Contacts of the strand formed by residues 600 - 608 (chain A) in PDB entry 1MS4
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 VAL 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A LYS* 3.4 0.2 - - - -
455A PHE* 2.7 39.9 + - + +
489A THR 3.1 13.2 - - - +
490A ILE* 3.8 12.3 - - + -
491A HIS* 3.7 7.9 - - - -
500A LEU* 3.7 33.2 - - + -
518A TYR* 3.6 19.1 - - - +
587A GLY* 3.8 31.0 - - - +
598A SER* 4.2 5.8 - - - +
599A ARG* 1.3 81.1 - - - +
601A THR* 1.3 60.9 + - - +
602A VAL* 4.5 4.7 - - + -
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Residues in contact with THR 601 (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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449A VAL* 4.0 20.2 - - + +
453A LEU 3.5 9.4 - - - +
454A LYS* 3.3 18.7 - - - +
487A SER 3.6 1.0 - - - +
488A VAL* 3.3 5.9 - - - +
489A THR* 2.8 44.1 + - - +
491A HIS* 2.8 28.4 + - - -
600A VAL* 1.3 69.1 - - - +
602A VAL* 1.3 65.6 + - - +
603A ASN* 3.9 21.6 + - - +
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Residues in contact with VAL 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.5 17.8 - - + -
452A GLY* 3.3 2.3 - - - -
453A LEU 2.8 35.7 + - - +
455A PHE* 4.3 6.5 - - + -
486A ALA* 3.9 19.3 - - + -
487A SER 3.3 9.0 - - - +
488A VAL* 4.2 13.5 - - + -
500A LEU* 5.0 1.3 - - + +
501A LEU* 5.5 0.4 - - + -
586A VAL* 3.7 22.9 - - + -
587A GLY* 4.1 26.5 - - - +
600A VAL* 4.2 8.3 + - + -
601A THR* 1.3 78.8 - - - +
603A ASN* 1.3 63.2 + - - +
605A VAL* 4.0 3.4 - - + -
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Residues in contact with ASN 603 (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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432A TRP* 4.8 0.4 - - - -
449A VAL* 4.6 1.0 - - - +
450A PRO 2.8 26.7 - - - +
451A ASN* 3.2 10.5 - - - +
452A GLY* 4.0 2.6 + - - -
486A ALA* 4.0 1.7 - - - +
487A SER* 2.9 38.8 + - - -
489A THR* 4.9 3.8 + - - -
544A ARG* 4.1 23.2 - - - +
601A THR* 3.9 22.2 + - - +
602A VAL* 1.3 75.8 - - - +
604A ASN* 1.3 84.1 + - - +
605A VAL* 3.6 3.1 + - - -
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Residues in contact with ASN 604 (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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422A PHE* 3.7 10.7 - - + -
423A LEU 3.3 10.4 + - - -
424A SER* 2.7 32.5 + - - -
432A TRP* 4.7 0.6 - - - -
451A ASN* 3.2 17.7 + - - +
485A VAL* 3.6 9.0 - - - +
486A ALA* 3.7 5.0 - - - -
487A SER* 4.3 7.0 + - - +
603A ASN* 1.3 87.5 - - + +
605A VAL* 1.3 63.5 + - - +
606A LEU* 3.7 5.7 + - - +
624A GLN 4.0 12.0 - - - +
627A ILE* 3.7 27.8 - - + +
628A GLY* 3.4 19.4 + - - -
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Residues in contact with VAL 605 (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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421A GLY 4.0 0.3 - - - +
422A PHE* 3.2 7.1 - - - -
423A LEU* 2.8 40.2 + - + +
432A TRP* 3.5 37.0 - - + -
464A TRP* 3.9 14.2 - - + -
484A LEU* 3.9 23.6 - - + -
485A VAL 3.0 14.6 - - - +
486A ALA* 4.4 4.7 - - + -
501A LEU* 5.1 0.7 - - + -
586A VAL* 4.4 12.3 - - + -
602A VAL* 4.0 16.4 - - + -
604A ASN* 1.3 73.1 - - - +
606A LEU* 1.3 59.6 + - - +
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Residues in contact with LEU 606 (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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392A LEU* 5.0 4.9 - - + -
414A VAL* 5.8 1.3 - - + -
419A LEU* 4.0 14.4 - - + -
421A GLY 3.5 1.6 - - - -
422A PHE* 2.9 51.1 - - + -
464A TRP* 4.9 0.2 - - - -
483A THR 3.5 1.1 - - - +
484A LEU* 3.3 9.5 - - - +
485A VAL* 2.9 46.9 + - + +
604A ASN 4.3 4.3 - - - +
605A VAL* 1.3 74.6 - - - +
607A LEU* 1.3 60.9 + - - +
608A TYR* 3.8 25.4 - - + +
620A LEU* 3.6 33.4 - - + -
627A ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 607 (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* 3.7 1.6 - - - +
420A VAL* 2.7 34.9 + - + +
421A GLY 2.9 13.5 + - - +
464A TRP* 3.8 21.3 - - + -
475A TYR* 3.8 41.1 - - + -
477A PHE* 4.0 19.1 - - + -
482A PHE* 4.2 10.8 - - + -
483A THR 3.4 10.5 - - - +
484A LEU* 4.2 7.9 - - + -
584A PHE* 3.8 32.5 - - + -
606A LEU* 1.3 74.7 - - - +
608A TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 608 (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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392A LEU* 5.6 0.3 - - - +
414A VAL* 4.4 2.4 - - - +
415A THR* 2.8 43.5 + - + +
417A VAL 3.7 8.3 - - - -
418A GLY 3.1 5.6 - - - +
419A LEU* 3.6 37.2 - - + +
477A PHE* 3.8 5.9 - - - -
482A PHE* 3.2 10.4 - - - +
483A THR* 2.9 36.5 + - + +
485A VAL* 4.7 1.1 - - + -
606A LEU* 3.8 38.8 - - + +
607A LEU* 1.3 78.0 - - - +
609A ASN* 1.3 57.5 + - - +
610A ARG* 3.2 19.1 - - + +
612A LEU* 3.7 34.1 - - + -
620A LEU* 4.0 12.1 - - + +
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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