Contacts of the strand formed by residues 530 - 538 (chain B) in PDB entry 3FO5
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 SER 530 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B 1PE 3.9 22.7 - - - -
395B LEU* 3.7 10.7 - - - +
507B ALA* 3.6 5.0 - - - +
508B LEU* 2.7 41.0 + - - -
527B THR* 3.0 22.6 + - - -
529B CYS* 1.3 77.1 + - - +
531B GLY* 1.3 56.8 + - - +
547B TYR 3.2 12.3 - - - -
548B ASN* 3.2 16.3 + - - -
549B GLN 4.2 0.2 + - - -
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Residues in contact with GLY 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B LEU* 3.8 6.0 - - - +
506B ILE 3.2 9.2 - - - -
508B LEU* 4.1 13.9 - - - -
530B SER* 1.3 77.7 - - - +
532B PHE* 1.3 66.5 + - - -
545B SER 3.8 0.2 - - - +
546B TYR* 3.3 10.6 - - - -
547B TYR* 2.7 41.1 + - - +
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Residues in contact with PHE 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 1PE 5.1 0.2 - - - -
395B LEU* 3.9 1.2 - - - +
443B LEU* 4.0 39.3 - - + -
446B LEU* 5.3 2.2 - - + -
449B ARG* 3.9 21.5 - - - -
452B TRP* 3.6 37.7 - + - -
504B TYR 3.9 0.2 - - - +
505B VAL* 3.5 2.4 - - - -
506B ILE* 2.8 60.1 + - + +
508B LEU* 5.3 2.9 - - + -
531B GLY* 1.3 77.0 - - - -
533B CYS* 1.3 66.2 + - - +
534B LEU* 4.4 11.2 - - + -
544B VAL* 4.5 4.7 - - + -
545B SER 3.1 14.8 - - - +
546B TYR* 3.8 29.4 - + + -
573B PHE* 5.0 2.5 - + - -
576B CYS* 4.6 5.8 - - - -
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Residues in contact with CYS 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLY* 5.6 0.2 - - - -
395B LEU* 4.2 15.3 - - - -
396B LYS* 5.6 0.7 - - - -
399B VAL* 3.5 29.6 - - - -
503B PRO* 4.1 6.5 - - + -
504B TYR 3.2 6.3 - - - +
505B VAL* 4.3 16.4 - - - -
531B GLY 4.3 0.2 + - - -
532B PHE* 1.3 78.6 - - - +
534B LEU* 1.3 64.6 + - - +
535B TRP* 3.6 28.6 - - + -
543B LYS 3.6 1.6 - - - +
545B SER* 3.0 31.4 + - - -
547B TYR* 4.5 5.5 - - + -
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Residues in contact with LEU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B ALA* 4.1 2.5 - - + +
439B ALA* 3.7 9.9 - - + +
440B PHE* 3.5 42.0 - - + +
443B LEU* 3.9 13.7 - - + -
502B ASP 4.8 0.2 - - - +
503B PRO* 3.2 2.5 - - - +
504B TYR* 2.8 52.3 + - + +
506B ILE* 4.4 9.2 - - + -
532B PHE* 4.4 6.5 - - + -
533B CYS* 1.3 86.3 - - - +
535B TRP* 1.3 61.9 + - - +
542B THR* 3.8 11.9 - - + -
543B LYS 3.1 5.4 - - - -
544B VAL* 3.6 36.8 - - + -
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Residues in contact with TRP 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CL 4.4 2.0 - - - +
481A GLY 3.0 29.6 + - - -
482A HIS* 4.2 8.8 + - - -
483A THR* 5.1 9.2 - - + -
399B VAL* 3.9 19.7 - - + -
436B ALA* 4.6 0.2 - - - -
501B GLY 3.6 23.1 - - - +
502B ASP 5.2 0.4 - - - -
503B PRO* 3.4 19.1 - - + +
533B CYS* 3.6 31.0 - - + -
534B LEU* 1.3 72.8 - - - +
536B ARG* 1.3 64.3 + - - +
537B GLU* 3.5 15.8 - - - +
542B THR* 3.4 5.0 - - - +
543B LYS* 2.9 61.7 + - + -
545B SER* 3.6 21.8 - - - -
547B TYR* 4.2 9.9 - - - -
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Residues in contact with ARG 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ASP* 2.6 39.8 + - - -
436B ALA* 3.9 19.1 - - + +
437B ALA* 4.0 5.9 - - - +
502B ASP 5.6 1.8 + - - -
504B TYR* 3.6 28.3 + - + -
534B LEU 4.1 1.2 + - - -
535B TRP* 1.3 75.2 - - - +
537B GLU* 1.3 63.0 + - - +
538B GLY* 3.9 21.2 + - - +
539B ASP* 5.7 2.8 + - - +
541B LEU 3.9 5.4 - - - +
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B VAL* 4.4 13.4 - - + +
535B TRP* 3.5 22.4 - - - +
536B ARG* 1.3 74.1 - - - +
538B GLY* 1.3 57.7 + - - +
541B LEU* 3.0 29.8 + - + +
542B THR 4.1 1.3 - - - -
543B LYS* 3.5 40.6 - - - +
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Residues in contact with GLY 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ASP* 5.5 0.9 - - - +
536B ARG* 3.6 20.7 + - - +
537B GLU* 1.3 78.1 - - - +
539B ASP* 1.3 68.4 + - - -
540B GLN 3.3 3.3 + - - -
541B LEU* 3.4 17.7 + - - +
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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