Contacts of the helix formed by residues 502 - 517 (chain C) in PDB entry 5U07
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 502 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ALA* 6.2 2.2 - - - -
429C LEU* 5.7 2.5 - - - -
492C GLY 3.6 5.4 - - - +
500C PRO* 3.3 8.8 - - - +
501C GLY* 1.3 91.0 - - - +
503C ALA* 1.3 64.1 + - - +
504C PHE 3.3 2.5 - - - +
505C ASN* 3.1 34.8 + - - +
506C LEU* 3.0 22.4 - - - +
537C PHE 5.3 3.8 + - - -
538C SER* 5.7 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 503 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C VAL* 4.4 14.5 - - + +
484C ILE* 4.3 17.7 - - + -
490C ALA* 5.5 0.2 - - + -
491C GLN* 4.4 8.1 + - - +
492C GLY 3.9 10.5 - - - +
493C TYR* 3.8 29.2 - - + -
500C PRO 4.4 2.0 + - - +
501C GLY 3.1 1.8 + - - -
502C ASN* 1.3 78.3 - - - +
504C PHE* 1.3 59.9 + - + +
506C LEU* 2.9 24.7 + - - +
507C VAL* 3.1 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 504 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TRP* 4.6 1.6 - + - -
422C ALA* 4.1 14.1 - - + -
425C ALA* 4.8 5.8 - - + -
426C ALA* 3.8 37.2 - - + -
429C LEU* 3.2 34.3 - - + +
473C TYR* 4.1 6.1 - - - -
477C ALA* 3.7 26.5 - - + -
480C VAL* 4.4 7.4 - - + -
481C PHE* 3.8 31.4 - + + -
484C ILE* 3.8 22.7 - - + -
500C PRO 6.0 0.9 - - - -
502C ASN* 3.3 0.4 - - - +
503C ALA* 1.3 75.5 - - + +
505C ASN* 1.3 58.3 + - - +
507C VAL* 3.1 20.8 - - + +
508C ALA 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 505 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU* 3.3 25.4 - - - +
432C ARG* 5.9 0.5 - - - -
502C ASN* 3.1 35.1 + - + +
503C ALA 3.0 1.2 - - - -
504C PHE* 1.3 77.1 - - - +
506C LEU* 1.3 61.8 + - + +
508C ALA* 3.8 2.0 - - - +
509C LEU* 2.8 39.9 + - + +
536C LEU* 2.7 28.0 - - - +
537C PHE 3.8 6.0 + - - +
538C SER* 3.4 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C GLN* 4.0 29.2 - - - +
492C GLY* 4.4 11.9 - - - -
502C ASN* 3.0 39.3 - - - +
503C ALA* 2.9 10.5 + - - +
505C ASN* 1.3 81.4 - - + +
507C VAL* 1.3 62.3 + - - +
509C LEU* 3.9 15.5 - - + +
510C ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C TYR* 3.5 20.6 - - + +
476C LYS* 3.8 43.7 - - + +
477C ALA* 4.4 3.4 - - + +
480C VAL* 4.8 13.0 - - + -
491C GLN* 5.2 3.0 - - - +
503C ALA 3.1 9.9 + - - +
504C PHE* 3.1 37.7 - - + +
506C LEU* 1.3 77.3 - - - +
508C ALA* 1.3 72.2 + - - +
510C ALA* 3.1 7.4 + - + +
511C ALA* 2.9 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU* 3.6 19.1 - - + -
433C LEU* 4.1 10.9 - - + +
473C TYR* 3.7 19.1 - - + -
504C PHE 2.9 17.9 + - - +
505C ASN* 3.9 3.1 - - - +
507C VAL* 1.3 77.6 - - - +
509C LEU* 1.3 57.4 + - - +
511C ALA* 3.7 1.5 - - - +
512C TYR* 2.8 31.2 + - - +
536C LEU* 3.8 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C ASN* 2.8 28.1 + - + +
506C LEU* 3.9 17.0 - - + +
