Contacts of the strand formed by residues 600 - 608 (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 VAL 600 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LYS* 3.6 0.3 - - - -
455B PHE* 2.8 32.4 + - + -
489B THR 3.1 13.5 - - - +
490B ILE* 4.1 5.8 - - - -
491B HIS* 3.6 8.0 - - - -
500B LEU* 3.5 30.1 - - + -
518B TYR* 3.6 21.8 - - + +
587B GLY* 3.8 36.8 - - - +
598B SER* 4.2 4.5 - - - +
599B ARG* 1.3 82.1 - - - +
601B THR* 1.3 62.5 + - - +
602B VAL* 4.3 6.5 - - + -
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Residues in contact with THR 601 (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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449B VAL* 3.7 23.4 - - + +
453B LEU 3.4 11.7 - - - +
454B LYS* 3.6 16.2 - - - +
487B SER 3.9 0.2 - - - +
488B VAL* 3.4 4.5 - - - +
489B THR* 2.9 37.8 + - - -
491B HIS* 2.6 28.2 + - - -
600B VAL* 1.3 74.0 - - - +
602B VAL* 1.3 66.1 - - - +
603B ASN* 4.0 20.6 + - - +
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Residues in contact with VAL 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TRP* 3.5 12.2 - - + -
452B GLY* 3.3 2.6 - - - -
453B LEU 2.8 34.4 + - - -
455B PHE* 4.1 8.3 - - + -
486B ALA* 3.9 11.2 - - + -
487B SER 3.4 8.7 - - - +
488B VAL* 4.3 12.8 - - + -
500B LEU* 4.9 1.6 - - + +
586B VAL* 3.8 12.6 - - + -
587B GLY* 4.0 27.8 - - - +
600B VAL* 4.3 6.7 - - + -
601B THR* 1.3 78.4 - - - +
603B ASN* 1.3 66.2 + - - +
605B VAL* 3.8 26.7 - - + -
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Residues in contact with ASN 603 (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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449B VAL* 4.4 0.7 - - - +
450B PRO 3.0 24.1 - - - +
451B ASN* 3.4 13.0 - - + +
452B GLY* 3.9 2.0 - - - -
486B ALA* 3.8 1.7 - - - +
487B SER* 2.8 43.4 + - - -
489B THR* 5.1 3.2 + - - -
544B ARG* 3.9 26.8 - - - +
601B THR* 4.0 19.2 + - - +
602B VAL* 1.3 80.0 - - - +
604B ASN* 1.3 85.2 + - + +
605B VAL* 3.5 1.7 + - - -
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Residues in contact with ASN 604 (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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422B PHE* 3.7 9.7 - - + -
423B LEU 3.3 10.0 + - - -
424B SER* 2.6 32.9 + - - -
432B TRP* 4.7 0.6 - - - -
451B ASN* 3.3 13.5 + - - +
485B VAL* 3.6 8.7 - - - +
486B ALA* 3.6 4.9 - - - -
487B SER* 4.3 6.2 + - - +
603B ASN* 1.3 88.4 - - + +
605B VAL* 1.3 62.9 + - - +
606B LEU* 3.7 6.1 + - - +
624B GLN 3.8 8.0 - - - +
627B ILE* 3.8 32.1 - - + +
628B GLY* 3.4 20.8 + - - -
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Residues in contact with VAL 605 (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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421B GLY 3.9 0.3 - - - +
422B PHE* 3.2 7.3 + - - -
423B LEU* 2.8 45.7 + - + -
432B TRP* 3.6 34.8 - - + -
464B TRP* 3.9 22.6 - - + -
484B LEU* 4.1 14.4 - - + -
485B VAL 3.0 13.5 - - - +
486B ALA* 4.1 6.3 - - + -
501B LEU* 5.1 0.7 - - + -
586B VAL* 4.2 12.8 - - + -
602B VAL* 3.8 18.8 - - + -
604B ASN* 1.3 72.7 - - - +
606B LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 606 (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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392B LEU* 4.8 7.4 - - + -
414B VAL* 6.0 0.9 - - + -
419B LEU* 4.1 17.7 - - + -
421B GLY 3.5 1.8 - - - -
422B PHE* 3.0 45.1 - - + -
483B THR 3.6 1.1 - - - +
484B LEU* 3.5 7.1 - - - +
485B VAL* 2.8 48.0 + - + +
604B ASN 4.3 2.2 - - - +
605B VAL* 1.3 75.5 - - - +
607B LEU* 1.3 60.9 + - - +
608B TYR* 3.9 21.8 - - + +
620B LEU* 3.8 30.1 - - + -
627B ILE* 3.9 16.8 - - + -
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Residues in contact with LEU 607 (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* 3.5 2.3 - - - +
420B VAL* 2.7 35.3 + - + +
421B GLY 2.9 12.4 + - - +
464B TRP* 3.7 21.8 - - + -
475B TYR* 3.6 42.2 - - + -
477B PHE* 4.0 17.5 - - + -
482B PHE* 4.2 9.9 - - + -
483B THR 3.5 12.3 - - - +
484B LEU* 4.1 8.3 - - + -
584B PHE* 3.7 30.7 - - + -
606B LEU* 1.3 75.0 - - - +
608B TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 608 (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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392B LEU* 5.7 0.3 - - - +
414B VAL* 4.4 2.4 - - - +
415B THR* 2.7 37.7 + - + +
417B VAL 3.5 23.1 - - - -
418B GLY 3.1 5.4 - - - +
419B LEU* 3.5 31.2 - - + +
420B VAL* 4.6 0.4 - - - -
477B PHE* 3.7 5.5 - - - -
482B PHE* 3.3 9.4 - - - +
483B THR* 2.9 36.4 + - + +
485B VAL* 4.7 1.6 - - + -
606B LEU* 3.9 30.1 - - + +
607B LEU* 1.3 77.5 - - - +
609B ASN* 1.3 58.6 + - - +
610B ARG* 3.3 17.9 - - + +
612B LEU* 3.8 35.2 - - + -
620B LEU* 4.0 18.8 - - + +
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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