Contacts of the strand formed by residues 507 - 520 (chain B) in PDB entry 2VXO
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 LEU 507 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470B ALA* 3.4 30.6 + - + +
471B ASP* 5.3 2.3 - - - +
501B ILE* 3.9 25.4 - - + +
502B THR* 4.5 11.4 - - + -
505B HIS* 3.8 19.1 + - + +
506B SER* 1.3 76.5 - - - +
508B ASN* 1.3 68.7 + - - +
532B ILE* 4.3 14.4 - - + -
533B SER 3.4 6.5 - - - +
534B SER* 3.6 26.0 - - - -
543B LEU* 4.5 11.7 - - + -
546B LEU* 3.7 27.4 - - + -
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Residues in contact with ASN 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ALA* 4.0 2.7 - - - -
506B SER 5.3 1.4 - - - +
507B LEU* 1.3 81.8 + - - +
509B ALA* 1.3 60.9 + - - +
510B PHE* 4.0 15.9 - - + -
532B ILE* 3.2 29.2 - - - +
533B SER* 3.0 29.8 + - - +
534B SER* 5.4 0.2 - - - -
535B LYS 5.7 0.2 + - - -
567B PRO* 3.8 18.7 - - - +
568B VAL 3.8 10.5 - - - +
569B LYS* 5.3 2.5 - - - +
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Residues in contact with ALA 509 (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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463B ASN 4.6 2.1 - - - +
466B LEU* 3.7 40.0 - - + +
467B LYS* 4.0 5.8 + - - +
469B VAL* 5.8 0.9 - - + -
470B ALA* 3.7 13.3 - - + +
508B ASN* 1.3 76.0 - - - +
510B PHE* 1.3 66.9 + - - +
530B CYS* 4.4 5.6 - - - -
531B GLY 3.2 9.9 - - - +
532B ILE* 4.4 12.1 - - + -
550B ILE* 4.8 7.2 - - + -
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Residues in contact with PHE 510 (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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463B ASN* 3.4 13.7 - - - +
466B LEU* 3.7 10.7 - - - +
508B ASN* 4.0 24.0 - - + -
509B ALA* 1.3 84.0 - - - +
511B LEU* 1.3 66.2 + - - +
512B LEU* 3.9 15.0 - - + -
530B CYS* 3.4 1.8 - - - -
531B GLY* 2.7 46.0 + - - -
532B ILE 4.6 0.4 - - - -
533B SER* 4.3 4.0 - - - -
563B ILE* 3.6 31.9 - - + -
568B VAL* 3.8 31.9 - - + -
571B PRO* 3.7 38.6 - - + -
620B PHE* 4.8 0.7 - + - -
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B PHE* 3.5 51.4 - - + +
462B THR* 3.7 40.8 - - + -
463B ASN* 2.8 16.9 + - - +
466B LEU* 3.8 9.6 - - + -
510B PHE* 1.3 83.7 - - - +
512B LEU* 1.3 64.1 + - - +
513B PRO* 4.2 2.6 - - - +
528B TYR* 3.7 38.1 - - + -
529B VAL 3.5 5.6 - - - +
530B CYS* 4.6 2.7 - - - -
557B VAL* 3.8 11.2 - - + -
571B PRO* 4.7 5.7 - - - +
572B PRO 5.1 0.7 - - - +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B PHE* 4.8 0.4 - - - -
510B PHE* 3.9 20.0 - - + -
511B LEU* 1.3 76.0 - - - +
513B PRO* 1.4 63.5 - - + +
514B ILE* 2.8 35.5 + - + +
528B TYR* 3.9 10.4 - - - -
529B VAL* 2.8 40.3 + - + +
531B GLY* 4.3 10.1 - - - +
561B VAL* 4.2 6.1 - - + -
563B ILE* 4.7 1.1 - - + -
571B PRO* 5.5 0.2 - - + -
572B PRO* 5.0 5.2 - - + -
618B LEU* 3.9 20.0 - - + -
620B PHE* 3.8 26.2 - - + -
679B MET* 4.1 20.2 - - - -
692B TRP* 6.0 0.2 - - + -
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Residues in contact with PRO 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B GLU 4.8 0.2 - - - +
453B PRO* 3.6 19.2 - - + +
454B TYR 2.7 44.4 + - - +
455B ILE* 4.2 10.5 - - + -
459B PHE* 4.7 6.7 - - + -
511B LEU 4.4 1.8 - - - +
512B LEU* 1.4 83.5 - - + +
514B ILE* 1.3 61.7 + - - +
572B PRO* 3.5 26.2 - - + +
573B THR* 4.2 4.9 - - - +
574B ASP 4.1 5.4 - - - +
575B VAL* 3.7 17.2 - - + +
618B LEU* 3.9 15.3 - - + -
