Contacts of the strand formed by residues 388 - 395 (chain A) in PDB entry 3A3K
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 PHE 388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.7 1.8 - - + -
257A GLN* 2.8 38.4 + - + +
259A PRO* 3.7 22.2 - - + -
260A TRP* 4.0 2.7 - + - -
274A PHE* 3.7 33.2 - + - -
277A ALA 3.5 27.4 - - - -
279A ILE* 3.6 29.2 - - + -
379A TRP* 3.9 14.3 - - + -
380A ASP* 3.4 26.7 - - - -
381A MET* 3.7 29.8 - - + -
386A GLY 3.9 7.9 - - - -
387A ALA* 1.3 75.1 - - - +
389A ARG* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TRP* 3.2 14.9 - - - -
380A ASP* 3.0 66.4 + - - +
381A MET 3.5 1.8 + - - -
382A ASP* 3.4 37.9 + - - +
383A PRO* 5.2 2.4 - - - +
387A ALA* 4.2 9.2 - - - -
388A PHE* 1.3 77.6 - - - +
390A VAL* 1.3 65.1 + - - +
391A VAL* 3.3 10.8 + - + +
407A HIS* 3.4 50.6 + - + +
408A LYS 4.8 6.9 + - - +
410A TYR* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A SER* 3.7 11.7 - - - +
378A LEU 3.5 5.6 - - - +
379A TRP* 3.6 38.3 - - + +
389A ARG* 1.3 75.3 - - - +
391A VAL* 1.3 60.9 + - - +
392A LEU 3.7 10.3 - - - +
393A ASN* 3.4 26.5 - - - +
404A VAL* 3.6 29.0 - - + +
407A HIS* 3.8 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 2.9 19.6 + - + +
380A ASP* 3.3 35.9 - - + +
389A ARG* 3.5 26.5 - - + +
390A VAL* 1.3 73.7 - - - +
392A LEU* 1.3 64.5 + - + +
403A ALA* 3.6 7.3 - - - +
404A VAL* 3.1 25.0 + - - +
407A HIS* 3.8 28.1 - - + +
408A LYS 4.5 7.2 - - - +
409A LEU* 3.8 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 5.8 1.5 - - + -
140A LEU* 4.2 12.3 - - + -
143A ARG* 4.2 22.9 - - - +
377A SER* 3.4 0.3 - - - -
378A LEU* 2.9 54.3 + - + -
390A VAL* 3.7 1.7 - - - +
391A VAL* 1.3 79.2 - - - +
393A ASN* 1.3 67.3 + - - +
401A LEU* 4.0 27.4 - - + -
402A MET 3.3 32.8 - - - +
403A ALA* 4.0 4.5 - - + +
404A VAL* 3.7 3.3 - - - +
409A LEU* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 5.6 0.2 - - - -
283A LYS* 2.9 42.2 - - + +
376A PHE 3.5 1.3 - - - -
377A SER* 3.0 23.2 + - - -
390A VAL* 3.4 8.1 - - - +
392A LEU* 1.3 77.4 - - - +
394A TYR* 1.3 62.5 + - - +
395A ASN 4.2 0.2 - - - -
400A GLU 3.5 1.0 - - - +
401A LEU* 3.3 7.3 - - - +
402A MET* 2.9 46.8 + - + +
404A VAL* 3.6 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 4.6 1.6 - - + -
135A ASP* 3.4 28.4 + - + +
136A PHE* 3.4 43.3 - + + -
139A ALA* 3.7 15.4 - - + +
283A LYS* 4.8 1.7 - - - +
374A THR 3.9 13.0 - - - -
375A ASP* 3.2 28.6 - - - +
376A PHE* 2.9 19.7 + + - +
393A ASN* 1.3 75.6 - - - +
395A ASN* 1.3 60.5 + - - +
396A GLY* 3.6 18.6 + - - -
399A GLN* 3.2 52.6 - - - +
400A GLU 3.5 7.4 - - - -
401A LEU* 3.9 14.4 - - + -
402A MET* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP* 3.4 9.9 - - - +
394A TYR* 1.3 74.7 - - - +
396A GLY* 1.3 54.0 + - - +
397A THR* 2.9 17.2 + - - -
398A SER* 3.1 16.1 + - - +
399A GLN* 2.8 36.4 + - - -
400A GLU 3.1 11.4 + - - +
402A MET* 4.1 15.3 - - + +
461A NAG 1.4 65.6 + - - +
----------------------------------------------------------
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