Contacts of the helix formed by residues 508 - 527 (chain C) in PDB entry 4P3N
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 ASP 508 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C GLY* 1.3 71.9 - - - -
509C ILE* 1.3 72.6 + - - +
510C GLU* 3.1 30.8 + - - +
511C VAL* 3.2 30.4 + - + +
512C TRP* 3.2 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C ARG* 3.2 46.7 - - - +
505C PHE* 4.5 12.2 - - + -
507C GLY 3.7 2.2 + - - -
508C ASP* 1.3 76.5 + - - +
510C GLU* 1.3 63.3 + - + +
512C TRP* 3.0 10.5 + - + +
513C ASP* 2.9 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 510 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ASP* 3.1 16.9 + - - +
509C ILE* 1.3 82.7 - - + +
511C VAL* 1.3 56.4 + - + +
513C ASP* 3.3 11.3 + - - +
514C GLN* 2.9 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C MET* 4.0 10.1 - - + +
507C GLY* 6.2 0.2 - - - -
508C ASP* 3.2 28.2 + - + +
509C ILE 3.2 0.4 - - - -
510C GLU* 1.3 73.9 - - - +
512C TRP* 1.3 65.7 + - - +
514C GLN* 3.1 10.9 + - - +
515C ALA* 2.9 21.8 + - - +
565C PHE* 3.7 39.5 - - + -
587C VAL* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C THR 4.6 0.2 - - - -
501C ARG* 3.4 43.1 - - + +
502C PRO* 4.0 5.4 - - + -
505C PHE* 3.2 24.8 - + + -
506C LEU 2.6 24.2 + - - -
507C GLY 4.3 1.1 - - - -
508C ASP 3.2 23.3 + - - -
509C ILE* 3.0 10.2 + - - +
511C VAL* 1.3 78.1 - - - +
513C ASP* 1.3 61.6 + - - +
515C ALA* 3.3 1.9 + - - +
516C GLU* 2.9 46.4 + - - +
538C ALA 3.3 23.3 - - - -
539C PHE 3.4 20.9 - - - -
540C TYR 4.2 1.1 - - - -
541C GLY* 3.4 15.9 - - - -
542C PRO* 3.4 26.9 - - + -
565C PHE* 4.0 21.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 513 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C ARG* 5.1 3.3 + - - -
509C ILE* 2.9 43.2 + - - +
510C GLU* 3.6 10.9 - - - +
512C TRP* 1.3 77.2 - - - +
514C GLN* 1.3 57.1 + - + +
516C GLU* 4.4 11.3 - - - +
517C LYS* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C MET* 3.6 28.6 - - + +
470C GLU* 5.5 4.2 - - - +
510C GLU* 2.9 26.3 + - - +
511C VAL* 3.1 8.0 + - - +
513C ASP* 1.3 76.3 - - + +
515C ALA* 1.3 60.6 + - - +
517C LYS* 4.3 4.5 - - - +
518C GLN* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C MET* 3.9 10.1 - - + -
472C ILE* 4.7 2.5 - - - +
511C VAL 2.9 12.0 + - - +
512C TRP 3.5 7.4 - - - +
513C ASP 3.1 0.2 - - - -
514C GLN* 1.3 76.4 - - - +
516C GLU* 1.3 66.5 + - - +
518C GLN* 3.0 8.4 + - - +
519C LEU* 2.9 25.7 + - - +
542C PRO* 4.3 5.8 - - + -
563C LEU* 3.9 17.9 - - + -
565C PHE* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 5.3 2.0 - - + -
500C THR* 3.4 22.5 - - + +
501C ARG* 2.8 41.5 + - - +
512C TRP* 2.9 31.5 + - + +
513C ASP* 4.2 12.5 - - - +
515C ALA* 1.3 72.9 - - - +
517C LYS* 1.3 61.8 + - - +
519C LEU* 3.3 9.6 + - + +
520C GLU* 2.9 40.4 + - + +
542C PRO* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C ASP 2.9 19.5 + - - +
514C GLN* 4.4 6.1 - - - +
516C GLU* 1.3 76.4 - - - +
518C GLN* 1.3 59.3 + - + +
520C GLU* 3.3 10.5 + - - +
521C ASN* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C MET* 3.0 25.7 - - - +
470C GLU* 3.2 32.3 + - - +
472C ILE* 3.5 7.1 - - + +
473C GLU* 3.5 44.6 + - + +
514C GLN 3.1 18.3 - - - +
515C ALA 3.0 7.2 + - - +
517C LYS* 1.3 77.7 - - + +
519C LEU* 1.3 66.7 + - - +
