Contacts of the helix formed by residues 335 - 353 (chain A) in PDB entry 3IO6
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 GLN 335 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 3.7 28.5 - - + -
178A ILE* 3.6 29.3 - - + +
333A ILE* 3.3 16.8 - - + +
334A PRO* 1.3 98.2 - - - +
336A MET* 1.3 62.5 + - - +
337A SER 3.3 0.4 - - - -
338A ALA* 3.3 18.7 + - - +
339A PHE 3.4 8.8 + - - -
372A ALA* 4.5 19.5 - - + +
376A LYS* 6.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 4.4 2.2 - - + -
169A PHE* 4.3 7.4 - - - -
258A PHE* 4.0 8.5 - - + -
330A MET* 4.0 7.2 - - + -
331A PRO* 3.5 53.6 - - + +
333A ILE* 3.2 21.8 + - + +
334A PRO 3.0 0.4 - - - -
335A GLN* 1.3 76.6 - - - +
337A SER* 1.3 65.1 + - - +
339A PHE* 3.2 43.9 + - + +
340A TRP* 3.2 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO* 3.2 16.9 + - - +
336A MET* 1.3 78.3 - - - +
338A ALA* 1.3 62.0 + - - +
340A TRP* 3.4 20.2 + - - +
341A TYR* 3.4 13.3 + - - +
371A MET* 5.7 5.9 - - - +
375A GLU* 4.0 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO 4.5 0.2 + - - -
335A GLN* 3.3 12.4 + - - +
336A MET 3.2 0.2 - - - -
337A SER* 1.3 76.2 - - - +
339A PHE* 1.3 65.7 + - - +
340A TRP 3.4 0.2 + - - -
341A TYR* 3.4 3.8 + - - +
342A ALA* 3.0 25.9 + - - +
367A ASN 5.4 0.2 - - - -
368A ALA* 3.5 29.6 - - + +
371A MET* 4.1 19.3 - - + +
372A ALA* 3.9 21.5 - - + +
375A GLU* 5.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TRP* 3.8 36.1 - + - -
168A ALA* 3.6 30.1 - - + -
169A PHE* 4.4 8.1 - + + -
181A VAL* 5.2 3.1 - - + -
183A VAL* 3.8 25.8 - - + -
258A PHE* 3.9 7.6 - + - -
335A GLN 3.4 6.9 + - - +
336A MET* 3.2 43.0 + - + +
338A ALA* 1.3 78.5 - - - +
340A TRP* 1.3 88.5 + + - +
342A ALA* 3.9 0.9 - - - +
343A VAL* 3.0 37.6 + - + +
368A ALA* 4.6 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PRO* 3.7 25.8 - - + +
155A TYR* 3.7 33.4 - + + -
158A TRP* 5.5 0.2 - - + -
258A PHE* 3.4 31.2 - + - -
330A MET* 3.9 23.9 - - + -
336A MET* 3.2 46.4 + - + +
337A SER* 3.6 11.2 - - - +
338A ALA 3.3 0.4 - - - -
339A PHE* 1.3 93.7 - + - +
341A TYR* 1.3 52.4 + - - +
343A VAL* 3.7 0.3 - - - -
344A ARG* 2.8 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER 3.4 8.1 + - - +
338A ALA* 3.4 9.2 + - - +
340A TRP* 1.3 78.7 - - - +
342A ALA* 1.3 64.6 + - + +
344A ARG* 3.5 19.1 + - + +
345A THR* 3.0 43.7 + - - -
367A ASN* 5.1 3.8 - - + -
371A MET* 4.8 22.4 - - + -
383C SER* 2.7 37.2 + - - -
386C SER* 4.2 4.2 - - - -
387C PHE* 2.3 70.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA 3.0 17.1 + - - +
339A PHE* 3.9 3.4 - - - +
341A TYR* 1.3 81.5 - - + +
343A VAL* 1.3 57.7 + - + +
345A THR* 3.6 3.8 + - - -
346A ALA* 3.0 26.0 + - - +
364A ALA* 3.1 36.9 - - + +
367A ASN* 3.9 14.6 + - + +
368A ALA* 3.9 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PRO* 3.8 22.4 - - + -
158A TRP* 4.2 21.1 - - + -
161A ILE* 5.2 0.9 - - + -
183A VAL* 4.4 19.7 - - + -
339A PHE* 3.0 44.9 + - + +
340A TRP 4.0 1.8 - - - +
342A ALA* 1.3 75.3 - - + +
344A ARG* 1.3 60.8 + - - +
346A ALA* 3.1 6.7 + - + -
347A VAL* 2.8 45.0 + - + +
