Contacts of the strand formed by residues 464 - 469 (chain D) in PDB entry 4G3D
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 TRP 464 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D LYS* 3.7 50.5 - - + +
431D VAL 3.6 17.9 - - - -
432D ARG* 3.8 38.8 - - + -
460D ARG* 3.2 6.5 - - - +
461D GLU* 2.8 38.8 + - + +
462D GLY 3.2 1.2 - - - -
463D PRO* 1.3 100.9 - - + +
465D VAL* 1.3 61.4 + - - +
466D ASN* 3.9 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D TRP* 3.8 31.4 - - + -
429D LYS 3.5 2.8 - - - +
430D LYS* 3.7 0.3 - - - -
431D VAL* 2.8 41.0 + - - +
433D LEU* 4.0 27.1 - - + -
436D PHE* 3.7 42.0 - - + -
458D ALA* 4.7 0.9 - - + -
459D VAL 3.8 2.5 - - - +
460D ARG* 4.2 4.7 - - + +
464D TRP* 1.3 75.7 - - - +
466D ASN* 1.3 64.4 + - - +
467D ILE* 3.6 12.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D GLU* 5.4 1.0 + - - -
399D TRP* 3.5 26.9 - - - -
428D VAL* 4.0 6.6 - - + +
429D LYS 3.8 3.4 - - - -
430D LYS* 3.4 30.0 - - - +
458D ALA* 3.3 4.5 - - - -
459D VAL* 2.8 45.2 + - + +
461D GLU* 4.2 16.2 + - - +
464D TRP* 4.1 16.4 + - - +
465D VAL* 1.3 72.1 - - - +
467D ILE* 1.3 61.6 + - - +
468D PHE* 3.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D ALA 3.7 0.7 - - - +
428D VAL* 3.4 2.8 - - - -
429D LYS* 2.7 44.5 + - + +
431D VAL* 3.7 27.1 - - + -
436D PHE* 4.1 11.4 - - + -
440D GLU* 3.9 21.5 - - + +
441D LEU* 3.8 21.8 - - + -
455D LEU* 3.5 25.8 - - + -
457D GLY 3.9 2.0 - - - -
458D ALA* 4.4 1.8 - - + -
465D VAL* 4.1 12.6 - - + +
466D ASN* 1.3 74.5 - - - +
468D PHE* 1.3 62.7 + - - +
469D MET* 3.7 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D LEU* 3.9 11.7 - - + -
386D LEU* 3.8 22.0 - - + -
393D TYR* 4.0 18.2 - + - -
399D TRP* 4.1 15.7 - + - -
417D MET* 3.5 32.3 - - - -
426D CYS* 4.4 1.6 - - - -
427D ALA 3.4 3.8 - - - +
428D VAL* 4.0 22.0 - - + -
455D LEU* 3.2 7.3 - - - +
456D TYR* 2.6 26.3 + - - -
457D GLY 2.8 33.6 + - - +
459D VAL* 3.8 24.7 - - + -
466D ASN* 3.4 28.5 - - + -
467D ILE* 1.3 71.6 - - - +
469D MET* 1.3 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D VAL* 5.9 3.1 - - + -
426D CYS* 3.3 3.1 - - - +
427D ALA* 2.9 44.2 + - + +
428D VAL 5.4 0.7 - - - -
429D LYS* 3.8 31.4 - - + +
453D VAL* 3.9 20.0 - - + -
454D PRO 3.4 15.0 - - - +
455D LEU* 4.1 6.7 - - + -
456D TYR* 3.7 11.1 - - - +
467D ILE* 3.7 30.5 - - + +
468D PHE* 1.3 74.8 - - - +
470D GLU* 1.3 65.7 + - - +
522D LEU* 5.8 3.4 - - + -
533D CYS* 4.9 13.7 - - - -
534D ASP 5.6 2.7 - - - +
----------------------------------------------------------
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