Contacts of the helix formed by residues 505 - 523 (chain A) in PDB entry 1R1H
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 GLU 505 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 2.8 47.8 + - - +
502A LYS* 3.2 30.5 + - + +
503A GLU 3.4 0.2 - - - -
504A ASP* 1.3 117.2 - - - +
506A TYR* 1.3 65.6 + - - +
507A PHE 3.2 3.3 + - - +
508A GLU* 2.7 23.9 + - + +
509A ASN* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.8 5.4 - - + -
141A SER* 3.4 32.8 + - - +
142A CYS* 3.4 45.7 - - + -
148A ILE* 4.0 27.5 - - + +
151A ARG* 5.9 0.8 - - - +
381A SER* 3.8 35.3 + - - -
413A TYR* 3.9 28.4 - + - +
504A ASP 3.8 2.2 + - - -
505A GLU* 1.3 73.0 - - - +
507A PHE* 1.3 59.7 + - - +
509A ASN* 2.9 5.2 + - - +
510A ILE* 2.9 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 5.8 0.2 - - - +
151A ARG* 5.4 2.6 - - - +
155A PRO* 3.2 50.0 - - + -
156A LEU* 4.1 6.7 - - - -
159A LEU* 3.7 18.2 - - + -
378A LEU* 4.2 31.0 - - + -
381A SER* 4.3 9.4 + - - +
382A LEU* 3.6 29.8 - - + -
505A GLU 3.2 1.0 - - - -
506A TYR* 1.3 78.7 - - - +
508A GLU* 1.3 68.1 + - + +
510A ILE* 2.8 43.5 - - + +
511A ILE* 2.9 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 2.6 28.6 + - - -
155A PRO* 4.6 5.0 - - - +
502A LYS* 5.4 9.9 - - + +
505A GLU* 2.7 48.6 + - + +
507A PHE* 1.3 82.6 + - + +
509A ASN* 1.3 61.5 + - - +
511A ILE* 3.7 6.6 - - - +
512A GLN* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.0 14.0 - - + +
141A SER* 3.2 17.2 + - - -
501A TYR* 3.4 31.4 - - + +
502A LYS* 2.8 43.5 + - - +
505A GLU 3.0 14.8 + - - +
506A TYR* 2.9 8.8 + - - +
508A GLU* 1.3 82.2 - - - +
510A ILE* 1.3 57.6 + - - +
512A GLN* 3.4 10.3 + - - +
513A ASN* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 5.2 5.4 - - + -
381A SER* 3.9 18.4 - - - +
413A TYR* 3.3 25.0 + - + +
506A TYR* 2.9 42.1 + - + +
507A PHE* 2.8 58.3 - - + +
509A ASN* 1.3 74.4 - - + +
511A ILE* 1.3 76.8 + - + +
513A ASN* 3.1 3.8 + - - +
514A LEU* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.6 26.5 - - + -
194A TYR* 3.9 12.1 - - + +
374A PHE* 4.4 2.9 - - + -
378A LEU* 4.2 7.2 - - + -
507A PHE* 2.9 39.2 + - + +
508A GLU* 3.7 6.7 - - - +
510A ILE* 1.3 86.1 - - + +
512A GLN* 1.3 67.3 + - - +
514A LEU* 2.9 34.2 + - + +
515A LYS* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLU 3.7 5.9 - - - +
499A LEU* 3.2 22.4 - - + +
500A ASN 2.8 46.7 + - - -
501A TYR* 4.3 8.6 - - - -
508A GLU* 2.8 20.7 + - - +
509A ASN* 3.5 11.5 - - - +
511A ILE* 1.3 75.4 - - - +
513A ASN* 1.3 58.6 + - - +
515A LYS* 3.3 9.9 + - + +
516A PHE* 2.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.0 5.1 - - - +
413A TYR* 3.0 34.0 + - - +
417A ASN* 3.7 26.3 - - - +
499A LEU* 3.7 11.6 - - - +
501A TYR* 2.7 33.4 + - - -
509A ASN 3.0 15.6 + - - -
510A ILE 3.5 7.9 - - - +
511A ILE 3.1 0.2 - - - -
512A GLN* 1.3 78.1 - - - +
514A LEU* 1.3 62.6 + - + +
516A PHE* 3.2 4.2 + - - +
517A SER* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS 3.9 2.5 - - - +
194A TYR* 3.8 26.6 - - + +
195A GLY* 5.3 1.0 - - - -
374A PHE* 3.8 34.5 - - + -
378A LEU* 4.8 4.7 - - + -
510A ILE* 3.0 15.9 + - + +