521C ASN* 3.3 7.8 + - - +
522C SER* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 4.6 5.6 - - + -
476C ILE* 3.6 33.7 - - + -
498C LEU* 4.3 23.6 - - + -
515C ALA 2.9 16.8 + - - +
516C GLU* 3.5 11.2 - - - +
518C GLN* 1.3 76.3 - - - +
520C GLU* 1.3 56.6 + - - +
522C SER* 3.5 4.5 - - - -
523C LEU* 2.9 34.0 + - - +
542C PRO* 3.7 39.7 - - + -
543C LYS 4.8 1.8 - - - +
544C ILE* 3.9 22.9 - - + +
561C ILE* 6.0 1.1 - - + -
563C LEU* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 520 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 3.7 22.8 - - + +
500C THR* 5.5 3.9 - - - +
516C GLU* 2.9 28.9 + - - +
517C LYS* 3.5 10.2 + - - +
519C LEU* 1.3 72.6 - - - +
521C ASN* 1.3 66.7 + - - +
523C LEU* 3.3 4.8 + - - +
524C ASN* 2.9 34.7 + - - +
530C TRP* 4.3 15.0 - - + -
532C LEU* 5.7 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 521 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLU* 3.5 32.0 - - - +
517C LYS* 2.8 29.0 + - - +
518C GLN* 3.5 3.8 + - - +
520C GLU* 1.3 75.1 - - - +
522C SER* 1.3 57.8 + - - +
524C ASN* 3.3 11.6 + - - +
525C GLU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 522 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLU* 2.6 33.8 + - - +
476C ILE* 4.1 18.8 - - - -
477C LYS* 3.6 11.6 + - - +
480C LEU* 4.3 3.3 - - - +
518C GLN 2.9 15.1 + - - -
519C LEU 3.5 4.3 - - - -
521C ASN* 1.3 72.8 - - - +
523C LEU* 1.3 67.6 + - - +
525C GLU* 3.3 15.2 + - - +
526C PHE* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 523 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C LEU* 3.8 22.7 - - + -
496C LEU* 4.6 19.7 - - + +
498C LEU* 3.7 33.9 - - + +
519C LEU 2.9 11.9 + - - +
520C GLU 3.6 4.7 - - - +
522C SER* 1.3 76.1 - - - +
524C ASN* 1.3 62.2 + - - +
526C PHE* 3.3 15.6 - - - +
527C GLY 3.6 3.3 + - - -
528C GLU 4.2 3.1 - - - +
530C TRP* 3.7 45.1 + - + -
544C ILE* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 524 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C GLU* 2.9 26.6 + - - +
521C ASN* 3.3 13.8 - - - +
523C LEU* 1.3 73.9 - - - +
525C GLU* 1.3 57.2 + - - +
526C PHE 3.0 3.8 - - - -
527C GLY* 2.9 23.4 + - - -
528C GLU 5.8 0.2 - - - -
530C TRP* 3.5 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 525 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLU* 4.4 13.2 - - - +
474C ASP* 5.8 0.2 - - - -
477C LYS* 3.8 42.5 + - - +
521C ASN 2.9 19.9 + - - +
522C SER* 3.3 21.1 + - - +
524C ASN* 1.3 73.0 - - - +
526C PHE* 1.3 61.4 + - - +
527C GLY* 3.1 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 526 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C LYS* 5.2 4.7 - - + -
480C LEU* 3.6 55.9 - - + -
481C ASP 4.3 0.7 - - - -
484C ARG* 3.5 34.5 - - - -
494C PHE* 4.1 21.3 - + - -
496C LEU* 3.9 24.2 - - + -
522C SER 2.9 17.8 + - - +
523C LEU* 3.3 8.1 - - + +
524C ASN 3.0 0.2 - - - -
525C GLU* 1.3 78.8 - - - +
527C GLY* 1.3 61.1 + - - +
528C GLU* 3.6 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 527 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C LEU 3.6 0.6 + - - -
524C ASN 2.9 16.1 + - - -
525C GLU 3.1 1.8 - - - -
526C PHE* 1.3 79.2 - - - +
528C GLU* 1.3 59.5 + - - +
----------------------------------------------------------
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