Contacts of the helix formed by residues 338 - 351 (chain B) in PDB entry 3AP1
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 ASP 338 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 2.9 20.6 + - - +
244B HIS* 2.8 43.8 + - - +
245B PRO* 3.8 6.2 - - + +
246B ARG* 4.7 8.3 + - - +
247B ARG* 4.3 7.7 + - - -
336B ASN 3.6 0.2 + - - -
337B PRO* 1.3 73.1 - - - +
339B PRO* 1.4 75.2 - - + +
340B PHE* 4.1 12.1 - - + +
341B VAL* 3.0 23.0 + - + +
342B ILE* 3.1 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PRO 3.7 3.3 - - - +
338B ASP* 1.4 86.9 - - + +
340B PHE* 1.3 52.0 + - - +
342B ILE* 3.2 15.2 + - + +
343B ASN* 2.7 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO* 4.0 33.4 - - + -
246B ARG* 5.6 2.2 - - + -
265B LEU* 3.3 45.5 - - + -
266B HIS* 4.3 16.8 - + - -
292B PRO* 6.1 0.2 - - + -
293B VAL* 5.1 4.5 - - + -
338B ASP* 3.1 8.7 - - + +
339B PRO* 1.3 79.8 - - - +
341B VAL* 1.3 58.4 + - - +
343B ASN* 3.4 8.9 + - + +
344B ASN* 2.9 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL 3.0 27.8 - - - +
243B LEU 3.5 14.4 - - - +
245B PRO* 3.2 28.0 - - + -
293B VAL* 3.9 16.4 - - + +
294B ASN* 5.1 0.4 - - - -
295B LEU* 3.9 11.0 - - + -
337B PRO* 3.8 11.9 - - + -
338B ASP* 3.0 19.5 + - - +
340B PHE* 1.3 79.5 - - + +
342B ILE* 1.3 62.6 + - - +
344B ASN* 3.7 5.5 - - - +
345B THR* 2.7 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.2 11.2 - - + -
337B PRO* 3.6 39.3 - - + +
338B ASP 3.1 13.1 + - - +
339B PRO* 3.5 15.0 - - + +
341B VAL* 1.3 76.8 - - - +
343B ASN* 1.3 68.9 + - - +
345B THR* 3.1 5.9 + - - -
346B GLN* 3.0 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PRO* 2.7 35.7 + - - +
340B PHE* 3.6 8.1 - - + +
342B ILE* 1.3 78.0 - - - +
344B ASN* 1.3 64.6 + - - +
346B GLN* 3.2 9.9 + - - +
347B ARG* 3.0 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PRO* 3.9 22.7 - - + +
293B VAL 3.0 32.9 + - - +
294B ASN* 4.5 0.4 - - - -
340B PHE* 2.9 61.1 + - - +
341B VAL* 3.7 2.4 - - - +
342B ILE 3.3 0.2 - - - -
343B ASN* 1.3 75.9 - - - +
345B THR* 1.3 56.7 - - - +
347B ARG* 3.3 25.0 + - - +
348B VAL* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASN* 3.5 8.9 - - + +
295B LEU* 3.0 45.8 + - + +
296B GLU* 4.4 17.5 - - + +
341B VAL 2.7 22.0 + - - -
342B ILE* 3.1 5.4 + - - -
344B ASN* 1.3 75.8 - - - +
346B GLN* 1.3 57.5 + - + +
348B VAL* 3.2 4.1 + - + +
349B LEU* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 3.0 23.0 + - + +
343B ASN* 3.2 11.6 + - - +
345B THR* 1.3 77.6 - - - +
347B ARG* 1.3 61.9 + - - +
349B LEU* 3.3 20.3 + - - +
350B LYS* 3.1 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B HIS* 5.9 1.6 + - - -
268B GLU* 3.6 22.8 + - - +
292B PRO* 3.8 20.9 - - - +
340B PHE* 6.2 0.2 - - - -
343B ASN* 3.0 14.9 + - + +
344B ASN* 3.5 29.3 + - - +
346B GLN* 1.3 76.4 - - - +
348B VAL* 1.3 63.5 + - - +
350B LYS* 3.6 6.4 + - + -
351B GLY 3.2 5.0 + - - -
352B ASP* 3.0 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LYS* 3.9 25.8 - - + +
292B PRO* 3.9 28.3 - - + -
294B ASN* 4.1 19.3 - - + +
296B GLU* 3.3 27.6 - - + +
344B ASN 3.0 17.6 + - - +
345B THR* 3.5 10.1 - - - +
347B ARG* 1.3 76.4 - - - +
349B LEU* 1.3 64.1 + - - +
351B GLY* 3.0 16.3 + - - -
352B ASP* 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLU* 4.1 24.7 - - + +
345B THR* 2.9 35.9 + - + +
346B GLN* 3.3 24.2 + - - +
348B VAL* 1.3 77.5 - - - +
350B LYS* 1.3 61.8 + - + +
351B GLY* 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLN* 3.1 35.9 + - + +
347B ARG* 4.1 9.6 - - + +
349B LEU* 1.3 76.2 - - + +
351B GLY* 1.3 58.9 + - - +
352B ASP* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ARG 3.2 0.4 + - - -
348B VAL 3.0 15.7 + - - -
349B LEU 3.1 1.5 - - - -
350B LYS* 1.3 80.0 - - - +
352B ASP* 1.3 67.9 + - - +
----------------------------------------------------------
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