Contacts of the strand formed by residues 419 - 427 (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 LEU 419 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B GLN* 4.2 3.1 - - - +
326B ARG* 2.9 30.4 + - - +
392B LEU* 3.6 22.0 - - + -
416B THR* 3.2 24.4 + - + +
417B VAL 3.2 2.4 + - - -
418B GLY* 1.3 75.8 - - - +
420B VAL* 1.3 60.1 + - - +
421B GLY 3.4 25.6 - - - +
436B TYR* 3.0 35.7 - - + +
606B LEU* 4.1 16.6 - - + -
607B LEU 3.5 8.5 - - - +
608B TYR* 3.5 27.8 - - + +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN 3.5 27.1 - - - +
326B ARG* 3.3 24.7 - - - +
418B GLY 3.3 15.3 - - - +
419B LEU* 1.3 74.0 - - - +
421B GLY* 1.3 56.6 + - - +
434B ASP* 4.4 3.5 - - - +
436B TYR* 3.8 11.1 - - - +
438B CYS* 5.5 1.8 - - + +
474B ARG 5.7 0.2 - - - +
475B TYR* 3.4 36.5 + - + -
477B PHE* 3.9 25.1 - - + -
607B LEU* 2.7 16.9 + - + +
609B ASN* 4.1 11.2 - - + +
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Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 3.4 8.3 - - - +
420B VAL* 1.3 80.4 - - - +
422B PHE* 1.3 63.1 + - - +
434B ASP* 3.5 10.5 - - - -
436B TYR* 4.2 2.7 - - - -
464B TRP* 3.8 22.0 - - - -
475B TYR* 4.3 5.8 - - - -
606B LEU* 3.5 0.5 - - - -
607B LEU* 2.9 26.6 + - - +
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Residues in contact with PHE 422 (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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388B TRP* 5.3 4.3 - + + -
391B HIS* 5.3 2.7 - + - -
392B LEU* 4.6 15.5 - - + -
421B GLY* 1.3 75.6 - - - +
423B LEU* 1.3 70.1 + - - +
424B SER* 3.8 4.7 + - - -
433B GLU 3.5 2.1 - - - +
434B ASP* 3.2 7.6 + - - -
435B ALA* 2.8 47.2 + - + +
436B TYR* 3.6 24.2 - + + -
464B TRP* 4.1 2.0 - - - -
604B ASN* 3.7 31.4 - - + -
605B VAL 3.2 9.9 - - - -
606B LEU* 3.0 31.0 - - + -
627B ILE* 3.6 26.9 - - + -
629B THR* 3.4 21.8 - - + -
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Residues in contact with LEU 423 (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* 1.3 72.5 - - - +
424B SER* 1.3 59.6 + - - +
432B TRP* 3.5 56.7 - - + +
433B GLU 3.7 12.1 - - - +
434B ASP* 3.7 12.8 - - - +
439B VAL 4.4 0.2 - - - +
441B ALA* 4.2 17.0 - - + +
464B TRP* 3.7 50.0 - - + +
586B VAL* 5.3 4.3 - - + -
604B ASN* 3.3 7.6 + - - -
605B VAL* 2.8 47.7 + - + -
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 3.8 9.9 + - - -
423B LEU* 1.3 73.6 - - - +
425B HIS* 1.3 73.4 + - - +
426B SER 3.5 3.0 + - - +
432B TRP* 2.9 24.6 + - - +
433B GLU 4.4 3.6 + - - -
435B ALA* 5.8 1.1 - - - +
451B ASN* 3.4 15.8 + - - +
452B GLY* 3.5 6.2 + - - -
604B ASN* 2.6 27.1 + - - +
629B THR* 3.1 36.7 + - - -
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Residues in contact with HIS 425 (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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424B SER* 1.3 83.7 + - - +
426B SER* 1.3 66.2 + - - +
427B ALA* 3.4 2.3 + - - +
448B ARG* 2.9 40.0 + - + -
449B VAL 3.8 6.3 + - - +
450B PRO* 3.8 14.8 - - + -
451B ASN* 2.9 27.2 + - - +
452B GLY 4.2 4.6 + - - +
629B THR* 3.1 14.2 + - - +
630B GLU* 3.5 47.9 + - + +
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Residues in contact with SER 426 (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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424B SER 3.5 1.5 - - - +
425B HIS* 1.3 80.9 - - - +
427B ALA* 1.3 62.4 + - - +
432B TRP* 3.6 8.7 - - - -
433B GLU* 3.4 43.6 + - - +
435B ALA* 6.6 0.4 - - - -
448B ARG* 3.9 5.6 - - - +
629B THR* 4.2 3.6 + - - -
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Residues in contact with ALA 427 (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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425B HIS 3.4 4.0 + - - +
426B SER* 1.3 77.9 - - - +
428B THR* 1.3 69.8 + - - +
431B GLU 3.3 14.6 - - - +
432B TRP* 4.1 9.0 - - + -
433B GLU* 4.0 8.3 + - - +
448B ARG* 3.4 35.1 + - - +
453B LEU* 4.1 22.4 - - + -
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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