Contacts of the helix formed by residues 510 - 521 (chain B) in PDB entry 4CQ8
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 510 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B PHE* 1.3 78.8 - - - +
511B GLY* 1.3 62.8 + - - +
512B LEU* 3.4 12.8 + - - +
513B ASP* 3.1 29.1 + - - +
514B ALA 3.0 18.5 + - - -
542B ILE* 3.5 14.7 - - - +
545B GLU* 3.3 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B SER* 1.3 72.7 - - - +
512B LEU* 1.4 55.5 + - - +
514B ALA* 3.3 4.1 + - - +
515B LEU* 2.9 30.5 + - - +
542B ILE* 3.8 7.5 - - - +
545B GLU* 3.0 31.2 + - - +
546B LEU* 3.9 18.4 - - - +
549B LEU* 3.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B SER* 3.2 10.2 - - - +
511B GLY* 1.4 72.7 - - - +
513B ASP* 1.4 65.8 + - - +
515B LEU* 3.4 3.3 + - + +
516B GLU* 3.1 42.7 + - + +
549B LEU* 3.5 21.2 - - + +
553B ARG* 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ARG* 5.1 2.9 + - - -
482B LYS* 3.0 35.6 + - + +
507B GLY 3.5 4.7 - - - +
508B ILE* 3.9 10.1 - - + -
509B PHE* 2.9 36.0 + - - +
510B SER* 3.1 24.2 + - - +
512B LEU* 1.4 77.9 - - - +
514B ALA* 1.4 61.9 + - - +
516B GLU* 3.3 12.1 + - - +
517B LYS* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 3.6 36.6 - - + -
508B ILE* 3.8 9.6 - - + +
510B SER 3.0 12.8 + - - +
511B GLY* 3.3 9.8 + - - +
513B ASP* 1.4 72.6 - - - +
515B LEU* 1.3 64.9 + - - +
517B LYS* 3.2 5.6 + - - +
518B ILE* 3.0 28.7 + - + +
525B CYS* 4.1 9.8 - - - -
546B LEU* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B GLY 2.9 16.5 + - - +
512B LEU* 3.4 4.9 + - + +
514B ALA* 1.3 75.2 - - - +
516B GLU* 1.4 57.0 + - - +
518B ILE* 3.3 6.6 + - + -
519B GLU* 2.8 59.7 + - + +
546B LEU* 4.1 8.2 - - + +
549B LEU* 3.7 33.0 - - + +
550B LEU* 4.0 24.2 - - + -
553B ARG* 3.8 30.3 - - + +
555B TYR* 4.2 2.0 - - + -
561B ALA* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LYS* 2.8 37.2 + - - +
486B THR* 4.3 17.2 + - + +
512B LEU* 3.1 32.9 + - + +
513B ASP* 3.4 12.0 - - - +
514B ALA 3.3 0.2 - - - -
515B LEU* 1.4 75.4 - - - +
517B LYS* 1.4 60.9 + - - +
519B GLU* 4.0 9.1 - - - +
520B ALA* 3.1 24.4 + - - +
565B LYS* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LYS* 3.3 11.3 + - - -
485B SER* 3.3 23.8 + - - -
486B THR* 3.0 27.6 + - - +
489B ILE* 3.7 18.4 - - + +
504B ALA* 3.6 20.0 - - + -
505B SER 4.6 1.4 + - - -
506B GLY* 2.9 31.1 + - - +
508B ILE* 3.7 27.4 - - + -
513B ASP 3.2 13.5 + - - +
514B ALA* 3.2 7.4 + - - +
516B GLU* 1.4 75.6 - - - +
518B ILE* 1.3 59.6 + - - +
520B ALA* 3.3 9.0 + - - +
521B GLY 3.2 6.9 + - - -
522B ALA* 3.0 23.5 + - + +
525B CYS* 4.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PRO* 4.9 3.4 - - + -
514B ALA 3.0 26.5 + - - +
515B LEU* 3.7 8.7 - - + +
517B LYS* 1.3 74.9 - - - +
519B GLU* 1.3 57.1 + - - +
521B GLY 3.0 9.2 + - - -
522B ALA 3.3 25.0 + - - +
523B SER 5.1 3.4 - - - -
525B CYS* 4.3 17.3 - - - -
546B LEU* 4.2 13.9 - - + -
558B LEU* 3.7 34.8 - - + +
561B ALA* 3.8 15.7 - - + -
562B ILE* 3.4 27.7 - - + +
563B GLY 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B LEU* 2.8 46.7 + - + +
516B GLU* 4.2 8.2 - - - +
518B ILE* 1.3 71.7 - - - +
520B ALA* 1.3 56.2 + - - +
521B GLY 3.2 0.2 - - - -
553B ARG* 4.6 10.4 + - - +
555B TYR* 2.7 32.7 + - - +
561B ALA 3.4 17.5 - - - +
563B GLY* 3.1 12.3 - - - -
564B ARG* 3.9 3.1 - - + +
565B LYS* 2.9 40.7 + - + +
566B HIS* 3.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B THR* 4.1 13.9 - - + -
489B ILE* 3.6 20.4 - - + +
490B CYS* 3.6 23.3 - - - -
493B TYR* 3.7 6.4 - - - +
516B GLU 3.1 19.8 + - - +
517B LYS* 3.3 8.7 - - - +
518B ILE 3.2 0.2 - - - -
519B GLU* 1.3 76.7 - - - +
521B GLY* 1.3 55.5 + - - +
565B LYS* 4.4 4.6 - - + +
566B HIS* 2.7 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 4.0 6.1 - - - -
493B TYR* 3.8 33.0 - - - -
501B PRO* 5.7 0.2 - - - +
502B ILE* 3.8 13.1 + - - +
518B ILE 3.0 8.0 + - - -
519B GLU 3.2 0.6 - - - -
520B ALA* 1.3 79.8 - - - +
522B ALA* 1.3 64.9 + - - +
523B SER* 3.9 1.0 + - - -
562B ILE* 3.8 7.0 - - - +
563B GLY* 3.8 9.6 - - - -
----------------------------------------------------------
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