Contacts of the helix formed by residues 335 - 352 (chain D) in PDB entry 3CM7
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 GLY 335 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D LEU 3.9 0.2 + - - -
331D LEU* 2.7 31.7 + - - -
332D GLU 4.6 0.6 + - - -
334D LYS* 1.3 78.5 - - - +
336D GLN* 1.3 65.2 + - - +
337D GLU 3.5 2.6 + - - -
338D TYR* 3.5 9.0 + - - +
339D ILE* 3.7 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C GLY* 5.5 7.2 - - - -
325D PRO 5.5 0.7 - - - +
331D LEU* 3.5 27.3 - - + +
335D GLY* 1.3 71.0 - - - -
337D GLU* 1.3 65.3 + - + +
339D ILE* 3.1 20.7 + - - +
340D ASN* 2.9 47.6 + - - +
700D X22 3.9 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LYS 4.9 3.8 - - - +
337B GLU* 3.6 20.4 - - + +
338B TYR* 3.5 33.2 - - + +
341B ASN* 2.8 40.3 + - - +
335D GLY 3.5 1.2 - - - -
336D GLN* 1.3 76.6 - - + +
338D TYR* 1.3 56.1 + - - +
340D ASN* 3.2 7.2 + - - +
341D ASN* 3.0 15.2 + - - +
700D X22 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 3.6 29.2 - - + +
315D ASP* 4.2 1.6 + - - -
317D TRP* 3.3 30.5 + - + +
318D GLU* 3.5 10.9 + - - +
321D ALA* 3.8 21.8 - - + -
330D LEU* 4.7 1.1 - - + -
334D LYS* 3.3 60.0 + - + +
335D GLY 3.5 1.6 + - - +
336D GLN 3.2 0.2 - - - -
337D GLU* 1.3 76.1 - - - +
339D ILE* 1.3 73.5 + - + +
341D ASN* 3.1 18.1 - - + +
342D ILE* 3.2 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ALA* 4.4 8.7 - - + +
325D PRO* 3.7 38.6 - - + +
330D LEU* 3.7 34.5 - - + -
331D LEU* 4.3 16.8 - - + +
334D LYS* 5.5 0.2 - - + -
335D GLY 3.7 15.7 - - - +
336D GLN* 3.1 23.5 + - - +
338D TYR* 1.3 81.1 - - + +
340D ASN* 1.3 66.6 + - - +
341D ASN 3.0 1.2 + - - -
342D ILE* 3.1 11.6 + - - +
343D HIS* 3.4 16.5 + - - +
700D X22 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.4 16.6 - - - +
336D GLN* 2.9 36.9 + - - +
337D GLU* 3.2 11.3 + - - +
339D ILE* 1.3 76.2 - - - +
341D ASN* 1.3 61.7 + - - +
343D HIS* 3.6 1.9 + - - +
344D LEU* 3.0 28.4 + - - +
700D X22 2.9 80.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 4.0 24.3 + - + +
340B ASN* 4.3 11.1 - - - +
341B ASN* 3.1 22.7 + - - +
344B LEU* 3.9 17.4 - - - +
337D GLU 3.0 14.9 + - - +
338D TYR* 3.1 13.8 - - + +
339D ILE 3.0 0.2 + - - -
340D ASN* 1.3 75.4 - - - +
342D ILE* 1.3 67.1 + - + +
344D LEU* 3.1 4.7 + - - +
345D THR* 2.5 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D GLU* 3.7 41.5 - - + +
321D ALA* 4.1 10.1 - - + -
322D LYS* 4.3 18.2 - - + -
338D TYR* 3.4 52.5 - - + +
339D ILE 3.1 5.3 + - - +
341D ASN* 1.3 79.4 - - - +
343D HIS* 1.3 62.3 + - - +
345D THR* 3.4 7.0 + - - -
346D HIS* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C HIS* 5.7 7.2 - + - -
321D ALA 2.9 29.6 - - - -
322D LYS* 3.0 26.5 + - + -
325D PRO* 3.7 20.5 - - + +
