Contacts of the strand formed by residues 497 - 504 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 4.1 22.9 - - + -
414B THR* 4.8 8.3 - - - +
440B HIS 3.9 0.7 - - - +
441B GLY* 3.5 0.9 - - - -
442B THR* 3.0 31.7 + - - +
444B LEU* 3.8 13.2 - - + +
447B ALA* 4.4 9.2 - - + -
482B ALA* 4.0 6.2 - - - +
496B GLY* 1.3 76.3 - - - +
498B LEU* 1.3 61.5 + - - +
499B LEU* 3.8 7.7 + - + +
573B THR* 4.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 5.8 0.2 - - - -
439B TYR* 4.4 8.3 - - + -
440B HIS 3.9 0.7 - - - -
441B GLY* 3.8 12.6 - - - +
475B PRO* 4.1 18.6 - - + +
478B ALA* 3.4 32.5 - - + -
479B TYR* 3.7 30.1 - - + +
482B ALA* 4.9 2.5 - - + -
497B ALA* 1.3 73.0 - - - +
499B LEU* 1.3 70.8 + - - +
568B PRO* 4.2 0.3 - - - +
569B SER* 3.2 34.2 + - - +
571B ILE* 3.7 40.3 + - + +
573B THR* 4.4 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 4.5 12.3 - - + -
439B TYR* 3.2 6.7 - - - +
440B HIS* 2.6 56.3 + - + +
442B THR* 3.9 12.3 - - + -
447B ALA* 4.0 22.0 - - + +
450B ILE* 3.8 35.7 - - + -
451B VAL* 4.6 5.4 - - + -
469B PHE* 6.1 0.2 - - + -
497B ALA* 3.9 13.7 - - + +
498B LEU* 1.3 85.7 - - - +
500B ARG* 1.3 62.7 + - - +
566B VAL* 3.5 18.6 - - + -
567B ILE 3.8 5.2 - - - +
568B PRO* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LEU* 3.9 15.2 - - - +
426B HIS* 3.8 0.8 + - - -
436B PHE* 3.9 17.6 - - + -
438B GLY 3.8 3.4 - - - -
439B TYR* 3.4 23.4 + - + -
498B LEU 4.2 0.4 + - - -
499B LEU* 1.3 71.5 - - - +
501B VAL* 1.3 60.4 + - - +
502B TYR* 3.1 42.0 + - + -
566B VAL* 2.9 21.5 - - - +
567B ILE* 2.9 22.7 + - + +
568B PRO 4.0 14.8 - - - -
569B SER* 4.1 5.4 - - - +
591B GLU* 3.2 27.8 + - - +
594B ILE* 2.7 42.3 + - - +
595B SER* 2.8 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B PHE* 3.3 8.0 - - - -
437B VAL* 2.7 49.2 + - + -
438B GLY 2.8 18.3 + - - +
440B HIS* 3.9 13.0 - - + -
469B PHE* 3.9 12.3 - - + -
471B ILE* 3.7 26.7 - - + -
500B ARG* 1.3 76.0 - - - +
502B TYR* 1.3 57.9 + - - +
556B LEU* 4.1 10.8 - - + -
564B THR* 4.0 25.1 - - + -
565B VAL 4.3 1.6 - - - -
566B VAL* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B HIS* 2.8 36.4 + + - +
429B LEU* 3.6 37.0 - - + -
430B GLU* 5.8 1.1 - - + -
434B TYR* 4.4 10.4 - - + -
435B VAL* 3.1 10.8 - - - +
436B PHE* 3.3 39.7 - + + -
437B VAL 4.5 0.2 - - - +
500B ARG* 3.1 39.2 + - + -
501B VAL* 1.3 74.4 - - - +
503B VAL* 1.3 62.8 + - - +
564B THR* 3.2 6.2 - - - -
565B VAL* 2.9 52.5 + - + +
567B ILE* 3.8 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B TYR* 3.2 7.9 - - - -
435B VAL* 2.9 36.6 + - + -
437B VAL* 3.8 20.8 - - + +
502B TYR* 1.3 72.8 - - - +
504B PRO* 1.3 77.5 - - + +
505B ARG 3.1 0.2 + - - -
507B SER* 3.5 16.8 - - - +
508B LEU* 5.3 1.6 - - + -
511B PHE* 3.6 29.6 - - + -
556B LEU* 4.5 1.6 - - + -
560B LEU* 4.0 14.1 - - + -
564B THR* 3.4 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLY 3.8 2.9 - - - +
434B TYR* 3.3 28.2 - - + +
503B VAL* 1.3 90.3 - - + +
505B ARG* 1.3 68.8 + - - +
506B SER* 2.8 18.0 + - - +
507B SER* 2.8 28.5 + - - +
560B LEU* 4.7 0.7 - - + -
563B ARG* 3.5 47.6 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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