Contacts of the strand formed by residues 514 - 522 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A SER* 1.3 74.4 - - - +
515A TRP* 1.3 64.2 + - - +
544A ILE* 3.8 24.5 - - + +
545A PHE 3.3 7.0 - - - +
546A ARG* 2.9 45.5 + - - -
590A SER* 3.0 46.4 + - - +
591A SER* 5.3 1.6 - - - -
597A ASP 4.0 2.3 - - - +
599A ASN* 2.9 35.4 + - - +
601A GLN* 5.4 0.4 + - - -
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Residues in contact with TRP 515 (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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442A TYR* 3.4 23.8 - + - -
504A LEU* 3.8 26.5 - - + -
506A ALA* 3.8 20.6 - - + -
507A SER 3.7 26.7 - - - -
508A THR* 4.5 2.7 - - - -
513A SER* 4.0 26.9 + - - -
514A ASP* 1.3 74.1 - - - +
516A VAL* 1.3 63.0 + - - +
517A VAL* 4.1 0.4 - - + -
543A ALA 3.9 1.0 - - - +
544A ILE* 3.4 1.4 - - - -
545A PHE* 2.9 38.3 + + + +
547A GLY* 4.6 1.3 - - - -
559A LEU* 4.5 1.7 - - + +
567A PHE* 3.2 49.5 - + + -
569A PHE* 4.0 13.2 - - + -
588A VAL* 4.6 4.7 - - + -
589A GLN 3.7 1.1 - - - -
590A SER* 3.6 11.9 - - - -
620A GLN* 3.7 20.0 - - + -
621A ARG 4.9 0.2 - - - -
622A VAL* 4.9 3.8 - - + -
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Residues in contact with VAL 516 (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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515A TRP* 1.3 73.7 - - - +
517A VAL* 1.3 67.1 + - - +
518A LYS* 4.5 12.8 - - + -
542A LEU* 5.2 2.7 - - + -
543A ALA 3.4 9.9 - - - +
544A ILE* 3.6 33.7 - - + -
587A GLN 3.6 0.3 - - - +
588A VAL* 3.2 8.9 - - - +
589A GLN* 2.9 54.3 + - + +
590A SER 4.7 0.7 - - - -
591A SER 4.1 20.4 - - - +
592A LEU* 4.1 22.4 - - + -
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Residues in contact with VAL 517 (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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502A VAL* 4.0 31.6 - - + -
504A LEU* 4.9 9.2 - - + -
516A VAL* 1.3 81.0 - - - +
518A LYS* 1.3 66.7 + - - +
542A LEU* 3.2 3.8 - - - +
543A ALA 3.0 30.6 + - - +
569A PHE* 3.9 21.1 - - + -
571A LEU* 3.8 8.5 - - + +
586A VAL* 4.0 22.0 - - + -
587A GLN 3.4 2.7 - - - -
588A VAL* 4.5 15.0 - - + -
632A ILE* 4.1 13.5 - - + -
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Residues in contact with LYS 518 (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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451A PRO 5.8 0.8 + - - -
468A TRP* 6.5 0.7 - - - -
473A GLN* 2.9 32.8 + - + +
475A PHE* 5.9 0.2 - - - -
476A VAL* 3.4 11.9 - - - +
516A VAL* 4.5 10.1 - - + -
517A VAL* 1.3 79.3 - - - +
519A LEU* 1.3 60.7 + - - +
520A ILE* 3.7 14.8 + - + +
539A PRO* 5.0 1.6 - - + -
541A SER 3.7 4.5 - - - +
542A LEU* 3.8 23.6 - - + -
585A MSE 3.6 0.5 - - - +
586A VAL* 3.2 9.0 - - - +
587A GLN* 2.8 60.0 + - + +
589A GLN* 2.9 36.7 + - - +
592A LEU* 4.9 6.7 - - - +
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Residues in contact with LEU 519 (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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419A LEU* 4.6 1.6 - - + -
496A ILE* 3.9 20.6 - - + -
500A PRO* 4.1 16.2 - - + -
517A VAL 4.2 0.4 - - - -
518A LYS* 1.3 71.2 - - - +
520A ILE* 1.3 59.9 + - - +
539A PRO* 3.6 2.4 - - - +
540A VAL* 2.9 27.2 + - + -
541A SER* 2.7 26.7 + - - +
571A LEU* 4.1 12.9 - - + +
578A PHE* 4.4 9.6 - - + -
584A VAL* 3.9 28.5 - - + -
585A MSE 3.6 4.3 - - - +
586A VAL* 4.3 12.3 - - + -
632A ILE* 4.5 6.1 - - + -
634A LEU* 3.8 29.6 - - + -
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Residues in contact with ILE 520 (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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473A GLN* 4.0 12.3 - - + -
518A LYS* 3.9 20.0 - - + +
519A LEU* 1.3 79.8 - - - +
521A ASP* 1.3 73.9 + - - +
522A VAL* 4.0 10.8 - - + -
537A GLU* 3.8 20.4 - - + -
538A LEU 3.3 7.9 - - - +
539A PRO* 3.9 16.2 - - + -
578A PHE* 3.7 8.7 - - - -
584A VAL* 3.5 5.7 - - - +
585A MSE 2.7 48.4 + - + +
587A GLN* 3.7 38.1 - - + +
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Residues in contact with ASP 521 (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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394A GLY* 5.5 0.2 - - - -
520A ILE* 1.3 72.9 - - - +
522A VAL* 1.3 64.2 + - - +
523A TYR* 3.6 8.4 + - - -
536A TYR 3.4 2.3 - - - +
538A LEU* 2.8 37.9 + - + +
540A VAL* 3.8 7.7 - - + +
576A HIS* 2.8 35.5 + - + +
577A THR 4.2 1.2 - - - +
578A PHE* 3.6 25.9 - - + -
582A HIS* 2.6 38.6 + - - +
583A ARG 3.7 1.3 - - - -
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Residues in contact with VAL 522 (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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486A VAL* 4.3 0.9 - - + -
520A ILE* 4.0 5.6 - - + -
521A ASP* 1.3 73.7 - - - +
523A TYR* 1.3 74.1 + - - +
535A GLY* 3.9 20.0 - - - +
536A TYR 3.4 3.8 - - - +
537A GLU* 4.3 7.4 - - + +
582A HIS* 3.1 6.1 - - - +
583A ARG* 2.9 58.7 + - + +
585A MSE 3.5 47.8 - - + -
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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