Contacts of the helix formed by residues 518 - 536 (chain A) in PDB entry 1W1J
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 518 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A GLU* 3.1 37.0 + - - +
516A THR* 3.0 11.3 + - - +
517A TYR* 1.3 73.9 - - - +
519A TRP* 1.3 72.7 + - - +
520A ASN 3.3 0.7 + - - -
521A ASN* 3.5 3.8 + - - +
522A SER* 2.9 36.7 + - - +
218B PRO* 3.6 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR 3.5 0.8 + - - -
518A ASN* 1.3 78.9 + - - +
520A ASN* 1.3 97.2 + - + +
523A SER* 3.1 16.5 + - - -
524A PHE* 4.6 2.4 + - - +
201B GLU* 4.1 6.1 - - - -
209B LEU* 3.8 24.9 - - + -
210B LEU* 3.7 6.7 - - - -
211B ARG* 3.1 69.6 - - + +
215B GLY 3.6 8.7 - - - +
216B ALA* 2.7 34.3 + - - +
217B LEU 5.4 0.2 - - - -
218B PRO* 3.9 25.2 - - + +
219B ASP 5.5 0.9 - - - -
230B PRO* 3.4 30.3 - - + -
233B GLN* 3.2 24.3 + - - +
234B PRO 5.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ASN 3.3 0.6 + - - -
519A TRP* 1.3 107.8 - - + +
521A ASN* 1.3 81.7 + - - +
523A SER* 3.2 12.2 + - - -
208B GLU* 5.2 2.1 - - - +
209B LEU* 3.0 32.1 + - - +
230B PRO* 3.8 28.5 - - + +
233B GLN* 5.4 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ASN* 3.5 3.3 + - - +
519A TRP 3.4 0.6 - - - -
520A ASN* 1.3 88.9 - - - +
522A SER* 1.3 70.0 + - - +
523A SER* 3.2 1.9 + - - -
526A ARG* 4.9 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A GLU* 3.2 24.4 + - - -
517A TYR 4.8 1.1 - - - -
518A ASN* 2.9 32.0 + - - +
519A TRP 3.8 0.4 - - - -
521A ASN* 1.3 77.8 - - - +
523A SER* 1.3 65.9 + - - +
524A PHE* 3.3 3.1 - - - -
525A LEU* 3.2 21.6 + - - +
526A ARG* 3.3 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TRP* 3.1 11.1 + - - -
520A ASN* 3.4 17.7 - - - -
521A ASN 3.2 3.5 + - - -
522A SER* 1.3 76.4 - - - +
524A PHE* 1.3 63.1 + - - +
526A ARG* 3.3 6.4 + - - +
527A PHE* 3.3 23.6 + - - +
204B LEU* 5.0 4.2 - - - +
208B GLU* 5.3 9.8 - - - +
209B LEU 3.0 26.6 + - - -
210B LEU* 3.5 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A MET* 4.2 22.0 - - + -
517A TYR* 4.2 11.2 + + + +
519A TRP* 4.6 2.6 + - - +
522A SER 3.3 0.6 - - - -
523A SER* 1.3 79.3 + - - +
525A LEU* 1.3 62.1 + - - +
527A PHE* 4.0 2.4 + - - +
528A ASN* 3.2 44.9 + - - -
210B LEU* 3.9 16.8 - - + +
211B ARG 4.2 17.7 + - - +
212B THR* 4.6 1.6 - - - -
213B GLY* 4.6 16.6 - - - -
216B ALA* 3.7 27.1 - - + -
244B TYR 6.0 0.7 - - - -
246B PHE 3.8 20.0 - - - -
248B PRO* 3.6 20.4 - - + -
250B ILE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A MET* 3.7 40.8 - - + -
515A GLU* 5.6 6.3 - - - +
517A TYR 5.0 2.5 + - - +
522A SER* 3.2 15.3 + - - +
524A PHE* 1.3 79.3 - - - +
526A ARG* 1.3 93.6 + - - +
528A ASN* 3.0 7.3 + - + +
529A GLU* 2.9 36.0 + - + +
547A GLY 3.3 25.8 - - - +
548A VAL* 3.8 11.2 - - + -
555A HIS* 6.0 0.9 - - + -
559A LYS* 5.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASN 4.9 4.4 + - - +
522A SER* 3.3 30.8 + - - +
523A SER* 3.3 9.7 + - - +
525A LEU* 1.3 94.9 - - - +
527A PHE* 1.3 62.2 + - - +
529A GLU* 2.8 52.9 + - - +
530A VAL* 3.1 19.0 + - + +
555A HIS* 4.1 15.0 + - - -
559A LYS* 5.8 2.8 - - - +
208B GLU* 5.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER 3.3 12.5 + - - +
524A PHE 4.2 2.0 - - - +
526A ARG* 1.3 76.8 - - - +
528A ASN* 1.3 67.0 + - - +
530A VAL* 3.2 20.7 + - + +
