Contacts of the strand formed by residues 514 - 522 (chain D) in PDB entry 1MPX
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 ASP 514 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513D SER* 1.3 74.4 - - - +
515D TRP* 1.3 63.5 + - - +
516D VAL* 5.2 0.2 - - + -
544D ILE* 3.8 24.2 - - + +
545D PHE 3.4 6.3 - - - +
546D ARG* 2.9 45.7 + - - -
590D SER* 2.9 47.7 + - - +
591D SER* 5.3 1.4 - - - -
597D ASP 3.9 4.7 - - - +
599D ASN* 2.9 33.5 + - + +
601D GLN* 5.3 0.4 + - - -
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Residues in contact with TRP 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D TYR* 3.4 24.5 - + - -
504D LEU* 3.9 26.9 - - + -
506D ALA* 3.8 19.5 - - + -
507D SER 3.5 28.9 - - - -
508D THR* 4.4 3.6 - - + -
513D SER* 4.1 26.7 + - - -
514D ASP* 1.3 75.2 - - - +
516D VAL* 1.3 61.7 + - - +
543D ALA 4.0 1.2 - - - +
544D ILE* 3.5 1.0 - - - -
545D PHE* 2.9 39.4 + + - +
547D GLY* 4.5 0.7 - - - -
559D LEU* 4.6 0.8 - - - +
567D PHE* 3.2 50.3 - + - -
569D PHE* 4.0 12.9 - - + -
588D VAL* 4.6 5.4 - - + -
589D GLN 3.7 1.8 - - - -
590D SER* 3.6 13.7 - - - -
620D GLN* 3.7 18.8 - - + -
621D ARG 4.8 0.4 - - - -
622D VAL* 4.9 4.3 - - + -
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Residues in contact with VAL 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D TRP* 1.3 76.2 - - - +
517D VAL* 1.3 66.4 + - - +
518D LYS* 4.5 13.0 - - + -
542D LEU* 5.0 2.2 - - + -
543D ALA 3.4 11.0 - - - +
544D ILE* 3.7 28.5 - - + -
587D GLN 3.6 0.6 - - - +
588D VAL* 3.2 8.7 - - - +
589D GLN* 2.8 55.1 + - + +
590D SER 4.7 1.1 - - - -
591D SER 4.1 21.3 - - - +
592D LEU* 4.2 22.4 - - + -
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Residues in contact with VAL 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D VAL* 4.0 26.0 - - + -
504D LEU* 4.8 9.0 - - + -
515D TRP 4.2 0.2 + - - -
516D VAL* 1.3 81.0 - - - +
518D LYS* 1.3 66.4 + - - +
542D LEU* 3.3 4.2 - - - +
543D ALA 3.0 30.6 + - - -
569D PHE* 4.0 20.2 - - + -
571D LEU* 3.9 8.5 - - + +
586D VAL* 4.0 13.5 - - + -
587D GLN 3.4 2.5 - - - -
588D VAL* 4.3 16.4 - - + -
632D ILE* 3.9 28.3 - - + -
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Residues in contact with LYS 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D TRP* 6.5 0.2 - - - -
473D GLN* 2.9 33.7 + - + +
476D VAL* 3.4 10.7 - - - +
516D VAL* 4.5 9.4 - - + -
517D VAL* 1.3 79.9 - - - +
519D LEU* 1.3 61.1 + - - +
520D ILE* 3.8 14.4 + - + +
539D PRO* 5.0 1.6 - - + -
541D SER 3.7 3.4 - - - -
542D LEU* 3.9 24.2 - - + -
585D MSE 3.6 0.3 - - - +
586D VAL* 3.2 10.0 - - - +
587D GLN* 2.7 62.1 + - + +
589D GLN* 2.9 38.0 + - - +
592D LEU* 4.9 6.7 - - - +
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Residues in contact with LEU 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D LEU* 4.7 2.0 - - + -
496D ILE* 4.0 15.0 - - + -
500D PRO* 4.0 22.0 - - + -
517D VAL 4.2 0.2 - - - -
518D LYS* 1.3 70.9 - - - +
520D ILE* 1.3 62.7 + - - +
539D PRO* 3.6 2.3 - - - +
540D VAL* 2.9 26.8 + - + -
541D SER* 2.8 26.8 + - - +
571D LEU* 4.1 11.8 - - + +
578D PHE* 4.5 10.3 - - + -
584D VAL* 3.8 26.9 - - + -
585D MSE 3.6 4.0 - - - +
586D VAL* 4.4 11.0 - - + -
632D ILE* 4.9 4.5 - - + -
634D LEU* 3.7 30.1 - - + -
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Residues in contact with ILE 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D GLN* 4.2 12.3 - - + -
518D LYS* 4.0 17.7 - - + +
519D LEU* 1.3 79.3 - - - +
521D ASP* 1.3 74.6 + - - +
522D VAL* 4.0 10.5 - - + +
537D GLU* 3.7 20.6 - - + -
538D LEU 3.3 8.5 - - - +
539D PRO* 3.9 15.7 - - + -
540D VAL* 4.6 0.2 - - - -
578D PHE* 3.7 8.0 - - - -
584D VAL* 3.5 6.4 - - - +
585D MSE 2.7 48.3 + - + +
587D GLN* 3.6 42.0 - - + +
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Residues in contact with ASP 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D ILE* 1.3 73.4 - - - +
522D VAL* 1.3 60.8 + - - +
523D TYR* 3.5 9.0 + - - -
536D TYR 3.4 3.5 - - - +
538D LEU* 2.8 36.0 + - + +
540D VAL* 3.8 7.3 - - + +
576D HIS* 2.6 32.8 + - + +
577D THR 4.4 1.2 - - - +
578D PHE* 3.6 28.5 - - + -
582D HIS* 2.6 38.2 + - - +
583D ARG 3.7 1.6 - - - -
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Residues in contact with VAL 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D VAL* 4.3 0.9 - - + -
520D ILE* 4.0 5.6 - - + -
521D ASP* 1.3 71.7 - - - +
523D TYR* 1.3 77.0 + - - +
535D GLY* 3.8 21.1 - - - +
536D TYR 3.5 4.3 - - - +
537D GLU* 4.2 7.2 - - + +
582D HIS* 3.2 4.9 - - - +
583D ARG* 2.9 61.0 + - + +
585D MSE 3.5 46.9 - - + -
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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