Contacts of the helix formed by residues 560 - 572 (chain A) in PDB entry 1LSH
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 SER 560 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 5.0 0.8 + - - +
558A LYS 3.7 0.8 + - - -
559A PRO* 1.3 76.7 - - - +
561A VAL* 1.4 59.0 + - - +
562A ALA* 3.4 9.1 + - - +
563A LEU* 3.2 27.8 + - - +
564A VAL* 2.9 27.9 + - - +
604A ALA* 4.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A SER* 1.4 73.2 - - - +
562A ALA* 1.3 54.9 + - - +
564A VAL* 3.4 2.1 + - - +
565A SER* 2.7 39.7 + - - +
600A ASP 5.7 0.9 - - - +
603A ALA* 5.6 1.1 - - + -
604A ALA* 3.5 29.9 - - + +
607A VAL* 3.8 39.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
560A SER* 3.2 8.4 + - - +
561A VAL* 1.3 80.0 - - - +
563A LEU* 1.4 60.1 + - + +
565A SER* 3.1 7.8 + - - -
566A MET* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 3.3 37.7 - - + +
534A LEU* 3.7 19.8 - - + +
554A PHE* 3.7 22.8 - - + -
559A PRO* 4.2 4.3 - - + -
560A SER* 3.2 20.9 + - - +
562A ALA* 1.4 74.4 - - + +
564A VAL* 1.3 68.7 + - - +
565A SER 3.2 0.2 + - - -
566A MET* 3.3 18.1 + - + +
567A VAL* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A PHE* 4.2 5.4 - - + -
555A PHE* 3.9 24.5 - - + -
559A PRO* 3.5 32.5 - - + +
560A SER 2.9 20.8 + - - +
561A VAL 3.9 4.0 - - - +
563A LEU* 1.3 75.8 - - - +
565A SER* 1.3 62.5 + - - +
567A VAL* 3.2 5.3 + - - +
568A ALA* 3.0 19.2 + - - +
587A MET* 4.0 8.9 - - - +
601A VAL* 5.3 1.1 - - + +
604A ALA* 4.0 17.0 - - + +
605A CYS* 4.1 9.0 - - - -
608A ALA* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A VAL* 2.7 33.4 + - - +
562A ALA* 3.1 8.3 + - - -
564A VAL* 1.3 74.4 - - - +
566A MET* 1.3 61.9 + - - +
568A ALA* 3.1 1.4 + - - +
569A VAL* 2.8 34.4 + - - +
607A VAL* 4.4 1.4 - - - +
608A ALA* 4.1 14.0 - - - -
611A MET* 3.6 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 3.9 23.6 - - + -
538A LEU* 3.9 22.4 - - + -
562A ALA 3.0 12.3 + - - +
563A LEU* 3.4 21.3 - - + +
565A SER* 1.3 75.0 - - - +
567A VAL* 1.3 62.6 + - - +
569A VAL* 3.4 5.5 + - - +
570A ARG* 3.1 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 3.5 31.2 - - + -
537A PHE* 3.6 33.0 - - + -
538A LEU* 4.9 0.9 - - - -
551A CYS* 6.0 0.2 - - - -
554A PHE* 3.7 16.6 - - + -
555A PHE* 4.9 4.3 - - + -
563A LEU 3.2 9.4 + - - +
564A VAL* 3.2 10.2 + - - +
565A SER 3.1 0.4 - - - -
566A MET* 1.3 74.7 - - - +
568A ALA* 1.3 65.4 + - - +
570A ARG* 3.3 4.9 + - - +
571A LEU* 3.1 21.0 + - - +
583A VAL* 3.6 24.7 - - + -
587A MET* 4.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A VAL 3.0 6.0 + - - +
565A SER 3.1 7.1 + - - +
567A VAL* 1.3 79.5 - - - +
569A VAL* 1.3 63.2 + - - +
571A LEU* 3.1 21.0 + - - +
572A ARG* 3.5 3.9 + - - +
587A MET* 4.1 18.6 - - + -
608A ALA* 3.4 42.6 - - + +
611A MET* 4.6 3.1 - - + -
612A LEU* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A SER 2.8 19.6 + - - +
566A MET* 4.0 4.9 - - - +
568A ALA* 1.3 76.3 - - - +
570A ARG* 1.3 60.9 + - + +
572A ARG* 2.9 39.3 + - - +
573A ARG* 4.3 3.6 + - - +
611A MET* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A PHE* 4.9 3.6 - - + -
538A LEU* 3.6 57.9 + - + +
566A MET* 3.1 20.9 + - + +
567A VAL 3.3 4.9 + - - +
569A VAL* 1.3 76.3 - - + +
571A LEU* 1.3 61.1 + - - +
572A ARG 3.3 0.7 + - - -
573A ARG* 3.5 12.8 + - - +
574A GLU* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A PHE* 4.5 11.2 - - + -
567A VAL 3.1 8.6 + - - +
568A ALA* 3.3 11.0 - - - +
569A VAL 3.0 0.6 + - - -
570A ARG* 1.3 76.8 - - - +
572A ARG* 1.3 65.0 + - - +
573A ARG 3.1 0.7 + - - -
574A GLU* 3.2 21.0 + - + +
579A VAL 4.6 0.4 - - - +
580A ALA* 3.8 26.2 - - + +
583A VAL* 3.9 21.8 - - + -
584A TYR* 4.1 19.5 - - + +
587A MET* 3.7 30.5 - - + -
612A LEU* 3.9 19.6 - - + +
616A LEU* 4.3 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ALA 4.0 0.7 - - - +
569A VAL* 2.9 32.1 + - + +
571A LEU* 1.3 78.2 - - - +
573A ARG* 1.3 64.0 + - + +
574A GLU 4.1 0.3 + - - -
611A MET 3.1 26.7 + - - -
612A LEU* 3.5 34.3 - - + +
613A GLY 4.4 2.8 - - - +
----------------------------------------------------------
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