Contacts of the helix formed by residues 458 - 466 (chain C) in PDB entry 1F1H
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 HIS 458 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LYS* 5.2 0.4 - - - -
456C THR 3.3 1.4 + - - +
457C PRO* 1.3 73.3 - - - +
459C PRO* 1.3 73.0 - - + +
460C VAL* 2.9 50.6 - - + +
461C GLU* 2.7 51.6 + - + +
462C PHE* 3.5 6.4 - - - -
147I SER* 4.9 0.8 + - - -
320I LYS* 5.0 2.0 - - - -
453I VAL* 4.0 22.1 + - + +
456I THR* 2.8 39.6 - - - +
457I PRO 3.7 9.6 + - - -
458I HIS* 3.4 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C SER* 4.2 3.8 - - - +
457C PRO 4.0 5.1 - - - +
458C HIS* 1.3 92.1 - - + +
460C VAL* 1.3 56.2 + - - +
462C PHE* 3.0 34.4 + - + +
463C GLU* 3.5 4.2 + - - +
140I PHE* 4.4 5.5 - - - +
141I GLY 4.2 5.7 + - - +
147I SER* 3.7 13.2 - - - -
148I HIS* 3.6 39.7 - - - +
149I VAL* 4.2 10.7 - - + +
459I PRO* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C HIS* 2.9 29.5 - - + +
459C PRO* 1.3 72.6 - - + +
461C GLU* 1.3 58.8 + - - +
462C PHE 3.1 0.2 - - - -
463C GLU* 3.2 8.3 + - - +
464C LEU* 3.0 45.6 + - + +
142I ALA* 3.9 20.2 - - + -
147I SER* 5.4 0.2 - - - -
452I ARG* 3.9 36.1 - - + +
453I VAL* 4.1 7.9 - - + -
456I THR* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C HIS* 2.7 44.7 + - + +
460C VAL* 1.3 72.7 - - - +
462C PHE* 1.3 55.0 + - + +
464C LEU* 4.3 0.9 - - - -
465C TYR* 2.7 52.5 + - + +
256I MET* 4.0 5.1 - - + +
316I THR* 2.6 29.3 + - - +
317I ASN* 2.9 35.7 + - + +
320I LYS* 2.8 31.6 + - - +
453I VAL* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C PRO* 4.0 15.0 - - + -
458C HIS 3.5 17.7 - - - -
459C PRO 3.0 10.4 + - - +
461C GLU* 1.3 78.2 - - + +
463C GLU* 1.3 65.4 + - - +
464C LEU 3.2 0.2 - - - -
466C TYR* 3.0 34.7 + + - +
135I PHE* 5.9 0.2 - + - -
138I ILE* 4.0 19.3 - - + -
140I PHE* 3.6 26.4 - - + -
149I VAL* 3.7 40.8 - - + -
151I ILE* 4.4 3.1 - - + -
256I MET* 3.3 34.5 - - + -
259I PRO* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C PRO 3.5 2.2 + - - +
460C VAL* 3.2 14.9 + - - +
462C PHE* 1.3 79.3 - - - +
464C LEU* 1.3 61.8 + - + +
466C TYR 5.0 0.2 + - - -
140I PHE* 3.5 22.2 - - + -
141I GLY* 4.2 7.7 - - - -
142I ALA* 4.0 26.9 + - - +
452I ARG* 2.7 45.3 + - - +
160J SER* 4.8 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C VAL* 3.0 24.2 + - + +
463C GLU* 1.3 80.8 - - + +
465C TYR* 1.3 88.1 + - + +
466C TYR 4.0 0.2 - - - -
468C VAL* 5.2 1.9 - - - +
449I GLU* 3.6 45.3 - - + +
452I ARG* 4.0 32.3 - - + +
453I VAL* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C GLU* 2.7 39.2 + - + +
464C LEU* 1.3 101.1 - - + +
466C TYR* 1.3 67.1 + - - +
467C SER 3.2 3.1 - - - -
468C VAL* 3.0 31.9 + - + +
256I MET* 3.6 17.0 - - + +
257I PRO* 5.5 0.7 - - + -
314I PRO 4.8 0.4 - - - -
315I THR* 3.5 44.3 - - + -
316I THR* 3.4 38.4 + - - +
317I ASN* 4.1 7.2 - - + -
414I LEU* 4.5 2.3 - - - +
446I ARG* 4.8 3.1 - - - -
449I GLU* 3.6 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C GLU 3.9 1.0 + - - -
462C PHE* 3.0 31.2 + + - +
463C GLU 5.0 0.2 + - - -
464C LEU 4.0 0.6 - - - -
465C TYR* 1.3 77.2 - - - +
467C SER* 1.3 57.4 + - - +
468C VAL 3.3 2.9 + - - +
135I PHE* 3.9 8.2 - + - -
138I ILE* 3.5 39.5 - - + +
140I PHE* 4.3 9.4 - + + -
243I HIS* 5.0 0.2 + - - -
252I THR* 2.7 43.4 + - - +
253I ALA 4.3 0.3 - - - -
254I THR* 3.0 52.1 + - + -
255I PHE 4.4 1.4 + - - -
256I MET* 3.7 17.0 - - - +
169J LYS 4.0 2.2 - - - -
170J GLY 3.9 12.1 - - - -
171J HIS* 3.3 30.5 - + - -
----------------------------------------------------------
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