Contacts of the strand formed by residues 372 - 376 (chain P) in PDB entry 6K71
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 372 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370P GLU* 2.9 22.1 - - - +
371P LEU* 1.3 74.6 - - - +
373P ILE* 1.3 67.0 + - - +
424P LEU* 6.1 4.9 - - + -
425P GLY 3.4 9.9 - - - +
426P LYS* 4.5 9.2 - - + -
427P ILE 4.5 0.2 - - - +
459P ILE* 4.2 5.7 - - - +
460P ARG* 3.4 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371P LEU* 5.1 4.7 - - + -
372P GLU* 1.3 80.5 - - - +
374P SER* 1.3 59.1 + - - +
375P TYR* 4.2 12.1 - - + -
404P LEU* 6.1 0.2 - - + -
406P VAL* 5.6 0.2 - - + -
417P VAL* 6.0 1.1 - - + -
424P LEU* 3.3 2.4 - - - +
425P GLY* 2.4 59.3 + - - +
427P ILE* 3.9 41.3 - - + -
441P ILE* 4.9 11.0 - - + -
443P LEU* 4.0 35.4 - - + -
457P GLY* 5.7 0.7 - - - -
458P GLN 3.3 9.6 - - - +
459P ILE* 4.3 18.8 - - + -
460P ARG* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373P ILE* 1.3 70.6 - - - +
375P TYR* 1.3 61.0 + - - +
423P ASP 3.3 10.8 - - - -
424P LEU* 3.6 14.5 - - - +
457P GLY* 3.2 2.1 - - - -
458P GLN* 2.5 57.5 + - - +
460P ARG* 3.9 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 375 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373P ILE* 4.2 11.9 - - + -
374P SER* 1.3 74.9 - - - +
376P PHE* 1.3 82.4 + - - +
377P LEU* 3.6 32.3 - - + -
397P LYS* 4.9 3.0 - - + +
398P LEU* 3.9 27.1 - - + +
420P VAL* 3.4 17.7 - - - +
421P LYS 2.7 24.1 + - - -
422P ALA 4.5 7.0 - - - -
423P ASP* 2.6 34.5 + - - +
424P LEU 3.5 31.9 - - - -
425P GLY* 3.7 9.9 - - - -
443P LEU* 4.9 16.6 - - + -
456P TRP 3.3 14.8 - - - +
457P GLY* 4.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569J ILE* 5.4 11.7 - - + -
570J SER* 4.9 6.3 - - - -
573J ASN* 4.0 29.2 - - + -
179P ILE* 4.4 10.5 - - + -
375P TYR* 1.3 85.1 - - - +
377P LEU* 1.3 97.4 + - - +
422P ALA 5.3 0.9 - - - -
423P ASP* 4.7 8.5 - - - +
443P LEU* 6.1 0.3 - - - +
455P GLY* 3.5 1.6 - - - -
456P TRP* 3.3 71.1 + + + +
----------------------------------------------------------
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