339D ILE* 3.4 12.3 + - - +
340D ASN 3.9 2.7 - - - +
341D ASN 3.3 0.4 - - - -
342D ILE* 1.3 80.8 - - - +
344D LEU* 1.3 49.8 + - - +
346D HIS* 3.1 10.1 + + + +
347D SER* 2.7 42.8 + - - +
700D X22 3.5 42.2 - + + -
701D X22 4.2 15.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.5 40.6 - - - +
344B LEU* 4.7 14.8 - - + +
345B THR* 4.0 17.9 - - - +
348B LEU* 4.0 24.1 - - + +
323C TRP* 6.0 1.8 - - + -
600C X22 6.2 1.3 - - + -
340D ASN 3.0 19.0 + - - +
341D ASN* 3.5 3.6 - - - +
343D HIS* 1.3 74.1 - - - +
345D THR* 1.3 64.3 + - - +
347D SER* 3.0 3.1 + - - -
348D LEU* 2.9 26.4 + - - +
700D X22 3.4 49.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 4.6 17.8 - - + +
341D ASN* 2.5 41.5 + - - +
342D ILE* 3.5 6.0 + - - -
344D LEU* 1.3 73.5 - - - +
346D HIS* 1.3 64.7 + - - +
348D LEU* 3.2 8.3 + - + +
349D GLU* 3.2 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C SER* 5.8 3.2 + - - -
322D LYS* 3.0 40.2 + - - +
342D ILE* 2.9 21.4 + - + +
343D HIS* 3.4 10.3 - + + +
345D THR* 1.3 78.4 - - - +
347D SER* 1.3 66.2 + - - +
349D GLU* 3.5 7.2 + - - +
350D GLU* 3.1 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.8 20.8 - - - +
323C TRP* 5.9 0.9 - - - -
343D HIS* 2.7 27.5 + - - +
344D LEU 3.6 3.6 - - - -
346D HIS* 1.3 76.9 - - - +
348D LEU* 1.3 57.5 + - - +
350D GLU* 3.5 7.6 - - - +
351D CYS* 3.1 27.5 + - - +
700D X22 3.3 24.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.8 47.8 - - + +
347B SER* 4.2 26.7 - - - +
348B LEU* 4.3 12.5 - - + +
351B CYS* 4.8 2.0 - - + -
344D LEU 2.9 14.9 + - - +
345D THR* 3.6 7.0 - - + +
347D SER* 1.3 74.9 - - - +
349D GLU* 1.3 65.8 + - - +
351D CYS* 3.2 7.5 + - - +
352D LEU* 2.9 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D THR* 3.2 15.2 + - - +
346D HIS* 3.8 7.3 + - - +
348D LEU* 1.3 77.0 - - - +
350D GLU* 1.3 67.3 + - - +
352D LEU* 2.9 27.9 + - + +
353D VAL* 3.3 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C GLU* 3.2 59.2 - - + +
351C CYS* 4.9 2.3 + - - -
354C ARG 4.2 9.0 - - - +
346D HIS* 3.1 47.6 + - + +
347D SER* 3.5 9.6 - - - +
349D GLU* 1.3 79.4 - - - +
351D CYS* 1.3 60.8 + - - +
353D VAL* 3.3 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 5.7 2.0 - - + -
351B CYS* 2.1 63.0 - - + -
352B LEU* 3.7 23.6 - - + -
355B THR* 4.7 8.9 - - - +
350C GLU* 4.7 9.6 + - - +
347D SER 3.1 11.0 + - - +
348D LEU* 3.5 8.5 - - - +
350D GLU* 1.3 74.7 - - - +
352D LEU* 1.3 57.1 + - - +
353D VAL 3.0 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B CYS* 3.3 29.6 - - + -
354B ARG* 5.6 5.8 - - - +
348D LEU* 2.9 43.3 + - + +
349D GLU* 2.9 17.0 + - + +
351D CYS* 1.3 74.4 - - - +
353D VAL* 1.3 63.1 + - + +
----------------------------------------------------------
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