Contacts of the helix formed by residues 318 - 329 (chain C) in PDB entry 5CQD
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 LEU 318 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C PHE* 3.4 44.0 - - + +
286C SER* 3.9 11.0 - - - +
316C ASP* 2.8 12.6 + - - +
317C PRO* 1.3 86.4 - - + +
319C TYR* 1.3 65.3 + - - +
320C LYS 3.2 2.7 - - - -
321C GLU* 3.0 30.4 + - + +
322C ALA 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO 4.6 0.9 + - - -
320A LYS* 5.3 1.1 - - + +
321A GLU* 2.5 35.6 + - - -
282C SER* 5.4 2.2 - - - +
283C PRO 5.1 2.2 - - - +
284C CYS* 6.2 0.2 - - - -
285C PHE 5.4 0.2 - - - +
312C ILE* 3.3 26.0 - - + -
313C TYR 3.1 25.4 - - - +
314C ASP* 3.6 17.7 - - + -
316C ASP* 2.9 24.9 + - - +
317C PRO* 4.4 5.8 - - + -
318C LEU* 1.3 77.0 - - - +
320C LYS* 1.3 86.6 + - + +
322C ALA* 3.2 9.8 + - - +
323C LEU* 3.1 29.7 + - + +
372C ARG* 3.1 30.7 + - - -
376C ILE* 3.8 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 3.7 23.3 - - + -
321A GLU* 2.8 37.6 + - - +
317C PRO 4.5 10.3 + - - -
318C LEU 3.2 0.8 - - - -
319C TYR* 1.3 106.0 - - + +
321C GLU* 1.3 68.5 + - - +
323C LEU* 3.4 2.9 + - - +
324C GLN* 3.0 44.1 + - - +
376C ILE* 4.0 24.0 - - + +
379C LEU* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C PHE* 4.0 21.2 - - + -
317C PRO 4.3 2.1 - - - +
318C LEU* 3.0 44.9 + - + +
320C LYS* 1.3 85.5 + - - +
322C ALA* 1.3 60.1 + - - +
324C GLN* 3.9 13.5 - - - +
325C MET* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PRO 3.5 24.9 - - - +
284C CYS 3.7 20.4 - - - +
285C PHE* 3.8 9.8 - - + +
290C ALA* 3.9 13.4 - - + +
318C LEU 3.0 7.0 + - - +
319C TYR* 3.2 10.5 + - - +
321C GLU* 1.3 76.0 - - - +
323C LEU* 1.3 62.8 + - - +
325C MET* 3.3 2.8 + - - +
326C LEU* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C SER* 3.9 27.4 - - - +
283C PRO* 5.1 2.2 - - + +
312C ILE* 4.3 10.3 - - + -
319C TYR* 3.1 30.7 + - + +
320C LYS 3.8 4.0 - - - +
322C ALA* 1.3 76.0 - - + +
324C GLN* 1.3 63.3 + - - +
326C LEU* 3.3 11.9 + - + +
327C ARG* 3.0 18.9 + - - +
333C VAL* 4.1 17.4 - - + +
373C LEU* 3.6 28.9 - - + -
376C ILE* 4.1 20.9 - - + -
377C LEU* 3.6 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LYS* 3.0 31.5 + - - +
321C GLU* 4.0 15.3 - - - +
323C LEU* 1.3 75.7 - - - +
325C MET* 1.3 57.7 + - - +
327C ARG* 3.3 24.9 + - - +
328C ASP* 2.9 40.2 + - - +
376C ILE* 3.6 25.9 + - + +
377C LEU* 4.3 6.5 - - + -
379C LEU* 3.7 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C PHE* 3.8 25.4 - - + -
290C ALA* 3.8 9.4 - - + +
291C GLY* 3.8 30.3 - - - -
294C ARG* 3.4 49.3 - - + +
321C GLU 2.9 18.6 + - - +
322C ALA* 3.6 4.9 - - - +
324C GLN* 1.3 77.0 - - - +
326C LEU* 1.3 62.7 + - - +
328C ASP* 3.3 9.3 + - - +
329C ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PRO* 3.6 37.0 - - + -
290C ALA* 4.4 14.6 - - + +
293C VAL* 3.5 39.0 - - + -
294C ARG* 5.1 1.6 - - - +
297C LEU* 5.7 0.4 - - + -
307C ILE* 4.0 15.7 - - + -
322C ALA* 3.0 25.7 + - + +
323C LEU* 3.7 10.1 - - + +
325C MET* 1.3 74.9 - - - +
327C ARG* 1.3 62.9 + - - +
329C ALA* 3.3 10.9 + - - +
330C GLY 3.4 0.2 + - - -
331C ALA* 3.0 29.3 + - + +
333C VAL* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU 3.0 13.6 + - - +
324C GLN* 3.6 31.9 + - - +
326C LEU* 1.3 77.7 - - - +
328C ASP* 1.3 79.4 + - - +
330C GLY* 2.8 21.8 + - - -
331C ALA 3.7 14.2 + - - +
333C VAL* 4.6 2.8 - - + +
377C LEU* 2.0 60.5 + - + +
379C LEU 3.9 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 5.6 4.5 - - - -
324C GLN* 2.9 25.4 + - - +
325C MET* 3.3 8.8 + - - +
327C ARG* 1.3 99.8 + - - +
329C ALA* 1.3 58.9 + - - +
330C GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 3.9 37.9 - - + +
297C LEU* 4.0 26.9 - - + +
298C GLN* 5.5 5.9 - - + +
325C MET 3.0 16.2 + - - +
326C LEU* 3.7 7.9 - - + +
327C ARG 3.1 0.8 - - - -
328C ASP* 1.3 74.8 - - - +
330C GLY* 1.3 57.8 + - - +
331C ALA 3.5 0.6 + - - -
----------------------------------------------------------
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