511A ILE* 2.9 21.6 + - + +
513A ASN* 1.3 76.5 - - + +
515A LYS* 1.3 64.2 + - - +
517A SER* 3.4 3.7 + - - -
518A GLN* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 6.0 0.2 - - - -
192A SER 5.0 1.4 - - - +
193A LYS* 2.4 79.1 + - + +
194A TYR* 4.2 5.2 - - + -
511A ILE* 2.9 35.1 + - + +
512A GLN* 3.6 11.0 - - + +
514A LEU* 1.3 77.4 - - - +
516A PHE* 1.3 63.5 + - - +
518A GLN* 4.0 0.9 - - - +
519A SER* 3.0 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A GLU 3.7 16.2 - - - -
496A TYR* 5.3 1.1 - + - -
498A GLU* 3.7 32.5 - - + -
499A LEU* 3.8 37.7 - - + -
512A GLN* 2.8 18.6 + - + +
513A ASN* 3.2 4.5 + - - +
515A LYS* 1.3 78.9 - - - +
517A SER* 1.3 64.4 + - - +
519A SER* 3.8 4.4 - - - -
520A LYS* 2.6 75.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASN* 4.5 8.8 + - - -
513A ASN* 2.8 18.2 + - - +
514A LEU* 4.2 3.8 - - - -
516A PHE* 1.3 85.0 - - - +
518A GLN* 1.3 56.8 + - - +
520A LYS* 3.4 9.7 - - - +
521A GLN* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 3.0 45.3 + - - +
192A SER* 3.3 18.2 - - - +
193A LYS 4.9 0.7 - - - +
195A GLY* 4.0 17.5 - - - +
197A LYS* 3.8 19.1 + - - +
202A LEU 5.1 0.6 + - - -
203A PHE* 5.9 0.8 - - - +
514A LEU 3.2 16.7 + - - +
515A LYS 4.1 1.1 - - - +
516A PHE 3.2 0.2 - - - -
517A SER* 1.3 76.0 - - - +
519A SER* 1.3 64.5 + - - +
520A LYS 3.1 1.1 - - - -
521A GLN* 3.2 10.4 + - - +
522A LEU* 3.0 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER 4.6 3.2 + - - -
332A THR* 5.1 7.1 + - - -
333A VAL* 3.7 22.7 - - - +
515A LYS 3.0 18.8 + - - -
516A PHE* 3.8 4.9 - - - -
518A GLN* 1.3 77.2 - - - +
520A LYS* 1.3 61.5 + - - +
522A LEU* 3.5 3.1 + - - -
523A LYS* 3.2 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A GLU* 3.7 28.1 + - - +
516A PHE* 2.6 61.1 + - + +
517A SER* 3.4 10.3 - - - +
518A GLN 3.1 0.2 - - - -
519A SER* 1.3 79.1 - - - +
521A GLN* 1.3 60.2 + - - +
523A LYS* 3.7 23.1 - - + +
524A LYS* 3.8 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 6.0 2.5 - - + -
204A VAL* 2.8 40.6 + - + +
205A GLY* 4.3 5.5 - - - -
214A HIS* 5.3 2.8 - - - -
517A SER 3.1 16.8 + - - +
518A GLN* 3.2 15.4 + - - +
520A LYS* 1.3 74.1 - - - +
522A LEU* 1.3 68.6 + - + +
524A LYS* 3.2 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 4.9 0.4 - - - +
192A SER* 4.3 5.4 - - - -
202A LEU* 5.4 3.4 - - + -
203A PHE* 5.6 0.9 - - - -
204A VAL* 3.9 27.1 - - + +
329A ILE* 4.1 24.7 - - + +
330A MET* 3.8 25.5 - - + +
332A THR* 4.3 23.1 - - + -
333A VAL* 4.0 9.4 - - + -
335A ILE* 4.4 0.2 - - - +
518A GLN* 3.0 49.8 + - + +
519A SER 3.9 3.1 - - - +
520A LYS 3.3 0.2 - - - -
521A GLN* 1.3 74.4 - - + +
523A LYS* 1.3 58.7 + - - +
524A LYS 2.8 11.0 + - - -
525A LEU* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A VAL* 3.1 35.5 - - + +
335A ILE* 4.2 9.4 - - + +
519A SER* 3.2 19.9 + - - +
520A LYS* 3.7 16.8 - - + +
521A GLN 3.3 0.6 - - - -
522A LEU* 1.3 77.6 - - - +
524A LYS* 1.3 64.5 + - + +
525A LEU 3.1 3.3 + - - -
526A ARG* 4.3 3.1 + - - +
527A GLU* 3.8 17.2 - - + +
----------------------------------------------------------
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