Contacts of the helix formed by residues 312 - 323 (chain C) in PDB entry 5MLE
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 THR 312 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LYS* 2.7 31.9 + - - +
310C ASP* 2.8 17.2 + - - +
311C PRO* 1.3 79.6 - - + +
313C THR* 1.3 63.0 + - - +
314C PRO* 3.4 1.3 - - - -
315C ASP* 3.3 11.8 + - - +
316C PHE* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLU* 5.2 0.7 + - - -
256C MET 3.6 23.3 - - - +
257C SER* 4.1 1.1 - - - -
258C LYS* 3.9 32.4 - - + +
308C SER* 3.3 13.7 + - - -
310C ASP* 2.8 27.1 + - - +
312C THR* 1.3 77.0 + - - +
314C PRO* 1.3 67.8 - - - +
316C PHE* 3.2 2.6 + - - +
317C LEU* 2.9 30.5 + - + +
607C EDO 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C SER 3.6 14.1 - - - +
283C LEU* 3.4 20.6 - - - +
284C GLY 4.3 1.6 - - - +
285C THR* 3.6 17.5 - - - +
286C ASP* 4.7 3.6 - - + +
310C ASP 4.4 1.1 - - - +
311C PRO* 3.3 20.0 - - + +
312C THR 3.4 1.8 - - - -
313C THR* 1.3 90.4 - - - +
315C ASP* 1.3 58.2 + - - +
317C LEU* 3.5 1.7 + - + +
318C ASN* 2.8 36.8 + - - -
368C LYS* 4.6 13.0 - - - -
607C EDO 3.4 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C PRO 4.9 6.8 - - - +
312C THR* 3.3 10.0 + - - +
313C THR 3.3 0.4 - - - -
314C PRO* 1.3 77.8 - - - +
316C PHE* 1.3 62.6 + - - +
318C ASN* 3.4 3.6 + - - +
319C SER* 3.0 27.1 + - - -
368C LYS* 4.0 23.5 - - - +
374C LYS* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LYS* 3.5 60.8 - - + -
261C ALA* 4.5 0.7 - - + -
262C GLU* 4.4 17.0 - - + -
312C THR* 3.1 9.8 + - - +
313C THR 3.6 5.6 - - - +
315C ASP* 1.3 74.0 - - - +
317C LEU* 1.3 70.9 + - + +
319C SER* 3.2 8.6 + - - -
320C LEU* 3.1 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 4.0 12.6 - - + +
256C MET 4.2 4.7 - - - +
257C SER 3.7 12.1 - - - +
261C ALA* 3.6 31.4 - - + -
278C PRO* 4.7 2.2 - - + -
282C SER* 3.7 36.6 - - - +
283C LEU* 4.0 16.6 - - + +
313C THR* 2.9 36.8 + - + +
314C PRO* 4.1 2.9 - - + +
316C PHE* 1.3 78.4 - - + +
318C ASN* 1.3 57.5 + - - +
320C LEU* 3.3 3.5 + - - +
321C LEU* 2.9 30.0 + - - +
326C LEU* 4.0 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.0 39.7 + - - +
314C PRO 2.8 28.6 + - - +
315C ASP* 3.8 5.8 - - - +
316C PHE 3.2 0.2 - - - -
317C LEU* 1.3 76.2 - - - +
319C SER* 1.3 53.4 + - - +
321C LEU* 3.4 12.1 + - - +
322C SER* 2.6 39.0 + - - -
365C ILE* 4.5 7.8 - - - +
368C LYS* 3.5 37.1 - - + +
369C ALA* 3.8 16.0 + - + +
374C LYS* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ASP 3.0 12.0 + - - -
316C PHE* 3.5 12.7 - - - -
318C ASN* 1.3 76.5 - - - +
320C LEU* 1.3 66.6 + - - +
322C SER* 3.2 8.6 + - - -
323C CYS* 3.1 25.7 + - - +
374C LYS* 3.3 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ALA* 3.8 31.9 - - + +
262C GLU* 4.6 4.0 - - - +
265C ALA* 4.6 6.1 - - + -
316C PHE* 3.1 60.7 + - + +
317C LEU* 3.8 4.3 - - - +
319C SER* 1.3 80.3 - - - +
321C LEU* 1.3 60.4 + - - +
323C CYS* 3.4 8.7 + - - -
324C GLY 3.2 4.9 + - - -
325C ASP* 3.1 51.7 + - + +
326C LEU* 3.4 12.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PRO* 4.8 2.2 - - + -
283C LEU* 4.1 20.2 - - + -
317C LEU 2.9 17.9 + - - +
318C ASN* 3.5 11.4 - - - +
320C LEU* 1.3 74.8 - - - +
322C SER* 1.3 54.0 + - - +
324C GLY 3.7 1.9 + - - -
326C LEU* 3.6 33.0 - - + +
327C GLN 4.4 4.0 - - - +
328C VAL 4.6 1.8 - - - +
329C THR* 3.7 29.6 - - + -
365C ILE* 4.7 5.6 - - + -
375C MET* 4.0 17.5 - - + -
379C GLN* 2.8 31.9 + - - +
383C VAL* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ASN 2.6 21.6 + - - -
319C SER 3.2 5.8 + - - -
321C LEU* 1.3 78.2 - - - +
323C CYS* 1.3 56.7 + - - +
369C ALA* 3.7 2.4 - - - +
374C LYS* 3.3 40.2 - - - +
375C MET* 3.4 28.8 - - - +
379C GLN* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C SER 3.1 19.0 + - - +
320C LEU* 3.4 12.7 + - - -
321C LEU 3.4 0.2 - - - -
322C SER* 1.3 78.0 - - - +
324C GLY* 1.3 55.4 + - - +
325C ASP* 3.6 25.8 - - - +
379C GLN* 4.6 0.4 - - - -
----------------------------------------------------------
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