Contacts of the strand formed by residues 554 - 561 (chain A) in PDB entry 5ZF6
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 ILE 554 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA* 3.2 19.2 - - - +
235A ASN* 3.3 11.0 + - - -
236A ILE 2.9 11.3 + - - +
238A GLN* 4.0 22.4 - - + +
241A PHE* 3.9 49.1 - - + -
547A ILE* 3.7 33.4 - - + -
548A ALA 3.6 12.6 - - - +
553A GLY* 1.3 78.1 - - - +
555A THR* 1.3 63.3 + - - +
556A ALA 4.0 7.4 - - - +
575A ILE* 4.1 13.5 - - + -
579A SER* 5.5 0.4 - - - +
582A LYS* 4.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.4 2.4 - - - -
233A ALA* 2.7 35.9 + - - +
235A ASN* 4.0 22.2 - - + +
456A LYS 3.7 6.1 - - - +
457A ALA* 2.7 36.1 + - - +
460A PRO* 4.1 11.8 - - + +
461A VAL* 5.1 1.8 - - + -
506A VAL* 4.4 2.4 - - + +
548A ALA 2.9 13.4 + - - -
549A GLY* 3.6 16.0 + - - -
550A THR* 4.3 9.9 - - + -
554A ILE* 1.3 77.2 - - - +
556A ALA* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 3.3 13.0 - - - +
232A SER* 4.2 1.1 - - - +
241A PHE* 6.1 0.7 - - - -
453A LEU* 4.2 12.6 - - + -
456A LYS* 3.9 11.2 - - + -
457A ALA* 3.7 31.2 - - + +
485A MET* 6.2 0.2 - - + -
547A ILE* 3.4 5.6 - - - +
548A ALA* 2.9 29.1 + - + +
554A ILE* 3.8 4.3 - - - +
555A THR* 1.3 82.4 + - - +
557A LEU* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 4.2 25.4 - - + +
230A GLU* 3.5 3.1 - - - +
231A ALA* 2.7 40.7 + - + +
241A PHE* 3.6 37.5 - - + -
245A ILE* 4.8 0.7 - - + -
453A LEU* 4.5 2.7 - - - -
456A LYS* 4.7 0.2 + - - -
545A PHE* 3.5 46.2 - - + -
546A LYS 3.3 14.1 - - - +
547A ILE* 3.8 11.7 - - + -
556A ALA* 1.3 77.8 - - - +
558A GLN* 1.3 80.3 + - - +
559A ALA 4.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 3.6 30.4 + - - +
136A ARG* 4.0 4.7 - - - +
229A LEU 3.4 4.7 - - - -
230A GLU* 2.9 25.1 - - - +
449A GLY 4.9 3.8 + - - +
453A LEU* 3.5 34.7 - - + +
544A ASP 3.3 5.2 - - - +
546A LYS* 2.8 42.2 + - - +
557A LEU* 1.3 74.4 - - - +
559A ALA* 1.3 58.9 + - - +
560A ASP* 3.6 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 3.5 17.5 + - - +
228A MET* 4.5 2.9 - - - -
229A LEU* 2.7 40.1 + - + +
543A MET* 5.4 0.2 - - + -
544A ASP 3.8 3.4 - - - -
545A PHE* 3.6 32.1 - - + -
557A LEU* 4.1 1.1 - - + +
558A GLN* 1.3 70.7 - - - +
560A ASP* 1.3 61.9 + - - +
561A ILE* 3.6 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 2.9 35.2 + - - +
543A MET* 3.2 4.4 - - - -
544A ASP* 2.9 47.9 + - + +
546A LYS* 2.5 33.5 + - - -
558A GLN* 3.6 12.0 + - - -
559A ALA* 1.3 69.5 - - - +
561A ILE* 1.3 62.0 + - - +
562A LYS* 3.6 5.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 5.1 1.7 - - - +
140A PRO* 3.5 19.2 - - - +
226A ILE* 3.6 36.8 - - + +
227A VAL 3.5 23.8 + - - +
228A MET* 4.3 0.9 - - - +
229A LEU* 5.1 0.2 - - + -
542A ASP 3.8 6.1 - - - +
543A MET* 4.1 16.4 - - + +
545A PHE* 5.7 0.2 - - + -
559A ALA* 3.6 23.0 + - + -
560A ASP* 1.3 72.1 - - - +
562A LYS* 1.3 62.6 - - - +
563A LEU* 3.5 21.5 - - + +
565A GLY 4.5 0.4 - - - +
566A ILE* 4.0 35.2 - - + -
571A VAL* 5.2 2.0 - - + -
----------------------------------------------------------
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