Contacts of the strand formed by residues 536 - 542 (chain A) in PDB entry 3C98
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 ARG 536 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 5.6 4.4 + - - +
9A VAL* 6.1 1.0 - - - +
183A LEU* 4.1 34.7 + - - +
185A GLU* 2.9 36.7 + - - +
225A LYS* 3.9 12.9 - - - +
228A SER* 3.0 16.2 + - - +
229A GLN 3.1 25.1 + - - +
532A ARG 5.7 0.2 + - - -
533A SER* 4.0 22.0 + - - +
534A GLY 4.1 4.3 - - - +
535A PRO* 1.3 75.5 - - - +
537A LEU* 1.3 58.9 + - - +
538A ILE* 3.9 13.4 + - + +
563A TRP* 4.0 3.1 - - - -
564A GLU* 2.8 39.1 + - - +
566A LEU* 4.0 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLN* 3.5 15.9 - - + +
231A LEU* 4.6 9.4 - - + -
486A MET* 3.8 26.7 - - + +
489A THR* 3.4 42.2 - - + +
490A ILE* 4.1 5.8 - - + -
536A ARG* 1.3 70.6 - - - +
538A ILE* 1.3 65.1 + - - +
539A ILE* 4.2 17.0 - - + -
563A TRP* 3.9 21.4 - - + -
564A GLU 3.1 7.9 + - - +
565A VAL* 3.4 20.1 - - + +
566A LEU 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.8 19.3 - - + +
179A LEU* 4.1 20.2 - - + -
180A CYS* 4.7 16.4 - - - -
183A LEU* 4.9 7.0 - - + -
185A GLU* 5.3 7.2 - - + -
187A PRO* 5.2 6.5 - - + -
228A SER* 6.4 0.7 - - - -
229A GLN 2.8 15.0 + - - +
230A LEU* 3.3 29.8 - - + +
231A LEU 2.8 26.5 + - - -
536A ARG* 4.5 15.0 - - + +
537A LEU* 1.3 78.0 - - - +
539A ILE* 1.3 63.0 + - - +
566A LEU* 3.3 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.1 6.8 + - - -
231A LEU* 3.8 25.1 - - + +
233A LEU* 4.0 14.1 - - + -
482A ILE* 3.5 34.1 - - + -
485A ILE* 4.6 4.3 - - + -
486A MET* 3.5 33.7 - - + -
537A LEU* 4.2 15.7 - - + +
538A ILE* 1.3 77.2 - - - +
540A PHE* 1.3 64.8 + - - +
541A ILE* 4.2 4.0 - - + -
565A VAL* 5.1 2.2 - - + -
566A LEU 2.7 13.9 + - - +
567A ILE* 3.5 13.7 - - + -
568A GLY 2.9 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.4 21.1 - + - +
147A LEU* 3.4 30.7 - - + -
172A LEU* 4.5 3.4 - - + -
176A ILE* 3.4 26.9 - - + -
201A LEU* 3.9 26.2 - - + -
230A LEU* 5.4 2.2 - - + -
231A LEU 3.0 13.2 + - - +
232A ILE* 3.7 12.7 - - + -
233A LEU* 2.9 27.0 + - - +
539A ILE* 1.3 73.5 - - - +
541A ILE* 1.3 71.2 + - - +
542A LEU* 3.9 16.4 - - + -
568A GLY 3.4 9.2 - - - -
569A SER* 3.8 16.8 - - - -
570A THR* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.6 8.5 - - + +
234A ASP 4.2 3.6 - - - -
235A ARG* 3.9 24.0 - - - +
237A PHE* 3.9 13.2 - - + -
482A ILE* 3.8 22.4 - - + -
539A ILE* 4.2 11.7 - - + -
540A PHE* 1.3 82.9 - - - +
542A LEU* 1.3 69.3 + - - +
543A GLY 3.4 0.3 + - - -
544A GLY 3.5 17.0 - - - +
545A VAL* 4.1 11.7 - - + -
549A GLU* 3.8 22.7 - - - +
567A ILE* 4.7 1.1 - - + -
568A GLY 3.1 11.0 + - - +
569A SER* 2.6 33.1 + - - +
570A THR 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.6 40.8 - - + -
157A TYR* 3.1 10.4 + - + +
169A LEU* 4.5 10.3 - - + -
172A LEU* 4.0 5.4 - - + -
195A TYR* 4.9 10.3 - - + -
197A ASP* 5.0 3.8 - - + -
198A ASN* 3.5 25.1 - - - +
201A LEU* 4.0 27.8 - - + -
232A ILE* 5.0 0.9 - - + -
233A LEU 2.9 15.2 + - - +
234A ASP* 4.2 4.9 - - + -
235A ARG* 2.9 29.8 + - - +
540A PHE* 3.9 18.5 - - + -
541A ILE* 1.3 69.3 - - - +
543A GLY* 1.3 58.4 + - - +
570A THR* 5.2 0.9 - - + -
----------------------------------------------------------
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