Contacts of the helix formed by residues 562 - 570 (chain A) in PDB entry 3S95
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 ASN 562 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A PRO* 3.0 35.0 + - + +
555A ARG 3.8 14.4 + - - -
556A THR* 3.7 12.2 - - + +
560A GLY 3.8 1.2 + - - -
561A LEU* 1.3 68.4 - - - +
563A VAL* 1.3 59.1 + - - +
564A ARG* 3.5 7.3 + - - +
565A GLY* 3.0 25.8 + - - +
566A PHE* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LEU* 3.2 25.0 + - + +
562A ASN* 1.3 72.4 + - - +
564A ARG* 1.3 65.9 + - - +
566A PHE* 3.3 4.3 + - - +
567A LEU* 2.9 23.6 + - + +
580A PHE* 3.9 12.5 - - + -
584A VAL* 4.1 21.3 - - + -
628A PHE* 3.7 30.7 - - + -
632A TYR* 3.9 15.3 - - + -
637A SER* 3.8 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ASN* 3.4 6.0 + - - +
563A VAL* 1.3 81.4 - - - +
565A GLY* 1.3 56.8 + - - +
567A LEU* 3.3 2.6 + - - +
568A ASP* 2.8 47.0 + - - +
632A TYR* 3.4 59.9 + - + +
635A GLY* 4.8 12.3 - - - -
637A SER* 5.8 2.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
554A PRO* 3.8 9.9 - - - -
562A ASN* 3.0 27.5 + - - +
564A ARG* 1.3 77.7 - - - +
566A PHE* 1.3 57.1 + - - +
568A ASP* 3.4 4.7 + - - -
569A ARG* 3.0 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A CYS* 3.6 33.4 - - + -
543A ILE* 3.9 15.5 - - + -
544A GLY* 3.7 16.8 - - - -
546A VAL* 4.3 2.7 - - + -
553A LEU* 3.6 29.2 - - + -
554A PRO* 3.9 7.9 - - + +
561A LEU* 4.2 12.6 - - + -
562A ASN 3.0 16.5 + - - +
563A VAL 3.7 4.3 - - - +
565A GLY* 1.3 72.2 - - - +
567A LEU* 1.3 61.6 + - - +
570A TYR* 2.8 44.8 + + + +
571A CYS* 2.9 29.5 + - + -
580A PHE* 3.3 33.9 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
11A GOL 3.9 7.4 + - - -
563A VAL* 2.9 24.0 + - + +
564A ARG* 3.7 4.0 - - - +
566A PHE* 1.3 79.6 - - - +
568A ASP* 1.3 66.0 + - - +
571A CYS* 3.8 31.4 + - + +
580A PHE* 3.5 28.7 - - + -
628A PHE* 4.5 0.7 - - + -
629A TRP* 3.9 29.6 - - + -
632A TYR* 3.5 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GOL 2.7 22.0 + - - -
564A ARG* 2.8 41.3 + - - +
565A GLY* 3.8 6.4 - - - +
567A LEU* 1.3 78.2 - - - +
569A ARG* 1.3 62.0 + - + +
632A TYR* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GOL 4.3 1.0 + - - -
5A GOL 2.8 55.7 + - - -
11A GOL 3.3 15.9 - - - -
552A TYR 5.3 0.4 - - - -
554A PRO* 4.1 18.3 - - - +
565A GLY* 3.0 24.4 + - - +
568A ASP* 1.3 83.0 - - + +
570A TYR* 1.3 74.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GOL 3.8 18.1 + - - -
5A GOL 3.8 33.9 + - - -
11A GOL 3.9 9.6 - - - -
544A GLY* 3.7 28.7 - - - +
546A VAL* 3.5 27.8 - - + +
552A TYR* 3.3 36.9 + - - +
554A PRO* 3.8 18.6 - - + -
566A PHE* 2.8 32.5 + + + +
568A ASP 3.7 0.2 - - - -
569A ARG* 1.3 97.7 - - + +
571A CYS* 1.3 63.0 + - - +
572A PRO* 3.1 10.4 - - - +
----------------------------------------------------------
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