Contacts of the strand formed by residues 450 - 457 (chain A) in PDB entry 6QHD
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 LEU 450 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 3.8 34.1 - - - +
310A VAL* 3.8 37.0 - - + +
313A PHE* 4.1 26.5 - - + -
314A ARG* 3.8 18.4 - - + +
445A VAL 3.5 1.2 - - - +
446A TYR* 3.3 7.9 - - - +
447A HIS 2.9 36.2 + - - +
449A GLY* 1.3 82.5 - - - +
451A LYS* 1.3 60.3 + - - +
452A ILE* 4.0 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 2.7 25.5 + - - +
444A GLU* 3.5 31.1 + - + -
445A VAL 3.4 4.7 - - - +
446A TYR* 3.4 42.6 + - + +
449A GLY 4.3 0.2 + - - -
450A LEU* 1.3 72.0 - - - +
452A ILE* 1.3 62.4 + - - +
453A ASP* 3.4 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 4.0 31.2 - - + -
314A ARG* 4.0 29.8 - - + +
317A MET* 4.0 20.4 - - + -
318A LYS* 3.9 24.2 - - - +
444A GLU* 3.5 1.2 - - - -
445A VAL* 2.9 43.9 + - + +
447A HIS* 5.8 2.9 - - + -
450A LEU* 4.4 15.3 - - + +
451A LYS* 1.3 79.2 - - - +
453A ASP* 1.3 70.0 + - - +
454A LEU* 3.8 13.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 3.4 32.8 + - - +
443A THR 3.7 8.5 - - - +
444A GLU* 4.4 4.9 - - - +
451A LYS* 3.4 34.2 + - - +
452A ILE* 1.3 73.0 - - - +
454A LEU* 1.3 62.9 + - - +
455A GLU* 5.4 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A MET* 3.6 31.4 - - + +
318A LYS* 4.0 9.0 - - - +
321A PHE* 3.6 32.8 - - + -
351A LEU* 3.9 20.9 - - + -
362A LEU* 5.0 1.1 - - + -
442A GLU* 3.5 2.8 - - - +
443A THR* 2.9 53.5 + - + +
445A VAL* 4.0 22.4 - - + -
452A ILE* 4.2 13.0 - - + +
453A ASP* 1.3 81.6 - - - +
455A GLU* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 4.8 8.4 + - - +
321A PHE* 3.7 7.1 - - - +
370A LYS* 4.5 11.2 - - - +
440A THR* 4.1 18.0 + - + +
441A PHE 3.5 13.0 - - - +
442A GLU* 4.1 14.4 - - + +
453A ASP* 4.2 1.9 + - + +
454A LEU* 1.3 76.0 - - - +
456A THR* 1.3 71.8 + - - +
457A HIS* 5.1 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 5.9 0.7 + - - -
321A PHE* 3.5 48.2 + - + +
322A VAL* 4.3 4.0 - - - -
323A VAL* 4.0 17.1 + - + +
349A VAL* 4.4 3.1 - - + -
440A THR* 3.4 5.2 - - - +
441A PHE* 2.8 35.1 + - + +
455A GLU* 1.3 77.7 - - - +
457A HIS* 1.3 83.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 3.6 13.5 - - - +
326A GLN* 5.1 0.7 + - - -
438A LEU* 4.2 22.2 - - + +
439A ILE 3.3 15.3 - - - +
440A THR* 3.6 14.6 - - - +
441A PHE* 4.3 1.8 - - - -
455A GLU* 5.1 6.0 + - - +
456A THR* 1.3 89.5 + - - +
458A SER* 1.3 83.5 + - - +
487A PRO* 3.9 18.9 - - + +
488A LYS* 3.2 46.6 + - + +
----------------------------------------------------------
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