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ILE* 4.2 13.9 - - + -
450B ALA* 5.5 2.5 - - + -
454B TYR* 3.7 12.2 + - - +
512B LEU* 2.8 23.2 + - + +
513B PRO* 1.3 81.0 - - - +
515B LYS* 1.3 59.7 + - - +
528B TYR* 3.6 23.2 - - - -
529B VAL* 3.7 27.0 + - + -
575B VAL* 4.2 3.1 - - + -
616B THR* 3.9 22.4 - - + -
617B PRO* 3.7 29.6 - - + -
618B LEU* 3.8 31.0 - - + -
692B TRP* 4.2 5.4 - - + -
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Residues in contact with LYS 515 (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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448B ILE* 3.9 26.2 - - + +
454B TYR* 3.6 49.7 - - + +
514B ILE* 1.3 75.0 - - - +
516B THR* 1.3 62.2 + - - +
526B TYR* 3.9 34.2 - - + +
527B SER 3.6 2.9 - - - -
529B VAL* 5.0 0.4 - - - -
692B TRP 4.7 0.2 - - - +
693B GLU* 4.9 4.0 - - - +
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Residues in contact with THR 516 (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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515B LYS* 1.3 76.6 - - - +
517B VAL* 1.3 56.4 + - - +
526B TYR* 3.4 7.1 - - - -
527B SER 2.9 38.8 + - - +
528B TYR 4.0 1.8 - - - +
529B VAL* 3.6 24.7 - - + -
558B ASN* 3.1 21.5 + - + -
559B ARG* 2.9 35.2 + - + +
692B TRP* 2.7 31.9 + - - +
693B GLU* 5.6 0.2 - - - -
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Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B THR* 1.3 77.3 - - - +
518B GLY* 1.3 61.8 + - - +
524B ARG* 3.7 36.3 - - + +
525B SER 3.1 10.5 - - - +
526B TYR* 3.4 35.9 - - + +
558B ASN* 3.6 2.5 + - - +
559B ARG* 3.0 28.2 + - - -
688B GLY* 4.9 0.2 - - - -
689B THR* 3.2 22.0 - - - +
691B GLU 3.6 6.3 - - - +
692B TRP 3.0 10.1 + - - +
693B GLU* 3.6 21.5 - - - +
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Residues in contact with GLY 518 (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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517B VAL* 1.3 77.2 - - - +
519B VAL* 1.3 59.4 + - - -
520B GLN* 4.1 1.8 - - - -
524B ARG* 3.4 3.9 - - - -
525B SER* 2.7 35.8 + - - -
558B ASN* 3.1 15.2 - - - +
687B PRO 3.2 14.8 - - - -
688B GLY 4.6 0.4 - - - -
689B THR* 4.3 9.6 - - - -
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Residues in contact with VAL 519 (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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522A ASP* 3.7 33.4 - - + +
518B GLY* 1.3 74.1 - - - +
520B GLN* 1.3 61.4 + - - +
521B GLY 3.9 16.8 - - - +
522B ASP 4.6 0.7 - - - -
523B CYS 3.5 9.2 - - - +
524B ARG* 5.0 0.4 - - + -
646B MET 5.7 0.4 - - - +
685B LYS* 4.3 12.3 - - + -
686B PRO* 3.4 19.6 - - + +
687B PRO* 2.9 26.0 + - - +
688B GLY 3.5 17.5 - - - +
689B THR* 4.0 12.0 - - + +
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Residues in contact with GLN 520 (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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376A SER* 5.6 3.8 - - - +
379A LEU* 3.5 30.3 - - + +
518B GLY 4.1 1.9 - - - -
519B VAL* 1.3 73.6 - - - +
521B GLY* 1.3 68.0 + - - +
522B ASP 3.2 0.7 + - - -
523B CYS* 3.1 31.0 + - - +
525B SER* 5.5 8.5 - - - -
551B PRO 4.2 16.8 + - - -
555B HIS* 4.5 33.7 + - + +
557B VAL 4.9 4.2 + - - -
558B ASN* 5.2 7.2 - - - +
686B PRO* 5.4 0.4 - - - -
687B PRO* 3.6 25.3 - - + +
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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