Contacts of the helix formed by residues 6118 - 6126 (chain L) in PDB entry 1F2I
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 ARG6118 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5008E C 3.8 2.2 - - - +
6006F C 3.4 32.3 - - - +
6007F G 2.5 48.7 + - - -
5118K ARG* 3.4 50.2 - - + +
5119K SER 5.8 1.1 - - - +
5120K ASP* 4.0 8.1 + - - +
6105L TYR* 3.3 15.4 - - - +
6116L PHE* 3.6 5.2 - - - +
6117L SER* 1.3 85.4 - - - +
6119L SER* 1.3 60.6 + - - +
6120L ASP* 2.9 41.4 + - - +
6121L GLU* 3.0 39.1 + - - +
6122L LEU 3.5 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER6119 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5099K VAL* 3.4 27.7 + - - +
5100K PRO 4.8 1.7 + - - -
5117K SER* 6.4 0.4 - - - -
5118K ARG* 5.4 3.6 - - - +
6105L TYR* 3.6 30.7 - - - -
6118L ARG* 1.3 70.0 - - - +
6120L ASP* 1.3 63.3 + - - +
6121L GLU 2.9 5.8 + - - -
6122L LEU* 3.1 12.4 + - - +
6123L THR* 3.1 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP6120 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5007E G 4.8 16.8 - - + +
5008E C 3.8 12.6 + - - -
5009E G 5.2 0.2 - - - +
6006F C 4.1 7.2 + - - -
5118K ARG* 4.8 7.5 + - - -
6118L ARG* 2.9 52.8 + - - +
6119L SER* 1.3 75.8 + - - +
6121L GLU* 1.3 62.8 + - - +
6123L THR* 4.0 7.7 + - - -
6124L ARG* 3.5 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU6121 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6004F G 4.9 1.5 + - + -
6005F G 3.3 28.9 + - + +
6006F C 3.3 34.2 + - + +
6116L PHE* 3.4 23.3 - - + +
6117L SER* 3.1 14.0 + - - -
6118L ARG* 3.0 41.2 + - + +
6119L SER 2.9 0.6 - - - -
6120L ASP* 1.3 82.0 + - - +
6122L LEU* 1.3 63.3 + - - +
6124L ARG* 3.6 23.3 + - - +
6125L HIS* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU6122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097K TYR* 4.6 6.1 - - + +
5099K VAL* 4.2 17.9 - - + -
6105L TYR* 3.9 16.2 - - + -
6106L ALA 3.1 23.6 - - - +
6107L CYS* 3.6 27.8 - - + +
6116L PHE* 3.5 32.5 - - + -
6118L ARG 3.5 7.7 + - - +
6119L SER* 3.1 9.0 + - - +
6121L GLU* 1.3 80.6 - - - +
6123L THR* 1.3 58.8 + - - +
6125L HIS* 3.4 1.9 + - + -
6126L ILE* 2.9 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR6123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097K TYR 5.3 6.7 - - - +
5099K VAL* 3.4 19.9 - - + +
6119L SER* 3.1 17.5 + - - -
6120L ASP* 4.0 7.1 + - - -
6121L GLU 3.4 0.2 - - - -
6122L LEU* 1.3 78.6 - - - +
6124L ARG* 1.3 61.7 + - - +
6126L ILE* 3.6 15.6 + - + +
6127L ARG* 3.7 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG6124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5009E G 3.9 7.2 + - - -
6003F G 5.4 2.1 + - - -
6004F G 3.6 13.3 + - - +
6005F G 3.0 47.9 + - - -
6006F C 3.8 11.6 - - - +
6116L PHE* 6.3 0.4 - - - -
6120L ASP 3.5 18.7 + - - +
6121L GLU* 3.6 16.6 + - - +
6122L LEU 3.3 0.2 - - - -
6123L THR* 1.3 75.8 - - - +
6125L HIS* 1.3 61.2 + - - +
6126L ILE 3.1 0.2 - - - -
6127L ARG* 3.1 47.9 + - - +
6128L ILE* 4.0 5.5 + - - +
6145L SER* 6.0 0.9 - - - -
6146L ARG* 3.4 55.6 - - + +
6148L ASP* 4.7 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS6125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6004F G 2.6 36.9 + - - +
6107L CYS* 4.4 6.7 - - + -
6112L CYS* 3.6 6.0 - - - -
6114L ARG* 3.7 18.0 - - + +
6116L PHE* 3.3 33.4 - + + -
6121L GLU 3.4 7.6 + - - +
6122L LEU* 4.0 2.5 - - + +
6123L THR 3.4 0.2 - - - -
6124L ARG* 1.3 80.6 - - - +
6126L ILE* 1.3 59.1 + - - +
6127L ARG 3.1 0.4 - - - -
6128L ILE* 3.3 34.9 - - + +
6129L HIS* 3.7 6.5 + + - -
6201L ZN 2.3 34.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE6126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097K TYR* 3.5 44.9 - - + +
5099K VAL* 4.2 2.5 - - + -
6107L CYS* 4.4 4.0 - - - -
6108L PRO* 4.1 15.7 - - + -
6109L VAL* 6.3 0.4 - - + -
6122L LEU* 2.9 52.8 + - + +
6123L THR* 3.9 12.3 - - + +
6124L ARG 3.1 0.8 - - - -
6125L HIS* 1.3 73.6 - - - +
6127L ARG* 1.3 59.4 + - - +
6128L ILE 3.0 8.8 + - - -
6129L HIS* 3.3 21.8 + - + +
6130L THR* 3.4 21.9 + - + +
----------------------------------------------------------
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