Contacts of the strand formed by residues 362 - 373 (chain B) in PDB entry 1AF6
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 ALA 362 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 5.4 0.2 - - - -
350B GLN* 3.8 30.7 - - + +
351B TRP 3.3 4.9 - - - -
352B GLN* 4.0 5.6 - - + -
359B SER 4.3 0.9 - - - +
360B ARG* 4.0 17.3 - - - -
361B PRO* 1.3 76.1 - - - +
363B ILE* 1.3 62.9 + - - +
364B ARG* 4.0 12.0 - - - +
416B GLN 3.9 0.2 - - - +
417B MET* 3.2 7.1 - - - +
418B GLU 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 4.2 9.6 - - + -
86A VAL* 4.0 28.0 - - + +
88A GLY 3.9 10.5 - - - +
100A ILE* 3.7 50.3 - - + +
101A TRP* 4.4 5.4 - - - +
102A ALA* 4.4 14.8 - - + +
350B GLN* 3.3 4.5 - - - +
351B TRP* 2.8 42.8 + - + +
362B ALA* 1.3 77.2 - - - +
364B ARG* 1.3 64.6 + - - +
365B VAL* 5.6 3.1 - - + -
415B ALA* 5.9 1.3 - - + -
416B GLN 3.5 6.7 - - - +
417B MET* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 6.1 1.8 - - - +
34B LEU* 3.9 27.6 - - + +
37B GLU* 4.4 4.9 + - - -
311B ARG* 4.0 10.7 - - - +
348B ALA* 4.6 11.7 - - + -
349B GLN 3.4 5.4 - - - +
350B GLN* 3.3 31.3 + - + +
360B ARG* 3.3 22.0 - - - +
362B ALA* 4.1 8.9 - - + +
363B ILE* 1.3 78.1 - - - +
365B VAL* 1.3 65.0 + - - +
366B PHE* 4.2 6.0 - - + -
415B ALA* 3.1 7.8 - - - +
416B GLN* 2.8 71.4 + - + +
418B GLU* 2.9 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU 4.0 0.2 - - - +
348B ALA* 3.1 2.6 - - - -
349B GLN* 2.8 41.2 + - + +
351B TRP* 4.4 19.3 - - + -
363B ILE* 5.6 3.8 - - + -
364B ARG* 1.3 76.5 - - - +
366B PHE* 1.3 65.6 + - - +
414B GLY 3.4 9.4 - - - +
415B ALA* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE 4.8 0.7 - - - -
20B GLN* 3.5 31.2 - - - -
34B LEU* 6.0 0.9 - - + -
35B GLY* 3.5 36.3 - - - +
346B THR* 4.2 7.0 - - + -
347B LEU 3.2 11.4 - - - +
348B ALA* 3.9 11.4 - - + -
364B ARG* 4.7 8.7 - - + -
365B VAL* 1.3 79.7 - - - +
367B ALA* 1.3 66.0 + - - +
368B THR* 3.8 7.6 - - - -
412B THR* 4.0 6.3 - - - -
413B PHE* 3.2 21.3 - - - +
414B GLY* 2.9 56.6 + - - +
415B ALA* 3.9 12.1 - - - -
416B GLN* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE 4.1 0.6 - - - +
346B THR* 3.4 3.1 - - - +
347B LEU* 2.9 38.5 + - + +
366B PHE* 1.3 75.0 - - - +
368B THR* 1.3 62.4 + - - +
411B TRP* 5.5 6.5 - - + -
412B THR 3.3 9.0 - - - +
413B PHE* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.3 14.6 - - + -
35B GLY* 3.0 22.9 + - - +
36B ASN* 5.2 0.4 - - + -
344B LYS* 3.8 21.8 - - + -
345B ILE 3.4 3.1 - - - -
346B THR* 2.7 32.6 + - - +
366B PHE* 3.8 1.4 - - - -
367B ALA* 1.3 72.5 - - - +
369B TYR* 1.3 67.2 + - - +
411B TRP* 3.0 9.4 - - - +
412B THR* 2.6 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 4.0 23.2 + + - -
344B LYS* 3.4 2.6 - - - +
345B ILE* 2.7 56.7 + - + +
368B THR* 1.3 76.9 - - - +
370B ALA* 1.3 62.8 + - - +
371B LYS* 3.8 20.5 - - + +
409B ASP* 2.4 44.5 + - - -
410B GLU 3.6 13.2 - - - -
411B TRP* 4.3 13.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.7 40.8 - - + -
342B GLN* 4.4 4.7 - - - +
343B TYR 3.4 8.7 - - - +
344B LYS* 4.2 7.4 - - + -
368B THR* 4.6 0.6 - - - +
369B TYR* 1.3 81.8 - - - +
371B LYS* 1.3 59.4 + - - +
372B TRP* 3.9 10.2 - - + -
409B ASP* 3.5 5.2 - - - +
410B GLU 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 4.9 3.7 + - - +
342B GLN* 3.3 3.2 - - - +
343B TYR* 3.0 68.4 + - + +
369B TYR* 3.8 8.2 - - + +
370B ALA* 1.3 73.3 - - - +
372B TRP* 1.3 86.6 + - - +
373B ASP* 4.5 6.3 - - - -
407B ASP* 3.0 25.1 + - - -
408B SER* 3.3 13.8 + - - +
409B ASP* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.9 17.7 - + - -
341B ASN* 3.3 12.8 - - - +
342B GLN* 3.9 18.2 - - + +
370B ALA* 3.9 10.8 - - + -
371B LYS* 1.3 89.4 + - - +
373B ASP* 1.3 61.9 + - - +
374B GLU* 4.2 4.9 - - + -
405B ARG* 3.0 66.4 + - + +
406B GLY 3.4 15.7 - - - -
407B ASP* 3.5 0.2 - - - -
408B SER* 2.9 58.4 + - - +
409B ASP 3.8 29.4 - - - -
410B GLU* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LYS 4.1 2.3 - - - +
340B ASN* 3.6 2.8 - - - -
341B ASN* 2.9 50.2 + - - +
371B LYS* 4.5 6.0 - - - -
372B TRP* 1.3 77.6 - - - +
374B GLU* 1.3 62.9 + - - +
375B LYS* 3.6 35.3 + - - +
406B GLY 3.5 2.9 - - - +
407B ASP* 4.1 23.6 - - - +
----------------------------------------------------------
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