Contacts of the strand formed by residues 419 - 427 (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 LEU 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A GLN* 4.2 2.8 + - - +
326A ARG* 2.8 30.3 + - - +
392A LEU* 3.5 22.0 - - + -
416A THR* 3.0 23.3 + - + +
417A VAL 3.3 1.4 + - - -
418A GLY* 1.3 76.2 - - - +
420A VAL* 1.3 59.3 + - - +
421A GLY 3.3 26.7 - - - +
436A TYR* 3.0 35.2 - - + +
606A LEU* 4.0 16.6 - - + -
607A LEU 3.8 5.6 - - - +
608A TYR* 3.6 30.0 - - + +
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLN* 3.1 31.4 - - + +
326A ARG* 3.4 25.5 - - - +
327A ILE 5.8 0.4 - - - +
418A GLY 3.7 12.3 - - - +
419A LEU* 1.3 74.9 - - - +
421A GLY* 1.3 57.1 + - - +
434A ASP* 4.3 3.8 - - - +
436A TYR* 3.9 9.7 - - - +
438A CYS* 5.4 2.5 - - + +
474A ARG 5.6 0.2 - - - +
475A TYR* 3.4 36.2 + - + -
477A PHE* 4.0 23.8 - - + -
607A LEU* 2.7 17.5 + - + +
609A ASN* 4.3 11.0 - - + +
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Residues in contact with GLY 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 3.3 11.5 - - - +
420A VAL* 1.3 83.3 - - - +
422A PHE* 1.3 61.7 + - - -
434A ASP* 3.5 12.8 - - - -
436A TYR* 4.2 2.0 - - - -
464A TRP* 3.9 19.5 - - - -
475A TYR* 4.4 1.8 - - - -
606A LEU* 3.5 0.3 - - - -
607A LEU* 2.9 28.0 + - - +
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Residues in contact with PHE 422 (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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388A TRP* 5.3 4.0 - + + -
391A HIS* 5.2 2.7 - + - -
392A LEU* 4.5 17.5 - - + -
419A LEU* 4.7 0.2 - - + -
421A GLY* 1.3 75.9 - - - +
423A LEU* 1.3 61.5 + - - +
424A SER* 3.7 9.9 + - - -
434A ASP* 3.4 7.5 + - - -
435A ALA* 3.0 43.6 + - + +
436A TYR* 3.6 24.0 - + + -
464A TRP* 4.0 2.2 - - - -
604A ASN* 3.7 37.2 - - + -
605A VAL 3.2 7.6 - - - -
606A LEU* 2.9 29.8 - - + -
627A ILE* 3.6 27.1 - - + -
629A THR* 3.6 18.2 - - + -
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Residues in contact with LEU 423 (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* 1.3 71.5 - - - +
424A SER* 1.3 58.7 + - - +
432A TRP* 3.6 50.0 - - + +
433A GLU 3.8 2.7 - - - -
434A ASP* 3.7 27.8 - - - +
439A VAL 4.4 0.4 - - - +
441A ALA* 3.9 17.5 - - + +
464A TRP* 3.7 52.0 - - + +
586A VAL* 5.6 3.4 - - + -
604A ASN* 3.3 6.1 + - - -
605A VAL* 2.8 43.7 + - + -
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Residues in contact with SER 424 (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 10.2 + - - -
423A LEU* 1.3 73.9 - - - +
425A HIS* 1.3 72.4 + - - +
426A SER 3.6 2.0 + - - -
432A TRP* 2.9 24.0 + - - +
433A GLU 4.3 4.6 + - - -
435A ALA* 5.7 1.3 - - - +
451A ASN* 3.4 14.8 + - - +
452A GLY* 3.5 8.0 + - - -
604A ASN* 2.7 27.8 + - - +
629A THR* 3.0 37.6 + - - -
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Residues in contact with HIS 425 (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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424A SER* 1.3 83.7 + - - +
426A SER* 1.3 67.0 + - - +
427A ALA* 3.4 2.4 + - - +
448A ARG* 3.1 36.2 + - + -
449A VAL 3.8 8.4 + - - +
450A PRO* 3.7 11.0 - - + -
451A ASN* 2.9 31.2 + - - +
452A GLY 4.8 4.0 + - - +
629A THR* 3.0 16.1 + - - +
630A GLU* 3.4 48.1 + - + +
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Residues in contact with SER 426 (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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388A TRP* 5.9 3.3 - - - -
424A SER 3.6 1.1 - - - +
425A HIS* 1.3 80.2 - - - +
427A ALA* 1.3 61.1 + - - +
432A TRP* 3.7 6.6 - - - -
433A GLU* 3.3 45.6 + - - +
448A ARG* 4.0 6.1 - - - +
629A THR* 4.3 4.3 + - - -
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Residues in contact with ALA 427 (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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425A HIS 3.4 4.5 + - - +
426A SER* 1.3 76.0 - - - +
428A THR* 1.3 70.8 + - - +
431A GLU 3.3 15.3 - - - +
432A TRP* 4.1 9.9 - - + -
433A GLU* 3.6 8.2 + - - +
448A ARG* 3.5 38.2 + - - +
453A LEU* 4.3 16.8 - - + -
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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