Contacts of the strand formed by residues 536 - 546 (chain A) in PDB entry 6T2C
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 CYS 536 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 4.4 10.3 - - - -
324A LYS 3.5 8.5 - - - -
326A HIS* 3.8 9.0 - - + -
331A ASN* 3.3 25.6 - - - -
334A TYR* 3.6 41.3 - - + -
535A TYR* 1.3 76.6 - - - +
537A VAL* 1.3 62.5 + - - +
538A LEU* 3.9 7.5 + - - +
560A VAL* 2.9 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 4.0 2.5 - - - +
323A ILE* 3.0 14.1 + - + +
324A LYS* 2.9 49.4 + - + +
525A PRO* 3.7 26.5 - - + -
532A TRP* 5.2 0.7 - - + -
535A TYR* 4.3 9.6 - - + -
536A CYS* 1.3 75.2 - - - +
538A LEU* 1.3 72.1 + - - +
557A TYR* 4.1 3.8 - - + -
558A LEU 3.5 9.9 - - - +
559A TYR* 3.6 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA* 5.0 0.4 - - + -
321A THR 3.3 14.1 - - - +
322A ILE* 4.1 17.9 - - + -
323A ILE* 3.8 2.5 - - - -
334A TYR 4.7 2.9 - - - +
335A LEU* 3.8 31.4 - - + +
338A TRP* 4.0 27.8 - - + -
536A CYS* 4.6 9.0 - - - +
537A VAL* 1.3 76.1 - - - +
539A GLU* 1.3 61.4 + - - +
540A ILE* 4.0 10.8 - - + -
557A TYR* 3.3 14.0 - - - +
558A LEU* 3.0 53.6 + - + +
560A VAL* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 4.1 26.1 + - + +
319A LYS 4.0 4.2 - - - +
320A ALA* 3.8 3.5 - - - -
321A THR* 3.0 32.1 + - - +
323A ILE* 3.8 21.5 - - + +
526A ARG* 6.0 0.9 - - - -
538A LEU* 1.3 74.7 - - - +
540A ILE* 1.3 63.2 + - - +
541A GLY 4.7 3.8 - - - +
542A ASP* 5.3 0.7 - - - +
555A PRO* 3.3 26.6 - - + +
556A VAL 4.0 2.0 - - - +
557A TYR* 3.7 28.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 5.5 0.7 - - + -
316A GLY 4.0 1.0 - - - +
317A TRP* 3.8 33.1 - - + -
318A LYS* 3.4 27.4 + - - +
320A ALA* 4.3 9.0 - - + +
338A TRP* 3.9 32.5 - - + +
520A PHE* 4.1 20.0 - - + -
538A LEU* 4.0 13.0 - - + -
539A GLU* 1.3 76.2 - - - +
541A GLY* 1.3 61.0 + - - +
556A VAL* 3.0 24.1 + - + +
558A LEU* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 4.5 5.4 - - - -
316A GLY 3.3 12.6 - - - -
318A LYS* 3.7 9.1 - - - +
539A GLU* 3.8 0.9 - - - +
540A ILE* 1.3 82.2 - - - +
542A ASP* 1.3 72.2 + - - +
555A PRO* 3.3 6.9 - - - +
556A VAL* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.6 17.4 - - - -
315A TRP 4.3 6.2 - - - +
316A GLY* 3.5 12.5 + - - +
318A LYS* 3.3 23.9 + - - +
539A GLU* 5.3 0.6 - - - +
541A GLY* 1.3 80.6 - - - +
543A MET* 1.3 60.5 + - - +
553A MET* 3.8 26.0 - - + +
554A LYS 3.4 10.7 - - - +
555A PRO* 4.5 9.1 - - - +
556A VAL* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET* 3.6 26.5 - - - +
289A LYS 5.7 1.6 - - - +
290A LEU* 4.0 26.7 - - + -
313A THR 5.8 1.8 - - - +
314A PHE* 4.0 20.2 - - + -
522A LEU* 4.9 9.4 - - + -
542A ASP* 1.3 74.8 - - - +
544A GLU* 1.3 72.0 + - - +
545A ILE* 3.9 7.2 + - + +
553A MET* 3.3 5.2 - - - -
554A LYS* 2.9 34.1 + - + +
556A VAL* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A MET* 1.3 78.7 - - - +
545A ILE* 1.3 63.0 + - - +
546A ARG* 3.8 34.2 + - + +
551A THR* 6.0 1.6 - - + -
552A ILE 3.4 5.6 - - - +
553A MET* 2.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LEU* 5.2 11.2 - - + -
543A MET* 4.8 11.2 - - + +
544A GLU* 1.3 75.0 - - - +
546A ARG* 1.3 62.5 + - - +
547A THR* 3.8 25.8 - - + -
550A SER 3.8 1.6 - - - +
551A THR* 3.3 3.6 - - - -
552A ILE* 2.9 44.3 + - + +
554A LYS* 3.4 46.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLU* 3.8 31.8 + - + +
545A ILE* 1.3 73.0 - - - +
547A THR* 1.3 61.5 + - - +
550A SER 4.0 3.8 - - - -
551A THR* 3.2 30.5 - - + +
----------------------------------------------------------
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