Contacts of the helix formed by residues 661 - 671 (chain F) in PDB entry 4MNE
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 ASN 661 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E MET* 3.4 22.2 - - - +
234E ARG* 3.0 54.1 + - - +
240E TYR* 5.3 1.6 + - - -
659F ILE* 3.3 4.5 + - + -
660F ASN* 1.3 82.9 + - - +
662F ARG* 1.3 65.7 + - - +
663F ASP 3.9 2.8 + - - -
664F GLN* 2.9 48.6 + - - +
665F ILE* 3.2 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 662 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ASN* 4.6 17.0 + - - +
190E ASP* 5.5 7.5 + - - -
192E LYS* 5.8 2.6 - - - +
219E MET* 3.2 45.8 + - - +
220E ALA* 4.2 9.8 - - - +
222E SER* 3.3 32.2 + - - +
223E PHE 4.7 2.9 - - - -
230E MET* 5.8 6.9 - - + +
901E ACP 5.5 3.8 + - - -
903E 573 4.2 12.3 - - - +
617F ILE* 3.8 6.0 - - + +
660F ASN 3.8 4.2 + - - -
661F ASN* 1.3 72.7 + - - +
663F ASP* 1.3 79.9 + - - +
665F ILE* 3.1 17.0 + - - +
666F ILE* 3.1 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 663 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E GLY* 5.5 2.3 + - - -
227E ARG 4.6 1.7 - - - +
228E SER* 2.9 31.1 + - - +
230E MET* 4.4 12.2 - - + +
235E LEU* 3.8 20.2 - - + -
310E ILE* 4.0 8.1 - - - +
314E LEU* 3.2 16.7 - - + +
661F ASN* 3.3 6.5 + - - +
662F ARG* 1.3 89.8 + - - +
664F GLN* 1.3 60.5 + - - +
666F ILE* 3.4 18.8 + - - +
667F PHE* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 664 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ARG 3.4 18.5 - - - +
235E LEU* 3.5 18.7 - - - +
237E GLY* 3.7 24.8 - - - -
659F ILE* 3.7 32.0 - - + +
661F ASN* 2.9 32.4 + - + +
663F ASP* 1.3 79.8 - - - +
665F ILE* 1.3 55.1 + - - +
667F PHE 4.5 0.2 - - - +
668F MET* 2.8 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 665 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E ALA* 4.5 8.5 - - + +
617F ILE* 3.9 31.4 - - + +
618F LEU* 4.4 14.6 - - + -
625F ILE* 6.0 0.7 - - + -
656F TYR* 4.1 24.9 - - + +
659F ILE* 3.7 39.0 - - + +
661F ASN 3.2 6.9 + - - +
662F ARG* 3.1 11.7 + - - +
664F GLN* 1.3 73.9 - - - +
666F ILE* 1.3 59.1 + - - +
669F VAL* 2.8 52.6 + - + +
674F LEU* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 666 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E PHE 5.7 0.4 - - - +
224E VAL* 4.0 28.5 - - + -
225E GLY 4.8 1.3 - - - +
310E ILE* 4.3 22.4 - - + -
311E PHE* 4.0 6.7 - - - -
314E LEU* 3.8 11.4 - - + -
613F LEU* 6.3 0.2 - - + -
617F ILE* 4.0 20.2 - - + -
625F ILE* 3.4 35.3 - - + +
662F ARG* 3.2 15.5 - - + +
663F ASP* 3.5 24.0 - - - +
665F ILE* 1.3 78.3 - - - +
667F PHE* 1.3 63.3 + - - +
670F GLY* 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 667 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E LEU* 3.2 29.4 - - + +
236E GLN* 3.9 15.9 - - + -
311E PHE* 3.7 13.1 - + - -
314E LEU* 3.8 28.7 - - + -
315E ASP* 3.7 24.7 - - - -
318E VAL* 3.7 32.3 - - + -
319E ASN* 4.8 1.3 - - - -
663F ASP 2.8 22.2 + - - +
664F GLN 3.9 1.6 - - - +
666F ILE* 1.3 77.8 - - - +
668F MET* 1.3 66.2 + - + +
671F ARG* 3.1 36.2 + - + +
673F TYR* 4.3 27.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 668 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E LEU 3.7 13.0 - - - +
236E GLN* 4.2 14.8 - - - +
659F ILE* 5.4 1.3 - - + -
664F GLN* 2.8 54.9 + - - +
667F PHE* 1.3 78.4 - - + +
669F VAL* 1.3 64.7 + - - +
671F ARG* 4.4 2.7 - - - -
672F GLY 3.2 2.9 + - - -
673F TYR* 2.9 53.9 + - + +
674F LEU* 3.3 35.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 669 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617F ILE 5.8 1.6 - - - +
620F MET 4.4 7.6 - - - +
622F PRO* 3.8 28.3 - - + +
625F ILE* 3.5 23.1 - - + -
640F TYR* 4.5 7.6 - - - +
656F TYR* 3.6 30.3 - - + +
665F ILE* 2.8 36.1 + - + +
668F MET* 1.3 73.0 - - - +
670F GLY* 1.3 56.9 + - - +
671F ARG 3.0 5.4 + - - -
672F GLY* 3.2 12.8 + - - -
674F LEU* 3.8 21.8 - - + +
699F LYS* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 670 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E PHE* 3.8 8.7 - - - -
622F PRO* 4.0 12.8 - - - -
625F ILE* 4.0 16.8 - - - +
626F ARG* 2.7 38.1 + - - -
666F ILE 3.1 17.4 + - - -
667F PHE 3.9 0.4 - - - -
669F VAL* 1.3 77.7 - - - +
671F ARG* 1.3 57.2 + - - +
672F GLY 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 671 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E PHE* 4.2 11.9 - - + -
315E ASP* 2.9 36.6 + - - -
319E ASN* 3.3 23.0 + - - +
626F ARG* 5.2 1.6 - - - -
667F PHE* 3.1 26.7 + - + +
668F MET 3.9 3.6 - - - +
669F VAL 3.0 0.6 - - - -
670F GLY* 1.3 79.3 - - - +
672F GLY* 1.3 60.1 + - - +
673F TYR* 3.2 52.2 + - + -
----------------------------------------------------------
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