Contacts of the helix formed by residues 518 - 536 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA 3.5 0.2 + - - -
218A PRO* 3.8 13.9 - - - +
515B GLU* 3.5 31.4 + - - +
516B THR* 3.1 8.2 + - - +
517B TYR* 1.3 73.7 - - - +
519B TRP* 1.3 69.7 + - - +
520B ASN 3.2 1.6 + - - -
521B ASN* 3.2 5.6 + - - -
522B SER* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 4.2 4.5 - - - -
209A LEU* 3.5 25.6 - - + -
210A LEU 3.9 0.9 - - - -
211A ARG* 2.9 67.1 - - + +
215A GLY 4.1 4.9 - - - -
216A ALA* 3.0 29.9 + - + +
218A PRO* 3.8 31.1 - - + +
219A ASP 5.2 0.7 - - - -
230A PRO* 3.6 33.7 - - + -
233A GLN* 3.0 26.8 + - - +
234A PRO 5.4 1.8 - - - -
517B TYR 3.3 2.5 + - - +
518B ASN* 1.3 81.3 + - - +
520B ASN* 1.3 92.5 + - + +
522B SER* 3.3 5.0 + - - -
523B SER* 3.4 11.1 + - - -
524B PHE 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 5.6 0.5 - - - +
209A LEU* 2.9 35.3 + - - +
230A PRO* 3.5 29.3 - - + +
233A GLN* 5.6 1.8 + - - +
518B ASN 3.2 0.6 + - - -
519B TRP* 1.3 103.4 - - + +
521B ASN* 1.3 81.1 + - - +
523B SER* 3.6 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ASN* 3.2 5.7 + - - -
520B ASN* 1.3 89.6 + - - +
522B SER* 1.3 72.3 + - - +
523B SER* 3.5 0.5 + - - -
526B ARG* 4.4 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B GLU* 4.3 10.2 + - - -
517B TYR 4.6 2.0 - - - -
518B ASN* 3.0 36.1 + - - +
519B TRP 3.9 3.1 - - - -
521B ASN* 1.3 76.3 - - - +
523B SER* 1.3 63.2 + - - +
524B PHE 3.2 3.6 - - - +
525B LEU* 4.1 14.8 - - - +
526B ARG* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 5.0 2.6 - - - +
208A GLU* 4.9 13.1 + - - +
209A LEU 3.0 29.7 + - - -
210A LEU* 3.5 17.4 - - - +
519B TRP* 3.4 11.5 + - - -
520B ASN* 3.7 14.4 - - - -
521B ASN 3.4 2.6 - - - -
522B SER* 1.3 76.1 - - - +
524B PHE* 1.3 61.5 + - - +
526B ARG* 4.0 6.2 - - - +
527B PHE* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 4.1 6.9 - - + +
211A ARG 4.3 15.0 - - - +
212A THR* 4.8 0.7 - - - -
213A GLY* 4.5 17.7 - - - -
216A ALA* 4.0 25.4 - - + -
244A TYR 5.9 1.6 - - - -
246A PHE 3.5 23.1 - - - -
248A PRO* 3.5 23.8 - - + -
249A TYR* 5.6 0.4 - - - -
250A ILE* 3.6 33.7 - - + -
251A ASP* 5.5 0.4 - - - -
514B MET* 4.4 20.2 - - + -
517B TYR* 4.2 11.9 - + + +
519B TRP 4.9 1.2 + - - -
522B SER* 3.2 1.4 - - - +
523B SER* 1.3 76.8 - - - +
525B LEU* 1.3 62.5 + - - +
527B PHE* 3.8 1.9 - - - +
528B ASN* 2.8 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B MET* 3.6 47.1 - - + +
515B GLU* 5.7 4.3 - - - +
517B TYR 5.4 1.6 + - - +
522B SER* 3.7 15.9 + - - +
524B PHE* 1.3 76.4 - - - +
526B ARG* 1.3 73.8 + - - +
528B ASN* 4.2 2.0 - - - -
529B GLU* 2.7 56.9 + - + +
547B GLY* 3.5 25.8 - - - +
548B VAL* 3.9 12.3 - - + -
555B HIS* 5.7 0.9 - - + -
559B LYS* 5.6 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 5.0 10.3 - - - +
521B ASN 4.4 6.7 + - - +
522B SER* 2.9 43.0 + - - +
523B SER* 4.1 5.8 - - - +
525B LEU* 1.3 94.1 - - - +
527B PHE* 1.3 61.4 + - - +
529B GLU* 2.6 47.2 + - - +
530B VAL* 3.0 29.1 + - + +
555B HIS* 4.2 10.5 + - - -
559B LYS* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.6 31.0 - - + -
210A LEU* 3.6 13.0 - - + -
250A ILE* 3.4 35.2 - - + -
253A LEU* 3.8 15.0 - - + -
254A PHE* 4.1 14.8 - + - -
259A MET* 4.9 4.5 - - + -
535A VAL* 3.7 31.4 - - + -
523B SER 3.2 17.5 + - - +
524B PHE 4.0 1.6 - - - +
