Contacts of the helix formed by residues 486 - 502 (chain B) in PDB entry 1XSK
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 486 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TYR* 3.2 24.9 + - - +
485B ALA* 1.3 76.9 - - - +
487B TYR* 1.3 64.2 + - - +
488B GLU* 3.5 16.8 - - - +
489B SER* 2.8 37.1 + - - -
490B MET 3.0 14.2 + - - -
517B ASN* 5.5 1.8 - - - +
523B VAL* 4.3 11.6 - - - +
527B TRP* 3.6 10.9 - - - -
133C GLN* 6.0 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ASN* 1.3 70.2 - - - +
488B GLU* 1.3 65.4 + - - +
490B MET* 2.6 37.1 + - + +
491B ALA* 2.8 12.8 + - - +
522B HIS* 2.7 50.9 + + - -
523B VAL* 3.8 17.2 - - + +
526B ARG* 3.6 23.0 - - + +
620B PHE* 3.2 36.6 - - + +
621B THR* 3.3 18.4 + - - -
622B GLU* 3.5 13.3 + - + -
158C VAL* 4.0 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ASN* 3.5 18.2 - - - +
487B TYR* 1.3 83.6 + - - +
489B SER* 1.3 56.2 + - - +
491B ALA* 3.2 4.0 + - - +
492B GLU* 2.9 30.0 + - - +
495B ARG* 5.2 1.0 + - - -
128C ARG* 5.8 2.3 + - - -
156C LEU 3.8 20.4 - - - +
157C GLY* 4.3 14.5 - - - -
158C VAL* 3.9 14.3 - - - +
226C SER* 4.3 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 5.2 1.1 - - - -
483B CYS* 3.5 4.9 - - - +
484B TYR* 2.9 41.3 + - - -
486B ASN* 2.8 25.3 + - - -
488B GLU* 1.3 71.1 - - - +
490B MET* 1.3 57.4 + - - +
492B GLU* 3.0 28.5 + - - +
493B SER* 2.6 34.5 + - - -
527B TRP* 4.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ASN 3.0 7.3 + - - +
487B TYR* 2.6 35.2 + - + +
489B SER* 1.3 72.2 - - - +
491B ALA* 1.3 60.4 + - - +
493B SER* 3.3 4.9 + - - -
494B LEU* 3.1 20.3 + - - +
523B VAL 4.9 0.9 - - - +
526B ARG* 4.3 4.7 - - + +
527B TRP* 3.6 66.6 - - + -
530B PHE* 3.9 17.6 - - + -
618B PRO* 4.9 6.3 - - + -
619B VAL 3.4 22.2 - - - +
620B PHE* 3.3 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B TYR 2.8 9.2 + - - +
488B GLU* 3.4 8.7 - - - +
490B MET* 1.3 74.8 - - - +
492B GLU* 1.3 66.5 + - - +
494B LEU* 2.9 15.4 + - - +
495B ARG* 3.0 27.2 + - + +
605B ASP 5.3 0.2 - - - +
606B ARG* 5.6 4.5 - - + -
620B PHE* 3.6 23.5 - - + -
158C VAL* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.3 14.5 - - - +
188B THR* 2.7 44.6 + - - +
189B SER* 2.8 19.4 + - - -
488B GLU 2.9 12.8 + - - +
489B SER* 3.0 33.5 + - - +
491B ALA* 1.3 74.5 - - - +
493B SER* 1.3 64.8 + - - +
495B ARG* 3.4 32.8 - - - +
496B GLY 3.1 16.1 + - - -
225C VAL* 3.4 17.0 - - + +
226C SER* 4.8 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 4.4 9.0 - - - -
188B THR* 4.7 2.1 + - - +
480B GLY* 6.0 2.7 - - - -
483B CYS* 3.6 23.3 - - - +
489B SER 2.6 22.7 + - - -
490B MET* 3.5 7.5 - - - -
491B ALA 3.0 0.6 - - - -
492B GLU* 1.3 79.0 - - - +
494B LEU* 1.3 65.3 + - - +
496B GLY* 3.1 2.5 + - - +
497B GLY 2.9 17.2 + - - -
508B TRP* 3.0 23.3 - - - -
510B HIS* 5.1 8.7 - - - -
527B TRP* 4.3 7.4 - - - -
530B PHE* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B MET 3.1 9.6 + - - +
491B ALA* 2.9 10.8 + - - +
493B SER* 1.3 74.6 - - - +
495B ARG* 1.3 64.4 + - - +
497B GLY* 2.9 3.3 + - - -
498B LEU* 2.8 34.1 + - + +
508B TRP* 4.3 1.6 - - - -
530B PHE* 3.6 31.3 - - + -
588B MET* 4.0 12.6 - - - -
