Contacts of the helix formed by residues 400 - 410 (chain C) in PDB entry 1MFQ
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 PRO 400 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C PHE 3.4 8.4 - - - +
397C SER 3.5 13.2 - - - +
398C LYS 3.2 11.4 - - - +
399C GLN* 1.3 79.1 - - - +
401C GLY* 1.3 58.4 + - - +
402C ARG 2.9 2.9 - - - -
403C ILE* 2.6 35.0 + - + +
404C GLN* 3.1 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A A 3.1 28.6 - - - +
185A C 5.8 0.2 - - - -
399C GLN 3.1 2.4 + - - -
400C PRO* 1.3 79.5 - - - +
402C ARG* 1.3 55.7 + - - +
404C GLN* 3.2 11.7 + - - +
405C ARG* 2.8 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A A 3.1 62.8 + - + -
383C ASN* 4.1 2.2 - - - +
385C GLN* 6.1 1.2 - - - +
386C GLU* 3.2 44.2 + - - +
395C VAL* 3.7 27.9 - - - +
396C PHE* 3.6 10.8 - - + +
399C GLN* 2.7 51.5 + - - +
401C GLY* 1.3 78.0 - - - +
403C ILE* 1.3 55.3 + - - +
405C ARG* 3.3 3.6 + - - +
406C VAL* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C PHE* 3.8 37.0 - - + +
397C SER* 5.7 1.1 - - - -
400C PRO* 2.6 21.8 + - + +
402C ARG* 1.3 69.5 - - - +
404C GLN* 1.3 59.4 - - - +
406C VAL* 3.1 4.8 + - - +
407C ALA* 2.8 28.9 + - - +
414C THR* 3.9 29.4 - - + +
417C VAL* 4.0 18.9 - - + +
418C GLN* 3.8 29.2 - - + +
421C LEU* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C PRO 3.1 7.3 + - - +
401C GLY* 3.5 12.6 - - - +
403C ILE* 1.3 82.2 - - - +
405C ARG* 1.3 64.6 + - - +
407C ALA* 4.4 5.4 - - + -
408C ARG* 3.1 76.5 + - + +
414C THR* 5.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A A 3.0 37.9 + - + -
185A C 3.3 30.7 - - - +
207A C 3.0 45.6 + - - +
208A A 3.9 5.7 - - - -
381C SER 3.4 19.2 + - - -
383C ASN* 4.6 0.2 - - - +
386C GLU* 2.8 37.1 + - - -
401C GLY 2.8 18.1 + - - +
402C ARG* 3.4 13.1 + - - +
403C ILE 3.2 0.2 - - - -
404C GLN* 1.3 72.5 - - - +
406C VAL* 1.3 63.4 + - - +
408C ARG* 4.0 4.3 - - - +
409C GLY* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ILE* 3.7 39.5 - - + +
381C SER* 4.0 13.1 - - - +
382C MET* 4.2 12.6 - - + -
396C PHE* 3.8 17.9 - - + -
402C ARG 2.9 20.0 + - - +
403C ILE* 3.6 5.4 - - - +
405C ARG* 1.3 94.5 - - - +
407C ALA* 1.3 67.9 + - - +
409C GLY* 3.0 2.0 + - - +
410C SER* 2.8 25.5 + - - -
417C VAL* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE 2.8 20.1 + - - +
404C GLN* 3.7 4.9 - - + +
406C VAL* 1.3 75.8 - - - +
408C ARG* 1.3 67.5 + - + +
410C SER* 2.9 12.6 + - - -
411C GLY 3.1 7.8 + - - -
412C VAL* 3.3 24.1 + - - +
413C SER 3.9 12.1 - - - +
414C THR* 4.0 18.4 - - - +
417C VAL* 3.7 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A G 3.6 7.8 + - - -
205A A 5.6 1.4 - - - -
206A G 4.6 4.8 + - - +
72B TRP* 3.4 60.6 + - + +
73B ASN* 4.2 16.2 + - - +
404C GLN* 3.1 57.4 + - + +
405C ARG* 4.1 3.6 - - - +
407C ALA* 1.3 82.1 - - + +
409C GLY* 1.3 62.2 + - - +
410C SER 3.2 1.0 + - - -
411C GLY* 3.3 11.3 + - - +
412C VAL 5.0 1.1 - - - -
601C CL 3.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A G 2.6 37.6 + - - +
194A G 3.9 1.9 + - - -
206A G 4.2 5.8 - - - -
207A C 3.3 29.2 - - - +
381C SER* 3.0 9.5 + - - -
405C ARG 2.9 14.2 + - - -
406C VAL 3.0 4.4 + - - -
408C ARG* 1.3 76.4 - - - +
410C SER* 1.3 49.7 + - - +
411C GLY 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A G 3.3 24.7 - - - +
194A G 2.9 23.7 + - - -
377C THR* 4.0 1.5 + - - -
378C ILE* 3.9 22.1 - - - -
381C SER* 3.4 6.3 - - - -
406C VAL* 2.8 15.3 + - - +
407C ALA 2.9 0.2 + - - -
409C GLY* 1.3 75.7 - - - +
411C GLY* 1.3 53.4 + - - +
412C VAL* 2.6 40.8 + - - +
----------------------------------------------------------
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