361A LEU* 6.1 3.4 - - + -
364A ALA* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN 3.6 19.0 - - - +
153A GLU* 3.3 34.7 + - - -
154A PRO* 3.6 18.4 - - + +
340A TRP* 2.8 33.1 + - - +
341A TYR* 3.7 28.5 - - - +
342A ALA 3.4 0.2 - - - -
343A VAL* 1.3 76.0 - - - +
345A THR* 1.3 58.9 + - - +
347A VAL* 4.2 3.1 - - - +
348A ILE* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.0 34.7 + - - -
342A ALA* 3.8 4.9 - - - -
343A VAL 3.2 0.4 - - - -
344A ARG* 1.3 75.9 - - - +
346A ALA* 1.3 56.4 + - - +
348A ILE* 3.1 6.2 + - + +
349A ASN* 2.8 56.9 + - - +
354A ARG* 6.2 0.2 - - - +
367A ASN* 5.1 11.3 + - - +
386C SER* 5.1 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.7 2.4 - - - +
342A ALA 3.0 19.6 + - - +
343A VAL* 3.1 8.0 + - + +
345A THR* 1.3 75.9 - - - +
347A VAL* 1.3 59.1 + - + +
349A ASN* 4.8 1.3 - - - +
350A ALA* 3.0 30.2 + - - +
360A ALA* 3.6 36.8 - - + +
361A LEU* 4.5 14.4 - - + -
364A ALA* 3.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.0 19.3 - - + +
152A GLN 6.1 0.2 - - - -
153A GLU 5.7 1.1 - - - +
154A PRO* 5.3 2.0 - - + -
157A THR* 4.0 25.6 - - + +
161A ILE* 3.7 28.3 - - + -
192A LEU* 4.1 13.4 - - + +
195A LEU* 4.5 10.8 - - + -
343A VAL* 2.8 32.2 + - + +
344A ARG* 4.3 4.3 - - - +
346A ALA* 1.3 71.9 - - + +
348A ILE* 1.3 57.6 + - + +
350A ALA* 3.4 1.7 + - - +
351A ALA* 2.8 38.4 + - + +
361A LEU* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU 4.1 7.9 - - - +
152A GLN* 3.3 48.0 - - - +
206A ALA 5.5 2.5 - - - +
344A ARG* 3.0 25.1 + - + +
345A THR* 3.1 7.0 + - + +
347A VAL* 1.3 76.5 - - + +
349A ASN* 1.3 64.5 + - - +
351A ALA* 3.8 6.2 - - + +
352A SER* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 2.8 42.3 + - - +
346A ALA* 3.9 4.1 - - - +
348A ILE* 1.3 75.6 - - - +
350A ALA* 1.3 61.1 + - - +
352A SER* 3.2 15.6 + - - -
353A GLY 3.2 11.8 + - - -
354A ARG* 3.2 46.6 + - + +
355A GLN* 3.4 35.3 + - + +
360A ALA* 4.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.7 27.4 - - + -
196A VAL* 3.6 30.0 - - + +
346A ALA 3.0 17.9 + - - +
347A VAL 3.9 2.7 - - - +
349A ASN* 1.3 76.3 - - - +
351A ALA* 1.3 60.6 + - - +
352A SER 3.4 0.7 + - - -
353A GLY* 3.5 10.4 + - - -
355A GLN 3.6 14.3 - - - +
357A VAL* 4.7 5.4 - - - +
360A ALA* 4.5 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 5.8 5.8 - - + +
195A LEU* 6.1 2.2 - - + -
196A VAL* 4.5 4.7 - - + +
199A ILE* 3.9 35.5 - - + +
206A ALA* 3.4 28.6 - - + +
347A VAL* 2.8 26.0 + - + +
348A ILE* 3.9 8.7 - - + +
349A ASN 3.3 0.2 - - - -
350A ALA* 1.3 77.1 - - - +
352A SER* 1.3 57.8 + - - +
353A GLY 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA* 5.0 4.0 - - - -
348A ILE* 2.9 20.8 + - - +
349A ASN* 3.2 14.0 + - - -
351A ALA* 1.3 79.2 - - - +
353A GLY* 1.3 56.2 + - - +
354A ARG* 3.4 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASN 3.2 5.9 + - - -
350A ALA 3.5 9.6 + - - -
352A SER* 1.3 77.8 - - - +
354A ARG* 1.3 65.9 + - - +
355A GLN* 3.1 11.3 + - - +
53C THR* 4.3 10.7 - - - +
----------------------------------------------------------
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