Contacts of the strand formed by residues 440 - 446 (chain T) in PDB entry 6O81
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 LYS 440 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146T LEU 5.0 3.8 - - - +
147T ASN* 3.0 44.9 + - - +
148T GLY* 4.4 5.3 - - - +
407T ASN 4.7 0.2 - - - +
408T ILE* 4.7 3.5 - - - -
438T GLY 4.0 0.4 + - - -
439T GLU* 1.3 72.1 - - - +
441T ILE* 1.3 60.4 + - - +
456T TRP* 6.2 3.1 - - + -
457T GLY 3.4 10.1 - - - +
458T GLN* 4.8 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 441 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146T LEU 5.7 0.2 - - - -
373T ILE* 5.4 8.5 - - + -
406T VAL* 5.3 6.3 - - + -
407T ASN 4.6 3.6 - - - -
408T ILE* 4.7 15.5 - - + +
439T GLU* 3.2 7.8 + - + +
440T LYS* 1.3 71.3 - - - +
442T ALA* 1.3 66.3 + - - +
456T TRP* 3.6 2.1 - - - -
457T GLY* 2.9 35.1 + - - +
459T ILE* 5.4 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143T ALA* 4.3 26.5 - - + +
146T LEU 4.7 2.4 + - - +
147T ASN* 5.1 0.4 - - - +
405T MET 5.5 0.2 - - - +
406T VAL* 3.4 21.1 - - - +
407T ASN* 3.7 27.2 + - + +
440T LYS 4.0 1.0 + - - -
441T ILE* 1.3 78.3 - - - +
443T LEU* 1.3 64.0 + - - +
444T SER* 6.4 0.4 - - - -
453T LEU* 6.0 1.8 - - + -
455T GLY 3.6 11.0 - - - +
456T TRP* 4.1 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404T LEU* 5.0 11.0 - - + -
405T MET 4.0 4.0 - - - -
406T VAL* 4.6 2.7 - - + +
442T ALA* 1.3 78.9 - - - +
444T SER* 1.3 60.8 + - - +
453T LEU* 4.1 1.7 - - - -
454T ILE* 2.9 24.5 + - + +
455T GLY* 2.9 28.2 + - - +
456T TRP* 5.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 444 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143T ALA* 5.7 7.0 - - - -
404T LEU* 3.5 12.5 - - - +
405T MET* 3.2 46.1 + - - -
442T ALA* 6.4 0.2 - - - -
443T LEU* 1.3 74.9 - - - +
445T ARG* 1.3 64.8 + - - +
451T TRP* 4.5 7.0 - - - -
452T ARG 3.3 24.2 - - - -
453T LEU* 3.9 4.5 - - - -
454T ILE* 3.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 445 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395T VAL* 4.7 3.5 - - - +
396T GLN* 3.3 52.0 + - - +
397T LYS 3.3 16.5 + - - -
398T LEU* 4.4 6.3 - - - +
399T SER 5.1 0.8 - - - +
403T VAL 5.0 10.1 + - - +
404T LEU* 5.9 0.4 - - + -
444T SER* 1.3 78.1 - - - +
446T ARG* 1.3 72.7 + - - +
447T VAL* 3.2 5.3 + - - +
451T TRP* 3.9 8.7 - - - -
452T ARG* 2.8 28.9 + - - +
454T ILE* 4.6 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.2 22.0 - - - +
265A ASP* 2.5 42.7 + - + +
266A TYR* 3.5 26.6 + - - -
445T ARG* 1.3 79.7 - - - +
447T VAL* 1.3 62.9 + - - +
448T GLU* 4.4 0.4 - - - +
449T LYS* 3.7 30.0 + - - +
450T HIS 3.3 23.7 - - - +
451T TRP* 3.1 50.2 - - + +
----------------------------------------------------------
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