Contacts of the helix formed by residues 315 - 324 (chain C) 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 ASP 315 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLN* 3.4 15.7 + - - +
310C TRP* 4.5 0.7 - - - -
313C SER 5.4 1.1 - - - +
314C GLU* 1.3 78.3 - - - +
316C PRO* 1.3 76.9 - - - +
317C TRP* 3.8 14.7 + - - +
318C GLU* 3.1 45.2 + - - +
319C GLN* 3.0 26.8 + - - +
338C TYR* 4.2 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C VAL* 4.5 7.9 - - + -
283C GLN* 3.7 38.8 - - + +
284C LEU* 3.7 26.0 - - + +
287C ALA* 3.7 22.7 - - + -
289C PHE* 4.0 4.5 - - + -
310C TRP* 4.0 14.5 - - + -
314C GLU 4.0 5.8 - - - +
315C ASP* 1.3 92.4 - - - +
317C TRP* 1.3 65.2 + - + +
319C GLN* 3.3 1.9 + - - +
320C HIS* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLN 5.5 1.6 - - - -
286C ARG* 3.5 30.4 + - - +
287C ALA* 3.7 26.0 - - + +
315C ASP* 3.3 12.2 + - - +
316C PRO* 1.3 78.2 - - + +
318C GLU* 1.3 64.5 + - - +
320C HIS* 3.0 13.9 + - - +
321C ALA* 2.9 22.9 + - - +
329C TYR* 3.6 19.3 - + - -
330C LEU* 3.7 33.2 - - + -
333C GLN* 3.5 33.4 - - + -
334C LYS* 3.7 37.2 - - + +
338C TYR* 3.4 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C GLU* 5.6 0.9 - - - -
315C ASP* 3.1 34.8 + - - +
317C TRP* 1.3 78.1 - - - +
319C GLN* 1.3 69.0 + - + +
321C ALA* 3.0 6.2 + - - +
322C LYS* 2.9 27.4 + - - +
338C TYR* 3.1 12.2 + - - +
342C ILE* 4.0 27.5 - - + +
346C HIS* 3.7 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C LEU* 4.3 4.5 - - + +
310C TRP* 3.7 31.6 - - + -
314C GLU* 3.8 27.0 + - + +
315C ASP 3.0 17.8 + - - +
316C PRO 3.9 0.4 - - - +
318C GLU* 1.3 85.0 + - - +
320C HIS* 1.3 65.3 + - - +
322C LYS* 3.5 20.4 + - - +
323C TRP* 3.1 54.8 + - + +
346C HIS* 5.3 3.6 - - - -
600C X22 3.9 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ZN 2.1 36.3 - - - -
287C ALA 2.9 28.7 + - - -
289C PHE* 3.4 20.4 - + + -
300C CYS* 3.4 17.0 - - + +
303C CYS* 3.8 0.6 - - - -
307C LEU* 4.4 4.1 - - - +
316C PRO 2.9 13.8 + - - +
317C TRP* 3.2 24.8 - + + +
319C GLN* 1.3 74.4 - - - +
321C ALA* 1.3 57.6 + - - +
324C TYR* 2.9 43.3 + + + +
327C CYS* 3.4 5.7 - - - -
329C TYR* 4.4 7.6 - + - -
330C LEU* 4.2 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TRP 2.9 11.3 + - - +
318C GLU 3.5 7.2 - - - +
320C HIS* 1.3 77.7 - - - +
322C LYS* 1.3 62.9 + - - +
325C PRO* 3.4 15.2 - - - +
330C LEU* 3.6 20.9 - - + -
338C TYR* 3.7 25.8 - - + -
339C ILE* 4.4 7.2 - - - +
342C ILE* 4.2 10.5 - - + -
343C HIS* 3.1 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LEU* 5.7 2.6 - - - +
318C GLU* 2.9 15.1 + - + +
319C GLN* 3.2 30.9 + - - +
321C ALA* 1.3 77.6 - - - +
323C TRP* 1.3 91.7 + - + +
325C PRO* 3.8 0.2 - - - +
342C ILE* 4.2 10.0 - - + +
343C HIS* 2.8 36.2 + - + +
346C HIS* 3.5 37.3 + - + +
600C X22 5.0 2.4 + - - -
700D X22 3.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.2 12.8 - - + -
352B LEU* 3.9 16.2 - - + -
307C LEU* 3.7 19.7 - - + -
319C GLN* 3.1 44.0 + - - +
322C LYS* 1.3 99.5 - - + +
324C TYR* 1.3 78.6 + - + +
325C PRO* 3.2 5.3 - - - +
600C X22 3.3 67.6 + + + -
344D LEU* 6.0 1.6 - - + -
347D SER* 5.9 0.4 - - - -
700D X22 2.7 76.3 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 5.7 1.8 - + - -
303C CYS* 3.9 20.9 - - + -
305C GLY* 3.4 27.0 - - - -
306C GLY 2.9 30.3 + - - -
307C LEU* 3.4 31.6 - - + -
320C HIS* 2.9 27.4 + + + +
323C TRP* 1.3 85.6 - - + +
325C PRO* 1.4 62.6 - - - +
326C GLY 3.2 3.1 - - - +
327C CYS* 3.2 18.6 + - + +
330C LEU* 3.4 2.6 - - - +
600C X22 3.4 25.0 - + - -
700D X22 2.9 48.6 - + - -
----------------------------------------------------------
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