Contacts of the strand formed by residues 430 - 434 (chain K) in PDB entry 6QX2
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 GLU 430 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428K GLU 4.8 4.6 - - - +
429K CYS* 1.3 75.4 - - - +
431K ILE* 1.3 53.0 + - - +
432K PHE* 4.0 10.9 - - + -
451K THR* 2.9 15.1 + - - +
452K GLN* 3.0 26.8 + - + +
453K ALA* 2.8 31.5 + - - +
500K TYR* 3.8 6.1 - - - -
502K LYS* 3.1 39.8 + - + +
504K VAL* 4.6 3.1 - - + -
598K PRO* 5.3 2.1 - - - +
601K ARG* 2.6 45.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 431 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418K LEU* 3.7 26.9 - - + -
430K GLU* 1.3 72.5 - - - +
432K PHE* 1.3 66.2 + - - +
433K LEU* 4.1 2.4 + - + -
453K ALA* 3.5 12.6 - - + +
455K LEU* 4.1 12.1 - - + +
484K ALA* 3.9 13.9 - - + -
485K PHE* 3.8 12.3 - - + -
500K TYR* 3.8 38.3 - - + -
502K LYS 2.9 6.5 + - - +
503K ILE* 3.7 31.8 - - + +
504K VAL* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 432 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430K GLU* 4.0 17.9 - - + -
431K ILE* 1.3 74.5 - - - +
433K LEU* 1.3 58.7 + - - +
434K VAL* 4.0 1.8 + - + +
443K THR* 4.7 0.9 - - + -
452K GLN* 3.6 42.2 - - + -
453K ALA 2.9 19.5 + - - +
454K ILE* 3.4 13.2 - - + +
455K LEU 2.9 30.9 + - - +
504K VAL* 3.4 34.3 - - + -
506K MET* 3.8 37.7 - - + -
595K THR 4.6 4.0 - - - -
596K MET* 4.0 25.1 - - + -
601K ARG* 4.1 8.3 - - - -
603K LEU* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431K ILE* 4.6 7.4 - - + +
432K PHE* 1.3 72.0 - - - +
434K VAL* 1.3 59.4 + - - +
455K LEU* 3.5 39.9 - - + +
457K LEU* 4.7 8.1 - - + -
481K MET* 4.5 10.3 - - + -
485K PHE* 4.4 11.0 - - + -
503K ILE* 3.7 16.2 - - + -
504K VAL 2.9 14.5 + - - +
505K ILE* 4.1 13.7 - - + +
506K MET* 2.9 30.7 + - - +
507K THR* 5.3 1.7 - - - +
520K LEU* 4.5 16.9 - - + +
524K PHE* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432K PHE 4.7 4.3 - - - +
433K LEU* 1.3 77.1 - - - +
435K GLU* 1.3 57.1 + - - +
439K ALA* 4.0 12.3 - - + -
440K GLY* 3.9 19.3 - - - +
443K THR* 4.0 12.6 - - + +
454K ILE* 4.0 12.1 - - + -
455K LEU 3.4 2.4 + - - -
456K PRO* 3.6 25.4 - - + -
457K LEU* 2.9 36.0 + - - +
506K MET* 3.6 43.1 - - + +
507K THR* 5.8 1.8 - - - +
583K LEU* 5.0 0.4 - - + -
----------------------------------------------------------
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