Contacts of the strand formed by residues 502 - 509 (chain A) in PDB entry 5LZ6
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 GLY 502 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 3.6 2.1 - - - +
409A THR* 3.0 32.2 + - - -
433A PHE* 3.7 4.7 - - - -
434A GLU 3.3 12.8 - - - -
436A THR* 4.5 9.9 - - - -
500A GLY 3.6 2.0 + - - -
501A ARG* 1.3 78.3 - - - +
503A VAL* 1.3 70.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 3.6 50.7 - - + +
407A VAL 3.8 11.2 - - - +
408A PRO* 4.2 13.9 - - + -
433A PHE* 4.1 4.2 - - - -
434A GLU* 2.7 49.7 + - + +
436A THR* 5.6 4.9 - - - +
502A GLY* 1.3 80.8 - - - +
504A TYR* 1.3 74.1 + - - +
505A LEU* 3.7 3.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL 3.4 3.8 - - - +
406A ARG* 3.5 3.3 - - - -
407A VAL* 2.9 45.3 + - + +
409A THR* 3.9 7.0 - - + -
416A LEU* 3.5 37.0 - - + -
431A VAL* 3.9 11.9 - - + -
432A TYR 3.3 14.1 - - - -
433A PHE* 3.7 26.7 - + + -
479A ILE* 4.6 1.1 - - + -
496A HIS* 3.1 35.9 + + + -
497A GLN 3.3 6.9 + - - -
498A TYR* 3.4 34.2 + + - -
499A PRO* 3.1 15.9 - - - +
503A VAL* 1.3 73.3 - - - +
505A LEU* 1.3 59.0 + - - +
506A LEU* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A THR* 3.9 17.9 - - + -
405A VAL 3.7 2.0 - - - -
406A ARG* 3.5 39.9 - - + +
431A VAL* 3.4 4.0 - - - -
432A TYR* 2.7 43.9 + - + +
434A GLU* 4.0 9.4 - - + +
476A LEU* 3.9 35.2 - - + -
503A VAL* 4.1 11.2 - - + +
504A TYR* 1.3 79.4 - - - +
506A LEU* 1.3 65.0 + - - +
507A LYS* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL 3.6 1.6 - - - +
404A THR* 3.5 3.8 - - - -
405A VAL* 3.0 43.3 + - + +
407A VAL* 4.2 13.5 - - + -
416A LEU* 4.3 9.6 - - + -
418A TRP* 4.1 17.9 - - + -
419A GLU 6.1 0.2 - - - +
420A PHE* 6.1 0.2 - - + -
429A PHE* 4.2 21.1 - - + -
430A GLY 3.7 3.6 - - - -
431A VAL* 4.3 16.2 - - + +
504A TYR* 4.1 20.2 - - + -
505A LEU* 1.3 72.4 - - - +
507A LYS* 1.3 61.6 + - - +
508A PHE* 3.7 18.3 + - + -
522A TYR* 5.5 2.0 - - + -
524A VAL* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 4.6 15.7 - - + +
403A VAL 3.8 1.1 - - - -
404A THR* 2.8 38.6 + - + +
428A GLY 3.4 0.9 - - - +
429A PHE* 3.3 12.5 - - - -
430A GLY 2.9 35.7 + - - +
432A TYR* 4.0 32.5 - - + -
476A LEU* 6.3 1.3 - - - -
482A VAL* 4.5 11.9 - - + -
505A LEU* 4.1 15.7 - - - +
506A LEU* 1.3 72.7 - - - +
508A PHE* 1.3 60.9 + - - +
509A ASP* 3.7 2.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 4.5 8.5 - - + -
397A VAL* 4.0 16.7 - - + +
402A VAL* 3.6 2.8 - - - +
403A VAL* 2.9 35.8 + - + +
405A VAL* 3.8 30.5 - - + -
420A PHE* 4.0 25.1 - + + -
427A ILE* 3.9 24.0 - - + -
428A GLY 3.5 4.3 - - - -
429A PHE* 3.7 31.4 - + - -
506A LEU* 4.1 17.0 - - + -
507A LYS* 1.3 68.8 - - - +
509A ASP* 1.3 61.2 + - - +
510A ASN 3.7 1.6 + - - -
520A VAL* 3.8 32.8 - - + -
522A TYR* 4.2 12.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 3.6 25.3 - - + +
427A ILE* 3.4 2.8 - - - +
428A GLY* 2.8 40.4 + - - +
482A VAL* 4.1 24.3 - - + +
507A LYS* 3.7 4.6 - - + +
508A PHE* 1.3 71.0 - - - +
510A ASN* 1.3 59.4 + - - +
511A SER* 2.7 31.3 + - - -
512A TYR* 3.5 10.3 - - - -
----------------------------------------------------------
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