Contacts of the strand formed by residues 544 - 552 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B SER* 4.1 25.4 - - - -
488B VAL 4.0 2.7 - - - +
489B THR* 3.4 19.1 + - - +
542B GLY 3.8 2.2 + - - +
543B LYS* 1.3 89.0 + - - +
545B TYR* 1.3 63.3 + - - +
546B HIS 4.4 0.2 + - - -
561B ASP* 4.5 3.3 - - - +
603B ASN* 3.9 18.1 - - - +
624B GLN* 4.2 20.7 + - - +
625B ASP* 4.2 19.6 + - - -
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Residues in contact with TYR 545 (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 ALA 3.8 0.2 - - - +
487B SER* 3.2 4.7 - - - -
488B VAL* 2.7 52.0 + - + +
489B THR* 5.6 0.7 - - - -
490B ILE* 5.5 4.0 - - + -
524B TRP* 3.8 30.3 - + + -
538B SER 4.1 7.0 + - - -
539B TRP* 3.4 14.5 - + + -
540B GLU* 2.9 43.2 + - - +
543B LYS* 3.3 55.1 - - + +
544B ARG* 1.3 74.2 - - - +
546B HIS* 1.3 62.6 + - - +
547B VAL* 3.9 2.0 + - + -
560B ILE* 4.0 11.0 - - + -
561B ASP* 3.7 20.9 - - - -
624B GLN* 3.8 3.4 - - - -
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Residues in contact with HIS 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B VAL* 3.4 26.7 - - + -
486B ALA 3.7 4.7 + - - -
487B SER* 4.2 2.0 + - - -
545B TYR* 1.3 72.7 - - - +
547B VAL* 1.3 60.3 + - - +
548B VAL* 3.5 26.4 - - + +
559B TYR 3.7 0.3 - - - +
560B ILE* 3.4 6.4 - - - +
561B ASP* 2.7 34.5 + - - +
562B GLY* 4.6 6.1 - - - -
617B ILE 4.4 1.9 + - - -
620B LEU* 3.7 25.3 - - + +
621B PHE* 3.5 41.6 + - + -
624B GLN* 3.3 34.3 + - + +
627B ILE* 6.1 3.1 - - + -
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU 3.8 0.2 - - - +
485B VAL* 3.4 3.5 - - - +
486B ALA 2.8 36.5 + - - +
488B VAL* 3.8 32.3 - - + -
500B LEU* 5.4 0.4 - - + -
501B LEU* 3.9 25.1 - - + -
516B LEU* 3.9 23.3 - - + -
524B TRP* 5.5 0.2 - - + -
545B TYR* 4.4 2.0 - - + +
546B HIS* 1.3 75.8 - - - +
548B VAL* 1.3 73.7 + - - +
549B LEU* 4.1 11.4 - - + -
558B VAL* 5.1 0.7 - - + -
559B TYR 3.4 7.2 - - - +
560B ILE* 3.9 15.5 - - + -
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Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B THR* 3.6 27.1 - - + -
484B LEU 3.5 2.9 - - - +
485B VAL* 4.0 10.3 - - + -
546B HIS* 3.5 27.1 - - + +
547B VAL* 1.3 80.6 - - - +
549B LEU* 1.3 66.9 + - - +
550B THR* 3.9 13.5 - - + -
558B VAL* 3.3 4.5 - - - -
559B TYR* 2.6 54.5 + - + +
617B ILE* 4.3 23.1 - - + -
620B LEU* 5.7 1.3 - - + -
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Residues in contact with LEU 549 (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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482B PHE* 3.8 9.3 - - + +
483B THR* 3.1 6.1 - - - +
484B LEU* 2.7 47.6 + - + +
501B LEU* 3.8 33.2 - - + +
502B GLY* 4.0 20.4 - - - -
514B LEU* 3.7 23.3 - - + +
515B GLY* 4.5 3.8 - - - -
516B LEU* 4.3 11.0 - - + -
547B VAL* 4.1 9.6 - - + -
548B VAL* 1.3 79.7 - - - +
550B THR* 1.3 61.5 + - - +
557B SER 3.4 3.6 - - - -
558B VAL* 3.9 28.7 - - + -
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Residues in contact with THR 550 (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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482B PHE* 3.4 7.0 - - - -
483B THR* 3.8 13.7 - - + +
514B LEU* 3.3 6.0 - - - +
548B VAL* 3.9 17.7 - - + -
549B LEU* 1.3 78.2 - - - +
551B MET* 1.3 62.2 + - - +
555B ILE 4.3 0.4 - - - -
556B GLY* 3.3 3.6 - - - -
557B SER* 2.9 48.5 + - - -
559B TYR* 4.1 14.3 + - + -
611B GLN* 3.6 30.2 + - + +
612B LEU 4.7 0.4 - - - +
617B ILE* 4.3 8.1 - - + -
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Residues in contact with MET 551 (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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478B ALA 3.5 25.1 - - - +
479B ASN 3.6 13.0 - - - +
480B HIS 3.5 21.5 - - - +
481B ALA* 3.1 6.4 - - - +
482B PHE* 2.9 55.2 + - + +
513B LEU* 4.5 14.1 - - + -
514B LEU* 4.5 4.3 - - + -
550B THR* 1.3 76.4 - - - +
552B ALA* 1.3 70.1 + - - +
554B LYS* 4.0 22.4 - - - -
555B ILE 3.2 9.6 - - - +
556B GLY* 4.7 1.1 - - - -
572B VAL* 3.9 21.1 - - + -
573B VAL* 4.8 3.1 - - + -
579B PRO* 5.2 2.7 - - + -
611B GLN* 4.6 2.2 - - - +
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Residues in contact with ALA 552 (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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480B HIS 4.0 4.9 - - - -
481B ALA* 4.0 13.9 - - + -
551B MET* 1.3 80.1 - - - +
553B ASN* 1.3 74.0 + - + +
554B LYS 3.0 2.9 - - - -
555B ILE* 2.8 21.7 + - - +
611B GLN* 4.0 30.9 + - + +
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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