* 4.8 0.7 - - - +
383A LEU* 5.3 2.7 - - - -
384A ILE 3.4 12.3 - - - -
385A TYR* 4.3 16.6 - - - +
386A VAL* 4.6 1.3 - - - +
537A TRP* 4.5 12.2 - - - -
559A LEU* 1.3 80.2 - - - +
561A VAL* 1.3 70.1 + - - +
611A GLU* 4.2 8.7 - - - +
612A PRO* 3.1 35.0 + - - +
614A VAL* 4.9 2.8 - - - +
801A 5W6 4.8 4.0 - - - +
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Residues in contact with VAL 561 (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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317A LEU* 5.9 1.6 - - + -
354A LEU* 3.8 24.0 - - + -
356A THR* 3.3 33.7 - - + +
382A TYR 4.0 0.2 - - - +
383A LEU* 3.8 1.0 - - - -
384A ILE* 3.1 50.3 + - + +
386A VAL* 5.0 0.9 - - + +
559A LEU* 5.9 0.2 - - + -
560A SER* 1.3 81.5 - - - +
562A ILE* 1.3 65.3 + - - +
563A VAL* 4.0 6.6 + - + -
609A MET* 4.4 22.9 - - + -
610A ILE 3.3 11.7 - - - +
612A PRO* 3.9 2.7 - - - -
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Residues in contact with ILE 562 (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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374A LEU* 3.4 22.2 - - + -
381A PRO* 4.2 11.4 - - + -
382A TYR 3.6 5.6 - - - +
383A LEU* 3.8 22.2 - - + -
561A VAL* 1.3 72.8 - - - +
563A VAL* 1.3 64.4 + - - +
564A LYS* 3.9 7.2 + - + +
609A MET* 3.1 8.8 - - - +
610A ILE* 2.6 49.7 + - + +
612A PRO* 4.1 5.4 - - + -
801A 5W6 3.3 66.4 - - + +
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Residues in contact with VAL 563 (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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317A LEU* 4.4 10.3 - - + +
318A MET* 3.1 35.4 - - + -
380A ALA 4.5 0.2 - - - +
381A PRO* 3.0 23.6 - - - +
382A TYR* 2.8 62.1 + - + +
384A ILE* 4.9 2.7 - - + -
561A VAL* 4.5 16.8 - - + +
562A ILE* 1.3 76.6 - - - +
564A LYS* 1.3 63.1 + - - +
565A CYS* 3.9 3.6 + - + +
608A GLY 4.0 2.2 - - - -
609A MET* 4.7 10.1 - - + +
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Residues in contact with LYS 564 (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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318A MET* 4.3 0.2 - - - +
379A LYS 5.8 0.2 - - - -
381A PRO* 3.9 18.0 - - + +
562A ILE* 4.4 8.3 - - + +
563A VAL* 1.3 74.8 - - - +
565A CYS* 1.3 60.4 + - - +
566A GLY 3.5 1.1 - - - -
567A ASP* 3.2 44.6 + - + +
569A LEU* 3.8 18.2 - - + -
607A SER* 3.2 6.2 - - - -
608A GLY 2.9 45.9 + - - +
610A ILE* 3.8 11.9 - - + -
801A 5W6 2.4 62.3 + - - +
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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