Contacts of the helix formed by residues 509 - 522 (chain A) in PDB entry 1U9J
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 509 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 3.1 42.0 + - - +
493A TRP 2.8 19.0 + - - +
494A MET* 4.9 0.2 - - - -
498A LEU* 5.0 0.4 - - - +
507A GLY 3.8 1.0 + - - -
508A SER* 1.3 69.4 - - - +
510A ARG* 1.3 54.4 + - - +
511A ALA* 3.4 3.6 + - - +
512A ILE* 3.2 34.7 + - - +
513A THR* 2.6 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA* 5.4 12.6 - - - +
394A THR* 3.6 33.6 - - + +
395A PRO* 5.3 8.5 - - + -
492A ASN* 5.2 0.4 - - - +
499A ASP* 3.4 31.8 + - - +
500A ASN 3.4 16.7 + - - -
501A LEU* 3.8 20.2 + - + +
503A ALA 3.0 27.7 + - - +
505A ARG 3.3 17.2 + - - -
506A ILE* 4.9 0.2 - - - +
507A GLY 4.1 4.4 - - - +
508A SER* 3.0 31.0 + - - +
509A SER* 1.3 72.6 + - - +
511A ALA* 1.3 62.8 + - - +
513A THR* 3.3 8.7 + - - +
514A GLN* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 4.7 8.7 - - - +
509A SER* 3.2 7.9 + - - +
510A ARG* 1.3 78.8 - - - +
512A ILE* 1.3 64.5 + - + +
514A GLN* 3.4 5.7 + - - +
515A LEU* 3.2 29.7 + - + +
535A ARG* 6.1 1.3 - - + -
537A PHE* 5.0 4.3 - - + -
574A ILE* 4.6 21.3 - - + -
577A LEU* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A MET* 3.7 26.9 - - + -
498A LEU* 4.2 7.9 - - + -
509A SER* 3.2 28.5 + - - +
511A ALA* 1.3 76.2 - - - +
513A THR* 1.3 64.1 + - + +
515A LEU* 3.4 6.4 + - - +
516A ILE* 3.0 42.1 + - + +
537A PHE* 3.3 33.7 - - + -
577A LEU* 3.8 14.4 - - + -
581A LEU* 5.3 6.0 - - + +
645A THR* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 3.9 33.7 - - + -
499A ASP 4.3 12.6 + - - +
501A LEU* 3.6 15.9 + - + +
508A SER* 4.8 3.8 - - - +
509A SER 2.6 33.7 - - - +
510A ARG* 3.6 11.0 - - - -
512A ILE* 1.3 80.4 - - + +
514A GLN* 1.3 56.9 + - - +
516A ILE* 4.0 4.1 - - - +
517A LEU* 3.0 36.8 + - - +
649A PHE* 5.2 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 3.1 29.4 - - + +
510A ARG 3.0 18.6 + - - +
511A ALA* 3.7 6.3 - - - +
512A ILE 3.2 0.2 - - - -
513A THR* 1.3 75.8 + - - +
515A LEU* 1.3 63.5 + - + +
517A LEU* 3.2 15.6 + - - +
518A ASN* 2.9 43.2 + - - +
521A GLU* 5.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ALA* 3.2 15.2 + - + +
512A ILE* 3.7 4.7 - - - +
514A GLN* 1.3 77.7 - - + +
516A ILE* 1.3 64.7 + - - +
518A ASN* 3.0 15.4 + - - +
519A LEU* 3.0 26.1 + - - +
525A ILE* 3.2 37.9 - - + +
526A LYS 5.2 2.7 - - - +
574A ILE* 4.2 17.0 - - + +
577A LEU* 3.7 35.0 - - + -
578A GLY* 4.0 19.5 - - - +
581A LEU* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 4.4 7.6 - - + -
512A ILE* 3.0 40.7 + - + +
513A THR* 4.0 4.9 - - - +
515A LEU* 1.3 75.3 - - - +
517A LEU* 1.3 58.7 + - - +
519A LEU* 3.2 10.0 + - - +
520A VAL* 2.8 29.1 + - + +
581A LEU* 4.2 19.5 - - + -
645A THR* 4.1 15.7 - - + +
646A LEU* 4.2 35.4 - - + -
649A PHE* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 4.1 30.1 - - + +
513A THR* 3.0 34.0 + - - +
514A GLN* 3.4 12.8 - - - +
515A LEU 3.2 0.2 - - - -
516A ILE* 1.3 77.4 - - - +
518A ASN* 1.3 54.6 + - - +
520A VAL* 4.3 4.7 - - + -
521A GLU* 2.8 65.1 + - + +
649A PHE* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLN* 2.9 39.5 + - - +
515A LEU* 3.1 23.0 - - - +
517A LEU* 1.3 77.0 - - - +
519A LEU* 1.3 57.8 + - - +
521A GLU* 5.3 0.3 - - - +
522A GLY* 2.9 26.9 + - - -
523A SER* 3.0 37.8 + - - +
524A PRO 3.3 19.2 + - - +
525A ILE* 3.5 22.6 - - + +
526A LYS 4.4 2.2 - - - +
597A PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU 3.0 17.1 + - - +
516A ILE* 3.6 10.5 - - + +
518A ASN* 1.3 77.6 - - - +
520A VAL* 1.3 62.8 + - + +
521A GLU 3.5 0.2 + - - -
522A GLY* 3.7 5.5 + - - -
525A ILE* 4.3 8.7 - - + -
581A LEU* 3.8 31.6 - - + +
582A LEU* 3.9 6.1 - - + +
585A PHE* 3.6 66.3 - - + -
594A PHE* 4.3 0.7 - - - +
595A PRO* 4.2 7.6 - - - +
596A PRO 6.1 0.2 - - - -
597A PHE* 3.6 38.2 - - + +
646A LEU* 5.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ILE* 2.8 20.9 + - + +
517A LEU* 3.6 9.6 - - + +
519A LEU* 1.3 78.3 - - + +
521A GLU* 1.3 65.0 + - + +
594A PHE* 3.6 27.0 - - + -
595A PRO* 3.2 20.3 - - - +
649A PHE* 3.9 21.5 - - + -
650A LEU* 3.7 29.8 - - + -
653A VAL* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLN* 5.5 2.4 + - - -
517A LEU* 2.8 44.8 + - + +
518A ASN* 4.4 1.6 - - - +
520A VAL* 1.3 80.7 - - + +
522A GLY* 1.3 62.5 + - - +
523A SER* 3.9 16.8 + - - +
595A PRO* 3.4 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ASN 2.9 7.7 + - - -
519A LEU 3.7 2.8 + - - -
520A VAL 3.4 0.6 - - - -
521A GLU* 1.3 80.6 - - - +
523A SER* 1.3 60.7 + - - +
524A PRO* 4.7 0.2 - - - +
595A PRO* 3.2 24.5 - - - +
596A PRO 4.2 9.9 - - - +
597A PHE* 5.8 0.4 - - - -
598A ALA* 3.4 16.2 - - - +
----------------------------------------------------------
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