Contacts of the strand formed by residues 582 - 588 (chain B) in PDB entry 1M2V
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 582 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557B VAL* 3.4 46.0 - - + -
558B MET 3.5 13.7 - - - +
559B ARG* 3.8 26.0 - - + +
571B PHE* 4.5 0.2 - - - -
576B PHE 4.1 0.7 - - - +
577B ASN* 2.8 26.8 + - - +
579B SER* 3.3 21.5 + - - +
580B SER 2.9 7.1 + - - +
581B ASP* 1.3 79.9 - - + +
583B CYS* 1.3 60.0 + - - +
584B ALA* 4.1 1.5 + - + +
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Residues in contact with CYS 583 (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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557B VAL* 3.5 6.0 - - - +
558B MET* 2.9 37.0 + - + +
571B PHE* 3.6 29.6 - - - -
575B PHE* 3.3 42.2 - - + -
576B PHE 3.5 4.0 - - - -
577B ASN* 4.1 2.2 - - - -
581B ASP 5.6 0.2 - - - -
582B LEU* 1.3 76.2 - - - +
584B ALA* 1.3 60.5 + - - +
585B PHE* 3.7 16.8 - - + -
596B PHE* 3.8 12.8 - - - -
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Residues in contact with ALA 584 (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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491B SER* 6.1 1.6 - - - -
494B GLN* 5.7 4.5 - - - +
519B THR 5.6 0.9 - - - -
520B ALA* 5.1 0.2 - - - +
556B THR 3.8 3.6 - - - +
557B VAL* 4.1 12.6 - - + -
575B PHE* 3.6 3.1 - - - +
576B PHE* 2.6 60.3 + - + +
582B LEU* 4.1 1.7 + - + +
583B CYS* 1.3 72.8 - - - +
585B PHE* 1.3 62.2 + - - +
586B SER 3.9 2.3 + - - +
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Residues in contact with PHE 585 (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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494B GLN* 4.9 1.1 - - - -
520B ALA* 3.8 20.0 - - + -
555B GLU 3.9 0.2 - - - -
556B THR* 2.7 44.0 + - - +
558B MET* 3.5 35.4 - - + -
574B HIS 3.7 7.2 - - - -
575B PHE* 3.5 28.9 - + + -
583B CYS* 3.7 19.1 - - + -
584B ALA* 1.3 76.3 - - - +
586B SER* 1.3 63.1 + - - +
587B THR* 2.8 21.8 + - - +
588B MET* 3.5 31.9 - - + -
594B TYR* 3.7 22.4 - + - -
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Residues in contact with SER 586 (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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490B CYS 3.6 5.4 + - - -
491B SER* 4.3 6.4 - - - -
494B GLN* 3.3 47.6 + - - +
495B ILE 3.2 26.7 + - - -
496B THR* 3.3 9.3 + - - -
519B THR* 4.4 7.0 + - - -
554B MET* 3.4 4.9 - - - +
555B GLU 3.1 18.2 + - - +
576B PHE* 6.2 0.2 - - - +
584B ALA* 3.9 3.8 + - - +
585B PHE* 1.3 69.7 - - - +
587B THR* 1.3 65.8 + - - +
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Residues in contact with THR 587 (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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440B GLY* 3.3 27.8 - - - +
441B LYS* 4.7 11.7 - - + -
494B GLN 4.9 0.2 - - - +
496B THR* 3.1 31.2 + - - +
520B ALA* 3.3 16.1 + - - +
552B PHE* 4.3 14.7 - - + +
553B CYS 2.9 16.4 - - - +
554B MET* 4.9 5.6 - - + -
585B PHE* 2.8 17.7 - - - +
586B SER* 1.3 80.8 - - - +
588B MET* 1.3 62.7 + - - +
589B PRO* 4.0 2.8 - - - +
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Residues in contact with MET 588 (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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209B PRO* 4.1 21.1 - - + -
210B TYR* 3.8 26.0 - - + -
552B PHE* 3.0 26.5 - - - -
553B CYS* 3.0 26.2 + - + -
556B THR* 4.0 19.1 - - + +
558B MET* 4.3 10.1 - - + -
585B PHE* 3.5 48.5 - - + -
587B THR* 1.3 74.3 - - - +
589B PRO* 1.3 81.9 - - + +
590B ARG* 3.1 2.9 + - - -
594B TYR* 4.5 5.8 - - + +
615B VAL* 4.4 5.2 - - + -
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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