531A LEU* 3.3 43.2 + - + +
204B LEU* 3.9 34.5 - - + -
210B LEU* 4.0 15.0 - - + -
250B ILE* 3.4 37.7 - - + -
253B LEU* 4.6 6.3 - - + -
254B PHE* 4.0 16.4 - + - -
259B MET* 5.1 4.5 - - + -
535B VAL* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 5.2 0.7 - - - +
259A MET* 5.6 0.7 - - - +
514A MET* 4.5 3.4 - - - +
524A PHE* 3.2 49.7 + - - +
525A LEU* 3.0 14.8 + - - +
527A PHE* 1.3 83.4 - - - +
529A GLU* 1.3 59.8 + - - +
531A LEU* 3.5 9.3 + - - +
532A LYS* 3.2 21.8 + - - +
548A VAL* 4.2 16.4 - - + +
248B PRO* 3.9 25.3 + - - +
250B ILE* 3.5 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LEU* 2.9 33.5 - - + +
526A ARG* 2.8 44.2 + - - +
528A ASN* 1.3 72.5 - - - +
530A VAL* 1.3 65.7 + - - +
532A LYS* 3.2 7.3 + - - +
533A ASN* 2.8 38.7 + - - +
547A GLY 4.6 0.5 - - - +
548A VAL* 4.5 4.5 - - + -
549A TRP 3.8 17.5 + - - +
555A HIS* 3.4 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ARG* 3.1 22.6 + - + +
527A PHE* 3.2 13.6 + - + +
529A GLU* 1.3 75.6 - - - +
531A LEU* 1.3 64.9 + - - +
533A ASN* 3.1 5.6 + - - +
534A ALA* 3.0 21.0 + - - +
206B ASN* 6.2 1.6 - - - +
534B ALA* 3.3 38.4 - - + +
535B VAL* 4.5 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.8 16.2 - - + -
259A MET* 4.0 12.8 - - + -
527A PHE* 3.3 40.0 + - + +
528A ASN* 3.8 10.5 - - - +
530A VAL* 1.3 78.3 - - - +
532A LYS* 1.3 64.8 + - - +
534A ALA* 3.3 7.2 + - - +
535A VAL* 3.2 26.9 + - - +
250B ILE* 4.3 5.2 - - + -
253B LEU* 3.7 19.3 - - + -
259B MET* 4.3 9.9 - - + -
531B LEU* 3.8 21.3 - - + +
534B ALA* 5.2 0.7 - - + -
535B VAL* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASN* 2.6 46.5 + - - +
259A MET* 3.9 15.4 - - - -
528A ASN 3.2 12.0 + - - +
529A GLU* 3.4 8.5 - - - +
531A LEU* 1.3 81.7 - - - +
533A ASN* 1.3 66.2 - - - +
535A VAL* 3.0 3.7 + - + +
536A ASP* 2.9 49.3 + - + +
541A ILE* 2.6 28.5 + - - +
548A VAL* 4.0 18.4 - - + -
549A TRP 5.0 0.4 - - - -
550A PRO* 4.3 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A GLU* 2.8 38.4 + - - +
530A VAL* 3.8 5.3 - - - +
532A LYS* 1.3 73.5 - - - +
534A ALA* 1.3 63.3 + - - +
536A ASP 3.4 7.4 - - - +
537A PRO* 3.3 23.4 - - - +
549A TRP 4.5 1.2 + - - -
550A PRO* 3.4 15.8 - - - +
551A SER* 2.8 45.7 + - - +
552A GLN* 3.9 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A VAL 3.0 12.0 + - - +
531A LEU* 3.3 12.1 - - - +
533A ASN* 1.3 80.7 - - - +
535A VAL* 1.3 61.3 + - + +
536A ASP 3.5 0.3 + - - -
537A PRO* 3.7 11.4 - - - +
530B VAL* 4.1 23.4 - - + +
531B LEU* 5.3 0.9 - - + -
534B ALA* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 5.6 3.3 - - + +
205A ALA* 3.3 21.7 + - + +
206A ASN* 4.1 9.0 + - - +
259A MET* 3.7 32.1 - - + +
531A LEU 3.3 12.8 - - - +
532A LYS* 3.0 16.0 + - + +
534A ALA* 1.3 76.2 - - + +
536A ASP* 1.3 62.0 + - + +
537A PRO* 3.3 9.0 - - - +
527B PHE* 3.7 30.7 - - + -
530B VAL* 4.1 12.6 - - + -
531B LEU* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 4.7 1.0 - - - +
205A ALA* 3.6 15.7 - - + +
532A LYS* 2.9 39.6 + - + +
533A ASN* 3.4 15.4 - - - +
535A VAL* 1.3 81.8 - - + +
537A PRO* 1.3 67.9 - - - +
538A ASN 3.2 4.9 + - - -
539A GLY* 2.9 34.5 + - - -
540A ILE* 2.9 19.6 + - - +
541A ILE* 2.9 24.6 + - - +
550A PRO* 5.0 0.5 - - - +
----------------------------------------------------------
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