Contacts of the helix formed by residues 506 - 515 (chain A) in PDB entry 2P6U
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 506 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU* 1.3 75.5 - - - +
507A ASP* 1.3 58.8 + - - +
508A ILE 4.2 0.5 + - - -
509A GLY* 3.4 8.8 + - - -
510A ALA* 2.5 39.1 + - - +
542A GLU* 3.4 36.3 + - - +
615A SER 5.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A SER* 1.3 81.0 - - - +
508A ILE* 1.3 54.0 + - - +
510A ALA* 2.7 4.8 + - - +
511A LEU* 2.7 40.1 + - + +
568A LYS* 3.0 32.1 + - + +
571A ILE* 5.4 1.3 - - + -
572A GLU* 4.2 0.3 - - - +
619A LEU* 4.6 15.5 - - + +
622A ARG* 3.2 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A SER* 4.2 1.0 + - - -
507A ASP* 1.3 78.5 - - + +
509A GLY* 1.3 59.5 + - - +
511A LEU* 4.2 4.4 - - + +
512A HIS* 2.7 37.2 + - + +
539A LEU* 3.9 28.9 - - + -
542A GLU* 4.4 18.4 - - + +
543A LEU* 4.0 15.0 - - + -
561A VAL* 6.3 0.2 - - - -
564A ALA* 3.8 29.2 - - + +
565A LEU* 3.7 26.2 - - + -
568A LYS* 4.1 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU* 2.9 28.9 - - - +
506A SER* 3.1 14.6 + - - -
507A ASP 3.1 1.2 - - - -
508A ILE* 1.3 84.7 - - - +
510A ALA* 1.3 54.8 + - - +
512A HIS* 3.7 8.0 - - - +
513A LEU* 3.1 17.2 + - - +
542A GLU 3.9 15.5 - - - -
543A LEU* 4.7 1.3 - - - -
544A SER 4.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU* 3.1 14.3 - - + +
506A SER 2.5 21.1 + - - +
507A ASP* 2.7 5.5 + - - +
509A GLY* 1.3 70.0 - - - -
511A LEU* 1.3 65.5 + - - +
512A HIS 3.1 1.6 - - - -
513A LEU* 3.1 11.4 + - - +
514A ILE* 3.1 19.5 + - - +
604A MET* 4.0 2.0 - - + +
615A SER 5.3 0.7 - - - +
616A VAL* 3.5 31.4 - - + -
619A LEU* 3.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ASP* 2.7 24.7 + - + +
508A ILE* 3.8 6.1 - - - +
510A ALA* 1.3 73.9 - - - +
512A HIS* 1.3 62.9 + - - +
514A ILE* 3.3 10.9 + - + +
515A CYS* 3.2 23.0 + - - -
564A ALA* 3.5 18.6 - - + +
567A LEU* 3.5 17.8 - - + +
568A LYS* 3.3 47.1 - - + +
571A ILE* 5.0 5.4 - - + -
619A LEU* 3.8 17.3 - - + -
623A ILE* 3.2 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A ILE* 2.7 18.7 + - + +
509A GLY 3.7 3.6 - - - +
511A LEU* 1.3 79.0 - - - +
513A LEU* 1.3 62.7 + - - +
515A CYS* 3.0 13.2 + - - -
516A ARG* 3.1 27.3 + - + +
543A LEU* 3.6 33.9 - - + +
544A SER* 3.8 17.0 - - - -
545A TYR* 3.8 8.5 - - - -
557A PHE* 3.8 19.8 - + - -
560A GLU* 3.6 44.3 - - + +
561A VAL* 4.2 9.1 + - + +
564A ALA* 3.5 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 3.7 25.9 - - + +
496A PHE* 3.7 31.8 - - + -
499A VAL* 3.8 31.0 - - + -
500A LEU* 4.4 9.4 - - + -
505A LEU* 3.7 26.5 - - + -
509A GLY 3.1 6.4 + - - +
510A ALA 3.1 9.7 + - - +
512A HIS* 1.3 74.7 - - - +
514A ILE* 1.3 64.5 + - - +
516A ARG* 2.9 25.1 + - - +
517A THR 3.4 3.1 + - - -
544A SER* 3.9 12.3 - - - +
604A MET* 4.2 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 4.0 16.4 - - + -
510A ALA 3.1 13.8 + - - +
511A LEU* 3.3 18.8 - - + +
513A LEU* 1.3 79.0 - - - +
515A CYS* 1.3 61.6 + - - +
517A THR* 2.8 34.1 + - - +
520A MET* 3.6 21.5 - - + +
567A LEU* 5.0 1.8 - - + -
597A ALA* 4.1 13.0 - - + +
600A LEU* 4.1 17.7 - - + -
601A SER* 3.9 33.4 - - - +
604A MET* 3.9 21.1 - - + -
619A LEU* 4.4 4.5 - - + -
623A ILE* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LEU 3.2 13.2 + - - -
512A HIS 3.0 10.3 + - - +
514A ILE* 1.3 73.0 - - - +
516A ARG* 1.3 56.7 + - - +
517A THR 4.2 2.0 - - - -
520A MET* 3.9 14.1 - - + -
522A ARG* 3.2 18.0 + - + -
560A GLU* 2.9 41.6 - - - +
563A THR* 3.3 35.7 - - + -
564A ALA* 3.7 10.8 - - - -
567A LEU* 3.9 12.1 - - - -
----------------------------------------------------------
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