507C VAL 3.2 0.2 - - - -
508C ALA* 1.3 76.1 - - - +
510C ALA* 1.3 63.8 + - - +
512C TYR* 3.7 3.3 - - - +
513C ASP* 3.0 30.7 + - - -
533C ARG* 3.9 31.9 - - + +
536C LEU* 3.8 29.8 - - + +
537C PHE* 3.3 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LYS* 6.1 4.0 - - - -
506C LEU 3.0 17.9 + - - +
507C VAL* 3.1 6.7 + - + +
509C LEU* 1.3 78.5 - - - +
511C ALA* 1.3 55.7 + - - +
513C ASP* 3.4 5.0 + - - +
514C GLU* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU* 5.0 2.5 - - + -
469C GLY* 4.3 7.5 - - - +
472C ARG* 4.6 8.5 - - + +
473C TYR* 4.1 34.5 - - + +
476C LYS* 5.8 3.1 - - + -
507C VAL* 2.9 16.3 + - + +
508C ALA* 3.7 5.2 - - - +
510C ALA* 1.3 77.0 - - - +
512C TYR* 1.3 62.0 + - - +
514C GLU* 3.0 14.9 + - - +
515C VAL* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU* 3.4 28.6 - - + +
436C ALA* 5.0 5.4 - - + -
437C CYS* 3.4 30.1 - - - -
440C ALA* 4.2 9.9 - - + +
465C TRP* 5.0 2.1 - + - -
469C GLY* 6.1 0.2 - - - -
508C ALA 2.8 21.5 + - - +
509C LEU* 3.7 6.3 - - - +
511C ALA* 1.3 73.1 - - - +
513C ASP* 1.3 68.5 + - - +
515C VAL* 3.0 10.0 - - + +
516C THR* 2.9 51.0 + - + +
529C VAL* 2.7 39.3 + - + +
532C HIS 4.6 0.9 - - - -
533C ARG* 3.4 38.5 + - + -
536C LEU* 4.5 4.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
509C LEU 3.0 17.8 + - - +
510C ALA* 4.0 4.6 - - - +
512C TYR* 1.3 80.1 - - - +
514C GLU* 1.3 57.9 + - - +
516C THR* 4.0 6.9 - - - +
517C GLY* 3.0 29.2 + - - -
533C ARG* 2.9 52.2 + - - -
219J ARG* 4.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C HIS* 4.7 1.0 - - - -
472C ARG* 3.1 56.7 + - - +
476C LYS* 4.9 16.7 + - - +
510C ALA* 2.9 34.7 + - + +
511C ALA* 3.0 8.9 + - - +
513C ASP* 1.3 79.0 - - - +
515C VAL* 1.3 59.9 + - - +
517C GLY 4.4 1.4 + - - -
518C PRO* 4.8 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C CYS* 4.8 10.5 - - - -
465C TRP* 3.7 40.3 + - + +
468C HIS* 3.8 30.7 - - + +
469C GLY* 4.4 12.8 - - - -
511C ALA 2.9 15.6 + - - +
512C TYR* 3.0 27.6 - - + +
514C GLU* 1.3 79.6 - - - +
516C THR* 1.3 66.1 + - - +
517C GLY 3.4 1.4 + - - -
518C PRO* 3.9 8.3 - - - +
519C TYR* 4.3 11.1 - - - -
34D GLU* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C TRP* 3.5 32.6 - - - -
512C TYR* 2.9 53.9 + - + +
513C ASP* 4.0 7.6 - - - +
515C VAL* 1.3 79.6 - - - +
517C GLY* 1.3 68.8 + - - +
518C PRO* 3.5 1.1 - - - -
519C TYR* 3.2 10.8 + - - +
520C CYS* 3.3 9.0 + - + +
529C VAL* 3.3 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C ASP 3.0 19.8 + - - -
515C VAL 3.3 0.6 - - - -
516C THR* 1.3 77.7 - - - +
518C PRO* 1.3 69.9 - - - +
519C TYR 3.1 1.9 + - - -
520C CYS* 3.3 13.6 + - - +
211J ARG* 3.1 22.1 + - - -
215J GLN* 5.4 2.2 - - - -
----------------------------------------------------------
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