Contacts of the strand formed by residues 514 - 522 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513B SER* 1.3 73.8 - - - +
515B TRP* 1.3 64.6 + - - +
544B ILE* 3.8 25.3 - - + +
545B PHE 3.3 7.2 - - - +
546B ARG* 2.9 46.6 + - - -
590B SER* 2.9 47.6 + - - +
591B SER* 5.7 0.9 - - - -
597B ASP 4.0 4.0 - - - +
599B ASN* 2.9 32.9 + - - +
601B GLN* 5.4 0.2 + - - -
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Residues in contact with TRP 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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442B TYR* 3.4 23.3 - + - -
504B LEU* 3.7 27.4 - - + -
506B ALA* 3.8 19.5 - - + -
507B SER 3.7 24.2 - - - -
508B THR* 4.4 7.4 - - + -
513B SER* 4.0 28.2 + - - -
514B ASP* 1.3 73.5 - - - +
516B VAL* 1.3 62.4 + - - +
517B VAL* 5.3 0.4 - - + -
543B ALA 3.9 1.2 - - - +
544B ILE* 3.4 1.2 - - - -
545B PHE* 2.9 38.9 + + - +
547B GLY* 4.5 1.3 - - - -
559B LEU* 4.5 0.8 - - - +
567B PHE* 3.2 49.2 - + + -
569B PHE* 4.0 12.1 - - + -
588B VAL* 4.7 5.2 - - + -
589B GLN 3.7 1.1 - - - -
590B SER* 3.6 14.8 - - - -
620B GLN* 3.7 20.4 - - + -
622B VAL* 4.9 2.9 - - + -
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Residues in contact with VAL 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B TRP* 1.3 74.3 - - - +
517B VAL* 1.3 65.5 + - - +
518B LYS* 4.5 14.8 - - + -
542B LEU* 5.3 2.5 - - + -
543B ALA 3.3 10.1 - - - +
544B ILE* 3.6 32.8 - - + -
587B GLN 3.6 0.5 - - - +
588B VAL* 3.2 9.0 - - - +
589B GLN* 2.8 53.7 + - + +
590B SER 4.7 1.1 - - - -
591B SER 4.0 20.2 - - - +
592B LEU* 4.1 22.4 - - + -
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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
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502B VAL* 4.0 32.1 - - + -
504B LEU* 4.9 9.9 - - + -
515B TRP 4.1 0.2 - - - -
516B VAL* 1.3 80.2 - - - +
518B LYS* 1.3 66.3 + - - +
542B LEU* 3.3 2.6 - - - +
543B ALA 3.0 31.6 + - - -
569B PHE* 3.9 21.3 - - + -
571B LEU* 3.9 9.5 - - + +
586B VAL* 3.9 22.7 - - + -
587B GLN 3.4 2.0 - - - -
588B VAL* 4.4 14.8 - - + -
632B ILE* 4.2 12.6 - - + -
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Residues in contact with LYS 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B PRO 5.8 0.6 + - - -
473B GLN* 2.8 35.5 + - + +
475B PHE* 5.8 0.2 - - - -
476B VAL* 3.5 11.7 - - - +
516B VAL* 4.5 9.9 - - + -
517B VAL* 1.3 79.4 - - - +
519B LEU* 1.3 59.3 + - - +
520B ILE* 3.8 14.2 + - + +
539B PRO* 5.0 2.0 - - + -
541B SER 3.7 4.3 - - - +
542B LEU* 3.8 24.0 - - + -
585B MSE 3.7 0.3 - - - +
586B VAL* 3.2 9.7 - - - +
587B GLN* 2.9 59.3 + - + +
589B GLN* 3.0 37.2 + - - +
592B LEU* 4.9 6.4 - - - +
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Residues in contact with LEU 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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419B LEU* 4.6 1.8 - - + -
496B ILE* 4.0 20.4 - - + -
500B PRO* 4.1 15.9 - - + -
518B LYS* 1.3 70.3 - - - +
520B ILE* 1.3 60.2 + - - +
539B PRO* 3.6 2.4 - - - +
540B VAL* 2.8 26.7 + - + -
541B SER* 2.8 26.2 + - - +
571B LEU* 4.2 12.3 - - + +
578B PHE* 4.4 9.9 - - + -
584B VAL* 3.9 27.6 - - + -
585B MSE 3.6 5.6 - - - +
586B VAL* 4.3 11.9 - - + -
632B ILE* 4.5 6.3 - - + -
634B LEU* 3.8 30.1 - - + -
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Residues in contact with ILE 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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473B GLN* 4.1 12.8 - - + -
518B LYS* 4.0 16.4 - - + +
519B LEU* 1.3 77.6 - - - +
521B ASP* 1.3 74.9 + - - +
522B VAL* 3.9 10.8 - - + +
537B GLU* 3.7 20.6 - - + -
538B LEU 3.2 7.9 - - - +
539B PRO* 3.8 17.5 - - + -
578B PHE* 3.6 12.5 - - - -
584B VAL* 3.6 1.6 - - - +
585B MSE 2.8 46.6 + - + +
587B GLN* 3.6 41.7 - - + +
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Residues in contact with ASP 521 (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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394B GLY* 5.5 0.2 - - - -
520B ILE* 1.3 75.0 - - - +
522B VAL* 1.3 61.0 + - - +
523B TYR* 3.6 7.9 + - - -
536B TYR 3.3 3.3 - - - +
538B LEU* 2.8 37.1 + - + +
540B VAL* 3.8 8.6 - - + +
576B HIS* 2.8 31.8 + - + +
577B THR 4.3 1.0 - - - +
578B PHE* 3.6 30.7 - - + -
582B HIS* 2.6 37.8 + - - +
583B ARG 3.7 0.9 - - - -
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Residues in contact with VAL 522 (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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486B VAL* 4.3 1.6 - - + -
520B ILE* 3.9 6.7 - - + -
521B ASP* 1.3 71.0 - - - +
523B TYR* 1.3 76.4 + - - +
535B GLY* 3.9 20.0 - - - +
536B TYR 3.4 3.1 - - - +
537B GLU* 4.2 6.7 - - + +
582B HIS* 3.1 5.7 - - - +
583B ARG* 2.9 61.7 + - + +
585B MSE 3.5 47.1 - - + -
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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