Contacts of the helix formed by residues 559 - 569 (chain A) in PDB entry 5SY1
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 VAL 559 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 4.1 15.3 - - + -
229A VAL* 4.6 7.4 - - + -
232A ILE* 4.3 15.0 - - + -
557A HIS* 2.9 26.2 + - + +
558A PRO* 1.3 80.9 - - - +
560A MET* 1.3 61.3 + - - +
561A LYS 3.2 1.3 - - - -
562A ALA* 3.2 5.7 + - - +
563A PHE* 2.7 27.0 + - - +
12C GLU* 4.7 5.2 - - + +
13C PHE* 3.6 32.5 - - + -
16C ALA* 4.0 12.6 - - + -
69C PHE* 5.2 7.6 - - + -
73C MET* 4.5 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A SER 4.7 3.1 - - - +
555A GLN* 3.5 34.1 - - - +
556A SER* 4.7 0.2 - - - -
557A HIS* 3.3 17.1 + - + +
559A VAL* 1.3 79.5 - - - +
561A LYS* 1.3 61.8 + - + +
563A PHE* 3.6 9.1 - - - +
564A CYS* 3.3 31.7 + - - -
16C ALA* 4.2 12.3 - - + +
19C LEU* 3.9 36.1 - - + +
20C PHE* 3.9 29.4 - - + -
36C VAL* 4.8 15.7 - - + -
40C LEU* 4.9 9.4 - - + +
69C PHE* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 5.9 0.4 - - - +
81A LEU 3.5 20.4 + - - -
82A ASP* 3.3 25.1 + - - +
83A HIS* 4.4 0.6 - - + +
218A GLU* 3.7 25.2 + - - +
219A ASP* 4.4 13.6 - - + +
225A TYR* 3.2 40.9 + - + +
556A SER* 4.7 19.3 - - - +
557A HIS 3.1 18.2 + - - +
558A PRO* 4.6 2.2 - - + -
560A MET* 1.3 79.8 - - + +
562A ALA* 1.3 59.7 + - - +
564A CYS* 4.2 2.9 + - - +
565A GLY* 4.0 10.9 + - - -
40C LEU* 4.4 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 3.4 41.8 - - + +
226A ARG* 5.2 1.1 - - - -
229A VAL* 3.7 16.4 - - + -
558A PRO 3.8 7.4 + - - +
559A VAL 3.2 8.3 + - - +
561A LYS* 1.3 79.1 - - - +
563A PHE* 1.3 61.8 + - - +
565A GLY* 3.4 10.2 + - - +
566A LEU* 3.7 10.6 + - - +
73C MET* 4.0 8.0 - - + +
77C MET* 4.8 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A VAL* 2.7 21.1 + - + +
560A MET* 3.7 8.3 - - - +
561A LYS 3.4 0.6 - - - -
562A ALA* 1.3 71.5 - - - +
564A CYS* 1.3 70.3 + - - +
565A GLY 3.1 1.3 - - - -
566A LEU* 3.2 13.0 + - + +
567A LEU* 3.4 45.6 + - + +
20C PHE* 3.7 28.9 - + - -
28C ILE* 5.9 3.4 - - + -
33C LEU* 5.3 5.6 - - + -
56C VAL* 4.8 10.1 - - + -
64C ILE* 5.7 5.2 - - + -
69C PHE* 3.6 39.0 - + + -
72C MET* 4.2 19.7 - - + -
73C MET* 3.4 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP* 4.5 13.0 - - + +
560A MET 3.3 17.3 + - - +
561A LYS 4.2 2.9 + - - +
563A PHE* 1.3 88.5 - - - +
565A GLY* 1.3 57.4 + - - +
567A LEU* 3.2 3.7 + - - +
568A LEU* 2.8 32.4 + - - +
20C PHE* 4.5 13.2 - - - -
36C VAL* 4.7 7.0 - - - -
37C MET* 3.7 38.3 - - + +
40C LEU* 4.5 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP* 4.8 8.5 + - - -
221A SER* 4.6 20.2 - - - -
561A LYS 4.0 7.1 + - - -
562A ALA* 3.4 11.0 + - - -
563A PHE 3.1 1.4 - - - -
564A CYS* 1.3 79.1 - - - +
566A LEU* 1.3 59.0 + - - +
568A LEU* 4.7 3.4 - - - -
569A GLN* 3.2 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ALA 3.7 5.6 + - - +
563A PHE* 3.2 10.1 + - + +
565A GLY* 1.3 78.4 - - - +
567A LEU* 1.3 59.9 + - + +
570A SER* 2.6 34.0 + - - +
55C GLU* 5.0 1.6 - - - +
72C MET* 3.9 21.1 - - + +
73C MET* 3.8 18.4 - - - -
76C LYS* 3.9 32.7 + - + +
77C MET* 3.6 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A PHE* 3.4 49.6 + - + +
564A CYS 3.2 7.2 + - - +
566A LEU* 1.3 81.8 - - + +
568A LEU* 1.3 60.8 + - - +
570A SER* 4.0 3.3 + - - -
571A SER* 3.2 21.3 + - - -
33C LEU* 4.8 12.1 - - + -
37C MET* 4.1 13.9 - - + -
52C MET* 3.6 52.0 - - + +
55C GLU* 5.6 4.7 - - - +
56C VAL* 4.5 13.7 - - + -
64C ILE* 6.0 1.8 - - + -
72C MET* 4.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 4.3 4.0 - - - +
219A ASP* 3.5 27.8 - - - +
564A CYS 2.8 16.4 + - - +
565A GLY* 4.4 3.1 - - - +
567A LEU* 1.3 76.1 - - - +
569A GLN* 1.3 67.4 + - + +
570A SER 3.1 3.1 - - - -
571A SER* 2.6 31.2 + - - +
572A GLY* 3.2 6.2 + - - -
37C MET* 5.8 7.4 - - - -
42C GLN* 3.8 31.6 - - + +
44C PRO* 5.8 6.1 - - + -
48C GLU* 5.6 2.9 - - - +
52C MET* 5.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP 5.0 0.8 + - - -
220A LEU* 3.9 16.6 - - - +
221A SER* 3.3 47.0 + - - +
565A GLY* 3.2 15.4 + - - +
568A LEU* 1.3 86.9 - - + +
570A SER* 1.3 58.5 + - - +
572A GLY* 4.5 2.5 - - - +
573A GLN* 3.6 33.7 - - - +
----------------------------------------------------------
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