Contacts of the helix formed by residues 304 - 314 (chain I) in PDB entry 6MZL
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 304 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I LEU* 6.5 0.7 - - + -
260I SER* 3.7 34.5 - - - +
263I ILE* 6.0 1.3 - - + -
264I SER* 3.5 13.5 - - - +
286I VAL* 6.2 5.4 - - + -
289I LEU* 6.3 2.5 - - + -
297I LEU* 4.1 26.9 - - + -
300I TYR* 3.2 28.3 - - + +
301I VAL* 2.8 8.4 + - - +
302I HIS 3.7 0.8 - - - -
303I GLU* 1.3 89.3 - - + +
305I ILE* 1.3 65.9 + - + +
306I PRO* 3.3 2.0 - - - +
307I ALA* 2.9 23.6 + - - +
308I VAL* 3.3 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I MET* 5.6 1.6 - - + -
297I LEU* 5.1 9.4 - - + -
301I VAL* 3.6 33.9 - - + +
302I HIS* 5.9 0.2 - - - -
304I LEU* 1.3 77.5 - - + +
306I PRO* 1.3 60.7 - - + +
308I VAL* 3.1 12.6 + - + +
309I MET* 3.0 34.5 + - + +
337I VAL* 6.0 2.5 - - + -
340I ILE* 3.7 43.5 - - + -
351I ILE* 5.7 6.3 - - + -
355I ILE* 4.5 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 306 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I ARG* 6.1 2.9 - - - +
302I HIS* 4.8 8.5 - - - +
303I GLU* 4.3 10.5 - - - +
304I LEU 3.5 12.1 - - - +
305I ILE* 1.3 92.7 - - + +
307I ALA* 1.3 56.3 + - - +
309I MET* 3.9 9.7 - - + +
310I THR* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I SER* 4.2 19.1 - - - +
267I VAL* 3.7 33.6 - - + +
268I ARG* 6.2 2.2 - - + -
283I MET* 5.2 3.4 - - + -
304I LEU 2.9 12.3 + - - +
306I PRO* 1.3 76.6 - - - +
308I VAL* 1.3 62.2 + - + +
310I THR* 3.4 5.7 + - - -
311I CYS* 2.9 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 4.7 14.4 - - + -
286I VAL* 4.7 20.9 - - + -
304I LEU 3.4 17.9 - - - +
305I ILE* 3.1 16.1 + - + +
307I ALA* 1.3 77.5 - - + +
309I MET* 1.3 57.2 + - + +
311I CYS* 3.1 11.1 + - - +
312I ILE* 2.9 28.4 + - + +
333I ALA* 4.2 13.9 - - + +
336I LEU* 4.9 7.2 - - + -
337I VAL* 3.7 29.8 - - + -
340I ILE* 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305I ILE* 3.0 24.6 + - + +
306I PRO* 3.9 7.9 - - + +
307I ALA 3.3 0.2 - - - -
308I VAL* 1.3 76.1 - - + +
310I THR* 1.3 61.9 + - - +
312I ILE* 2.8 30.4 + - + +
313I VAL* 3.0 25.0 + - + +
337I VAL* 5.3 3.8 - - + -
355I ILE* 3.9 32.8 - - + -
358I THR* 3.8 21.8 - - + +
359I PHE* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 310 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 5.4 1.8 - - + -
268I ARG* 6.1 4.0 - - + -
271I VAL* 3.8 36.8 - - + +
306I PRO* 2.8 23.6 + - - +
307I ALA* 3.7 7.0 - - - -
309I MET* 1.3 75.7 - - - +
311I CYS* 1.3 63.1 + - - +
312I ILE 3.4 0.3 + - - -
313I VAL* 3.5 13.3 + - + +
314I SER 4.4 9.5 + - - +
316I GLN* 4.4 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 311 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 4.1 9.9 - - - -
271I VAL* 5.3 2.2 - - - -
279I LEU* 3.9 24.5 - - - -
283I MET* 3.6 38.8 - - + -
307I ALA 2.9 19.3 + - - -
308I VAL 3.3 10.8 - - - +
310I THR* 1.3 78.1 - - - +
312I ILE* 1.3 60.3 + - - +
316I GLN* 2.4 32.0 + - - +
329I LEU 5.7 0.5 - - - -
330I ARG* 4.3 5.2 - - - +
333I ALA* 4.9 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I VAL* 2.9 17.7 + - + +
309I MET* 2.8 22.2 + - + +
311I CYS* 1.3 79.8 - - - +
313I VAL* 1.3 68.4 + - + +
330I ARG* 3.7 26.0 + - + +
333I ALA* 3.9 20.9 - - + +
334I ALA* 4.7 7.0 - - + +
337I VAL* 3.7 29.6 - - + -
359I PHE* 4.2 27.8 - - + -
375I GLY* 3.6 35.4 - - - +
376I SER 4.5 0.2 - - - +
379I GLY* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I MET* 3.0 23.7 + - + +
310I THR* 3.5 7.5 + - + +
311I CYS 3.5 1.4 - - - -
312I ILE* 1.3 83.6 - - + +
314I SER* 1.3 75.9 + - - +
359I PHE* 5.7 6.1 - - + -
371I THR* 3.0 23.3 + - - +
372I THR* 3.2 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I VAL* 5.9 2.6 - - - +
310I THR 4.4 7.3 + - - +
311I CYS 5.2 0.6 + - - -
312I ILE 3.8 0.8 + - - -
313I VAL* 1.3 88.9 - - - +
315I ARG* 1.3 82.6 + - - +
316I GLN* 3.0 18.7 + - - +
330I ARG* 5.2 0.6 - - - +
369I PRO* 5.6 1.8 - - - -
371I THR* 3.4 11.4 - - - -
372I THR* 3.6 20.0 - - - -
----------------------------------------------------------
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