Contacts of the strand formed by residues 497 - 504 (chain F) in PDB entry 1ZM9
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 ALA 497 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F PHE* 3.9 28.9 - - + -
414F THR* 4.5 6.3 - - - +
440F HIS 3.8 0.2 - - - +
441F GLY* 3.5 2.6 - - - -
442F THR* 3.0 29.7 + - - +
444F LEU* 4.3 6.6 - - + +
447F ALA* 4.1 13.5 - - + -
482F ALA* 3.9 6.1 - - - +
496F GLY* 1.3 73.7 - - - +
498F LEU* 1.3 63.0 + - - +
499F LEU* 3.7 9.6 + - + +
573F THR* 4.0 4.3 - - - -
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Residues in contact with LEU 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439F TYR* 4.3 8.1 - - + -
440F HIS 3.9 4.5 - - - +
441F GLY* 3.8 13.2 - - - +
475F PRO* 3.9 28.5 - - + +
478F ALA* 3.8 26.9 - - + -
479F TYR* 4.2 21.8 - - + +
482F ALA* 5.0 2.7 - - + -
497F ALA* 1.3 71.2 - - - +
499F LEU* 1.3 70.1 + - - +
568F PRO* 4.3 0.2 - - - +
569F SER* 3.0 29.2 + - - +
571F ILE* 3.9 44.1 + - + +
573F THR* 4.3 5.4 - - + +
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Residues in contact with LEU 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F PHE* 4.5 13.0 - - + -
439F TYR* 3.1 8.8 - - - -
440F HIS* 2.6 52.7 + - + +
442F THR* 4.3 4.7 - - + -
447F ALA* 3.9 29.2 - - + +
450F ILE* 3.8 32.8 - - + -
451F VAL* 4.3 5.8 - - + -
497F ALA* 3.8 17.0 - - + +
498F LEU* 1.3 82.9 - - - +
500F ARG* 1.3 61.9 + - - +
566F VAL* 3.5 24.2 - - + -
567F ILE 3.9 2.5 - - - +
568F PRO* 4.7 3.1 - - + -
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Residues in contact with ARG 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F LEU* 4.0 16.4 - - - +
426F HIS* 4.0 0.6 + - - -
436F PHE* 3.5 22.5 - - + -
438F GLY 3.4 3.8 - - - -
439F TYR* 3.0 44.8 + - + -
499F LEU* 1.3 71.4 - - - +
501F VAL* 1.3 62.6 + - - +
502F TYR* 3.0 38.0 + - + -
565F VAL 3.9 0.9 - - - +
566F VAL* 3.1 18.5 - - - +
567F ILE* 3.0 22.6 + - + +
568F PRO 3.6 18.4 - - - +
569F SER* 4.1 3.4 - - - +
591F GLU* 3.3 15.7 + - - +
594F ILE* 3.1 40.4 + - - +
595F SER* 3.0 9.0 + - - -
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Residues in contact with VAL 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436F PHE* 3.5 5.2 - - - -
437F VAL* 3.0 40.5 + - + +
438F GLY 2.6 19.2 + - - +
440F HIS* 3.9 28.3 - - + -
469F PHE* 4.0 6.5 - - + -
471F ILE* 3.9 15.0 - - + -
500F ARG* 1.3 75.9 - - - +
502F TYR* 1.3 64.7 + - - +
556F LEU* 4.3 9.4 - - + -
564F THR* 4.0 28.0 - - + -
565F VAL 4.2 1.6 - - - -
566F VAL* 3.9 16.8 - - + -
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Residues in contact with TYR 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426F HIS* 2.8 35.1 + + - +
429F LEU* 3.4 39.3 - - + -
430F GLU* 6.0 1.1 - - + -
434F TYR* 4.4 13.0 - - + -
435F VAL* 3.2 12.6 - - - +
436F PHE* 3.4 40.4 - + + -
437F VAL* 4.4 0.2 - - - -
500F ARG* 3.0 43.0 + - + -
501F VAL* 1.3 76.5 - - - +
503F VAL* 1.3 61.2 + - - +
564F THR* 2.9 6.3 - - - -
565F VAL* 2.6 49.5 + - + +
567F ILE* 3.9 14.8 - - + +
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Residues in contact with VAL 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F TYR* 2.9 15.3 - - - -
435F VAL* 3.2 31.3 + - + -
437F VAL* 4.1 14.8 - - + +
502F TYR* 1.3 72.8 - - - +
504F PRO* 1.3 79.9 - - + +
507F SER* 3.0 22.0 - - - +
508F LEU* 5.2 1.3 - - + +
511F PHE* 3.8 25.6 - - + -
556F LEU* 4.3 1.6 - - + -
560F LEU* 3.9 14.8 - - + -
563F ARG 4.1 0.7 - - - -
564F THR* 3.5 27.1 - - + -
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Residues in contact with PRO 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433F GLY 3.9 2.5 - - - +
434F TYR* 3.5 25.8 - - + +
503F VAL* 1.3 85.1 - - + +
505F ARG* 1.3 63.8 + - - +
506F SER* 4.1 15.0 - - - +
507F SER* 2.7 33.0 + - - +
560F LEU* 4.9 0.4 - - + -
563F ARG* 2.8 54.1 - - + +
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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