605B ASP 3.3 23.6 - - - +
606B ARG* 3.8 22.2 - - - +
607B GLN 4.1 2.9 - - - +
608B TYR* 3.7 26.9 - - + -
618B PRO* 4.6 5.4 - - + -
620B PHE* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG 3.8 3.8 - - - +
169B PHE 2.7 30.5 + - - +
170B THR 3.2 22.2 + - - +
171B ALA* 4.3 3.8 - - - +
172B LEU* 4.0 14.6 - - + +
488B GLU 5.2 0.6 + - - -
491B ALA* 3.0 22.4 + - + +
492B GLU* 3.4 31.6 - - - +
494B LEU* 1.3 76.2 - - - +
496B GLY* 1.3 57.7 + - - +
498B LEU* 3.4 9.9 + - - +
499B SER* 2.9 33.4 + - - +
605B ASP* 3.7 33.1 + - + +
225C VAL* 3.7 22.4 + - - +
226C SER* 5.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.6 18.5 - - - +
168B ARG 3.1 19.2 + - - -
169B PHE* 3.9 16.2 - - - -
492B GLU 3.1 4.8 + - - -
493B SER 3.1 7.1 + - - -
495B ARG* 1.3 80.2 - - - +
497B GLY* 1.3 55.7 + - - +
499B SER* 3.4 1.6 + - - -
500B ILE* 3.1 23.4 + - - +
508B TRP* 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B SER 2.9 7.1 + - - -
494B LEU 2.9 6.7 + - - -
496B GLY* 1.3 73.9 - - - +
498B LEU* 1.3 66.9 + - - +
500B ILE* 3.1 18.3 - - - +
501B GLY* 3.3 5.2 + - - -
508B TRP* 3.4 41.3 - - - +
588B MET* 4.7 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 4.0 18.2 - - + -
494B LEU* 2.8 26.7 + - + +
495B ARG* 3.7 4.9 - - - +
497B GLY* 1.3 75.2 - - - +
499B SER* 1.3 62.9 + - - +
501B GLY* 3.2 4.5 + - - -
502B LEU* 3.1 26.6 + - - +
588B MET* 3.9 20.6 - - + +
589B ARG 4.1 0.4 - - - -
590B ALA* 4.0 25.4 + - + +
593B MET* 5.5 0.3 - - - +
604B LEU 4.7 0.4 - - - +
605B ASP* 3.7 33.7 - - + +
607B GLN 4.0 12.3 - - - +
608B TYR* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLY* 4.1 3.4 - - - -
166B GLY 3.3 9.6 - - - +
168B ARG 3.8 7.7 + - - -
170B THR 5.6 0.2 + - - -
172B LEU* 3.3 17.6 - - - +
174B ARG* 2.8 33.9 + - - -
495B ARG* 2.9 20.9 + - - +
496B GLY 3.6 4.7 - - - -
498B LEU* 1.3 78.2 - - - +
500B ILE* 1.3 60.3 + - - +
502B LEU* 3.1 16.0 + - - +
503B SER* 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY* 3.9 4.0 + - - -
167B GLU* 3.9 19.3 - - + +
195B LYS* 3.7 31.0 - - + -
478B HIS* 4.2 11.0 - - + -
496B GLY 3.1 15.6 + - - +
497B GLY 3.1 18.6 - - - +
499B SER* 1.3 73.6 - - - +
501B GLY* 1.3 66.7 + - - +
503B SER* 2.9 21.2 + - - -
505B PHE* 3.2 55.4 + - + +
507B PHE 5.5 0.4 - - - +
508B TRP* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.7 9.2 - - - +
497B GLY 3.3 3.9 + - - -
498B LEU 3.2 8.2 + - - -
500B ILE* 1.3 79.4 - - - +
502B LEU* 1.3 57.5 + - - +
503B SER 3.0 9.1 + - - -
504B GLY* 3.5 8.3 + - - -
505B PHE 3.3 17.9 + - - +
586B PRO* 3.6 31.4 - - - +
588B MET 4.7 2.2 - - - -
593B MET* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR* 3.9 31.9 - - + -
164B GLY* 4.1 13.1 - - - +
172B LEU* 4.3 12.8 - - + -
199B PHE* 3.7 17.7 - - - -
201B MET* 3.5 33.1 - - + +
251B LEU* 4.3 5.4 - - - -
498B LEU 3.1 17.1 + - - +
499B SER* 3.1 12.5 + - - +
501B GLY* 1.3 74.4 - - - +
503B SER* 1.3 57.9 + - - +
504B GLY 3.6 1.3 - - - -
590B ALA* 4.1 18.6 - - + -
592B MET* 4.1 13.5 - - - -
593B MET* 3.3 26.0 - - + -
----------------------------------------------------------
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