Contacts of the strand formed by residues 544 - 552 (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 ARG 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A SER* 4.2 16.4 - - - -
488A VAL 3.5 6.3 - - - +
489A THR* 3.6 15.2 + - + +
542A GLY 3.7 2.4 + - - +
543A LYS* 1.3 89.8 + - - +
545A TYR* 1.3 61.5 + - - +
546A HIS 4.5 0.2 + - - -
561A ASP* 4.5 3.3 - - - +
603A ASN* 4.1 17.5 - - - +
624A GLN* 4.1 32.9 + - - +
625A ASP* 3.9 23.2 + - - -
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Residues in contact with TYR 545 (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 ALA 3.7 0.3 - - - +
487A SER* 3.2 4.9 - - - -
488A VAL* 2.8 50.2 + - + +
489A THR* 5.8 0.7 - - - -
490A ILE* 5.4 4.5 - - + -
524A TRP* 3.9 21.8 - + + -
538A SER 4.1 7.0 + - - -
539A TRP* 3.3 20.3 - + + -
540A GLU* 2.8 45.1 + - - +
543A LYS* 3.5 44.8 - - + +
544A ARG* 1.3 74.4 - - - +
546A HIS* 1.3 61.5 + - - +
547A VAL* 3.8 1.9 + - + -
560A ILE* 3.9 17.0 - - + -
561A ASP* 3.4 25.1 - - - +
624A GLN* 3.7 4.7 - - - -
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Residues in contact with HIS 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 3.5 28.6 - - + +
486A ALA 3.6 4.9 + - - -
487A SER* 4.3 2.5 + - - -
545A TYR* 1.3 71.6 - - - +
547A VAL* 1.3 60.9 + - - +
548A VAL* 3.7 22.4 - - + +
559A TYR 3.6 0.7 - - - +
560A ILE* 3.2 8.1 - - - +
561A ASP* 2.8 32.8 + - - +
562A GLY 4.6 4.4 + - - -
617A ILE* 4.3 2.8 + - + -
620A LEU* 3.5 29.6 - - + +
621A PHE* 3.3 44.7 + - + -
624A GLN* 3.4 31.3 + - + +
627A ILE* 5.9 4.3 - - + -
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU 4.0 0.2 - - - +
485A VAL* 3.4 1.9 - - - +
486A ALA 2.7 38.5 + - - +
488A VAL* 3.8 32.5 - - + -
501A LEU* 4.2 22.7 - - + -
516A LEU* 4.1 22.7 - - + -
545A TYR* 4.2 1.3 - - + +
546A HIS* 1.3 78.0 - - - +
548A VAL* 1.3 77.1 + - - +
549A LEU* 4.4 8.5 - - + -
558A VAL* 5.1 0.7 - - + -
559A TYR 3.4 8.1 - - - +
560A ILE* 4.1 12.3 - - + -
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Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR* 3.7 25.8 - - + -
484A LEU 3.5 1.8 - - - -
485A VAL* 3.9 11.2 - - + -
546A HIS* 3.7 27.8 - - + +
547A VAL* 1.3 81.7 - - - +
549A LEU* 1.3 66.5 + - - +
550A THR* 3.9 13.7 - - + -
558A VAL* 3.3 4.3 - - - -
559A TYR* 2.7 55.7 + - + -
562A GLY 6.2 0.2 - - - +
617A ILE* 4.2 23.1 - - + -
620A LEU* 5.8 0.9 - - + -
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Residues in contact with LEU 549 (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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482A PHE* 3.8 7.5 - - + +
483A THR* 3.1 5.5 - - - +
484A LEU* 2.8 48.5 + - + +
501A LEU* 3.9 25.8 - - + +
502A GLY* 4.0 24.5 - - - -
503A ALA 5.1 0.2 - - - +
514A LEU* 4.0 17.3 - - + +
515A GLY* 4.4 9.0 - - - +
516A LEU* 4.4 11.4 - - + -
547A VAL* 4.4 8.3 - - + -
548A VAL* 1.3 77.3 - - - +
550A THR* 1.3 63.8 + - - +
557A SER 3.4 2.7 - - - -
558A VAL* 3.8 31.9 - - + -
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Residues in contact with THR 550 (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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482A PHE* 3.4 8.3 - - - -
483A THR* 3.6 16.4 - - + +
514A LEU* 3.0 5.9 - - - +
548A VAL* 3.9 16.4 - - + -
549A LEU* 1.3 79.2 - - - +
551A MET* 1.3 61.2 + - - +
555A ILE 4.1 0.2 - - - -
556A GLY* 2.9 5.8 - - - -
557A SER* 2.8 51.4 + - - -
559A TYR* 4.1 13.3 + - + -
611A GLN* 3.5 30.6 + - + +
612A LEU 4.7 0.2 - - - +
617A ILE* 4.6 6.7 - - + -
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Residues in contact with MET 551 (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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478A ALA 3.6 12.8 - - - +
479A ASN 3.4 20.6 - - - +
480A HIS 3.4 26.7 - - - +
481A ALA* 3.2 4.1 - - - +
482A PHE* 3.0 45.9 + - + +
513A LEU* 4.3 15.9 - - + -
514A LEU* 4.4 2.5 - - + -
550A THR* 1.3 75.9 - - - +
552A ALA* 1.3 69.7 + - - +
554A LYS* 3.8 26.9 - - - -
555A ILE 3.1 6.1 - - - +
556A GLY* 4.5 0.9 - - - -
572A VAL* 3.8 25.6 - - + -
573A VAL* 4.6 6.5 - - + -
579A PRO* 5.1 0.2 - - + -
611A GLN* 4.2 3.4 - - - +
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Residues in contact with ALA 552 (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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480A HIS 4.0 8.1 - - - -
481A ALA* 4.1 11.7 - - + -
551A MET* 1.3 77.2 - - - +
553A ASN* 1.3 74.1 + - + +
554A LYS 3.1 2.2 - - - -
555A ILE* 2.9 21.8 + - - +
611A GLN* 3.7 31.9 + - + +
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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