Contacts of the strand formed by residues 498 - 506 (chain D) in PDB entry 4QG0
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 PHE 498 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D PRO* 3.7 35.0 - - + +
480D VAL* 3.7 23.3 - - + -
481D ALA* 3.9 19.1 - - + -
493D LEU* 3.8 31.0 - - + -
494D LYS 3.5 17.9 - - - -
495D ALA 3.0 14.2 + - - +
496D GLU* 4.4 4.0 - - - +
497D ASP* 1.3 81.2 - - - +
499D ILE* 1.3 67.8 + - - +
500D VAL* 4.8 3.6 - - + -
552D VAL* 4.1 10.1 - - + -
553D TYR 3.4 11.4 - - - +
554D CYS* 5.0 1.3 - - + -
555D LYS* 5.2 0.9 + - - -
565D ALA* 3.9 28.9 - - + -
568D TYR* 3.9 15.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 499 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D ILE* 4.1 12.3 - - + -
384D THR* 4.3 17.7 - - + +
388D ASP* 5.0 1.1 - - - +
454D PHE* 3.4 39.5 - - + -
477D PRO* 5.7 0.2 - - - -
497D ASP 4.1 0.2 + - - -
498D PHE* 1.3 77.2 - - - +
500D VAL* 1.3 71.5 + - - +
501D ASP* 4.5 5.4 - - + +
551D ARG 3.7 0.7 - - - +
552D VAL* 3.3 5.7 - - - +
553D TYR* 2.9 54.0 + - + +
555D LYS* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 500 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D TYR* 5.2 7.0 - - - +
476D LEU* 3.9 31.5 - - + +
477D PRO* 3.6 38.9 - - + +
480D VAL* 4.3 7.0 - - + -
498D PHE* 4.8 2.9 - - + -
499D ILE* 1.3 82.0 - - - +
501D ASP* 1.3 60.2 + - - +
502D VAL* 3.9 6.0 + - + +
550D ILE* 3.7 27.8 - - + -
551D ARG 3.5 1.8 - - - -
552D VAL* 4.1 15.3 - - + -
572D TRP* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 501 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ARG* 2.9 44.5 + - - -
380D ASN* 3.7 16.1 + - - +
384D THR* 5.0 1.9 + - - -
499D ILE* 4.1 6.0 - - + -
500D VAL* 1.3 71.2 - - - +
502D VAL* 1.3 66.3 + - - +
503D ILE* 3.9 11.6 + - - +
549D LEU 3.6 3.3 - - - +
550D ILE* 3.7 0.7 - - - -
551D ARG* 2.8 43.2 + - + +
553D TYR* 4.0 19.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 502 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE* 4.6 7.6 - - + -
473D TYR* 3.5 43.6 + - + +
476D LEU* 3.8 28.5 - - + -
500D VAL* 3.9 5.9 + - + +
501D ASP* 1.3 80.7 + - - +
503D ILE* 1.3 68.8 + - - +
504D ASN* 4.2 2.8 + - - -
548D GLN* 3.5 32.8 - - + +
549D LEU 3.7 5.4 - - - +
550D ILE* 4.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 503 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ARG* 5.4 1.1 - - - +
375D GLN* 3.9 19.1 - - + +
380D ASN* 3.5 17.5 - - - +
501D ASP* 4.0 14.8 - - - +
502D VAL* 1.3 81.3 - - - +
504D ASN* 1.3 67.1 + - - +
505D MET* 3.6 30.9 + - + +
548D GLN* 3.2 5.9 - - - -
549D LEU* 2.9 45.2 + - + +
551D ARG* 3.2 44.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 504 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS* 4.3 13.7 + - - +
470D ARG* 3.8 19.0 - - - +
473D TYR* 3.7 17.6 + - - -
502D VAL 4.9 2.8 + - - -
503D ILE* 1.3 76.2 - - - +
505D MET* 1.3 63.1 + - - +
506D ASP* 3.9 14.1 + - - +
547D GLU 3.7 4.5 - - - +
548D GLN* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 4.5 3.9 - - + +
367D ASN* 3.2 34.1 - - - +
370D HIS* 3.6 27.8 - - + -
371D ARG* 4.4 9.9 - - + +
375D GLN* 4.1 14.1 - - - -
503D ILE* 3.8 20.6 - - + +
504D ASN* 1.3 73.5 - - - +
506D ASP* 1.3 61.2 + - - +
546D ALA* 3.2 2.4 - - - +
547D GLU* 2.9 50.0 + - + +
549D LEU* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 506 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 5.0 2.2 - - - -
366D ARG* 2.9 27.3 + - - +
367D ASN* 5.1 6.7 + - - +
504D ASN* 3.9 14.6 + - - +
505D MET* 1.3 76.2 - - - +
507D TYR* 1.3 68.3 + - - +
508D GLY* 2.8 28.6 + - - -
510D GLN* 3.3 32.4 + - - +
545D PHE 3.1 16.8 - - - +
546D ALA* 3.7 5.6 - - + +
----------------------------------------------------------
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