526B ARG* 1.3 78.4 - - - +
528B ASN* 1.3 67.9 + - - +
530B VAL* 3.5 8.3 + - + +
531B LEU* 3.4 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO* 3.5 30.2 - - - +
250A ILE* 3.7 18.5 - - - +
253B LEU* 4.9 1.9 - - - +
259B MET* 5.5 2.8 - - - +
514B MET* 5.0 1.0 - - - +
524B PHE* 2.8 56.4 + - - +
525B LEU* 3.6 7.4 - - + +
527B PHE* 1.3 76.2 - - - +
529B GLU* 1.3 66.9 + - - +
531B LEU* 3.0 22.5 + - - +
532B LYS* 3.0 10.9 + - - +
548B VAL* 4.3 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU* 2.7 41.5 + - + +
526B ARG* 2.6 53.5 + - - +
528B ASN* 1.3 70.8 - - - +
530B VAL* 1.3 62.2 + - + +
532B LYS* 3.0 11.1 + - - +
533B ASN* 3.0 33.4 + - - +
547B GLY 4.8 0.2 - - - +
548B VAL* 4.4 5.8 - - + +
549B TRP 4.3 18.7 + - - +
555B HIS* 3.1 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN* 6.2 2.0 - - - +
534A ALA* 4.1 24.9 - - + +
535A VAL* 4.1 21.3 - - + -
526B ARG* 3.0 20.5 + - + +
527B PHE* 3.6 13.2 - - + +
528B ASN 3.1 0.4 + - - -
529B GLU* 1.3 76.9 - - + +
531B LEU* 1.3 60.9 + - - +
533B ASN* 3.7 6.9 + - - +
534B ALA* 3.6 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 4.5 0.4 - - + -
253A LEU* 3.5 18.4 - - + -
259A MET* 4.4 0.4 - - + -
531A LEU* 3.8 27.4 - - + +
534A ALA* 5.3 0.4 - - + -
535A VAL* 3.7 28.0 - - + -
253B LEU* 3.8 15.5 - - + -
259B MET* 3.3 24.8 - - + +
527B PHE* 3.4 42.8 + - + +
528B ASN* 3.0 15.5 + - - +
530B VAL* 1.3 74.5 - - - +
532B LYS* 1.3 66.2 + - - +
534B ALA* 3.6 4.8 + - - +
535B VAL* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASN* 3.0 46.6 + - - +
259B MET* 4.1 12.2 - - - +
528B ASN 3.0 5.6 + - - +
529B GLU* 3.0 8.9 + - - +
531B LEU* 1.3 73.6 - - - +
533B ASN* 1.3 58.5 + - - +
534B ALA 3.0 4.3 + - - -
535B VAL* 3.1 2.8 + - - +
536B ASP* 2.9 60.8 + - + +
541B ILE 2.7 30.2 + - - -
548B VAL* 3.8 23.6 - - + -
549B TRP 5.6 0.2 - - - +
550B PRO* 4.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B GLU* 3.0 27.1 + - - +
530B VAL* 3.7 6.1 + - - +
531B LEU 3.5 0.2 - - - -
532B LYS* 1.3 74.8 - - - +
534B ALA* 1.3 59.6 + - - +
536B ASP 4.1 6.8 - - - +
537B PRO* 3.7 22.3 - - - +
549B TRP 5.0 0.6 + - - -
550B PRO* 3.3 15.4 - - - +
551B SER* 3.0 45.0 + - - +
552B GLN* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A VAL* 3.3 28.6 - - + +
531A LEU* 5.2 1.6 - - - -
534A ALA* 3.7 23.6 - - + -
530B VAL 3.6 15.9 + - - +
531B LEU* 3.8 7.2 - - - +
532B LYS 3.0 0.8 + - - -
533B ASN* 1.3 80.1 - - - +
535B VAL* 1.3 62.6 + - + +
537B PRO* 4.4 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A PHE* 3.5 34.3 - - + -
530A VAL* 4.6 8.7 - - + -
531A LEU* 3.8 15.0 - - + -
204B LEU* 5.7 2.8 - - + +
205B ALA* 3.1 19.2 + - + +
206B ASN* 4.1 8.5 + - - +
259B MET* 3.7 36.6 - - + +
531B LEU 3.4 19.5 - - - +
532B LYS* 3.4 4.9 - - + +
534B ALA* 1.3 77.5 - - - +
536B ASP* 1.3 65.5 + - + +
537B PRO* 3.4 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN* 4.7 1.0 - - - +
205B ALA* 3.5 16.7 - - + +
258B ASN 5.3 0.4 - - - +
532B LYS* 2.9 42.7 + - + +
533B ASN* 3.9 9.1 - - - +
535B VAL* 1.3 79.0 - - + +
537B PRO* 1.3 69.4 - - - +
538B ASN 4.0 1.2 + - - -
539B GLY* 3.0 15.2 + - - -
540B ILE* 2.8 31.4 + - - +
541B ILE* 2.7 30.4 + - - +
550B PRO* 4.7 0.7 - - - +
----------------------------------------------------------
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