Contacts of the helix formed by residues 316 - 321 (chain F) 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 THR 316 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F THR* 1.3 73.9 - - - +
317F ASN* 1.3 61.7 + - - +
319F TYR* 3.3 24.5 + - - +
320F LYS* 3.7 10.9 + - - -
414F LEU* 4.0 11.4 - - + +
450F ASP* 3.2 36.1 - - - +
453F VAL* 3.5 21.3 - - + +
461L GLU* 2.7 35.2 + - - +
465L TYR* 3.4 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F MET* 3.5 18.7 - - - +
257F PRO* 3.2 13.7 - - + +
258F LYS* 2.7 52.7 + - - +
315F THR* 3.6 8.1 - - - +
316F THR* 1.3 80.5 + - - +
318F SER* 1.3 64.2 + - - +
320F LYS* 2.9 21.7 + - - +
321F ARG 3.8 2.4 + - - -
457L PRO* 4.1 5.1 - - - +
461L GLU* 2.9 31.6 + - + -
465L TYR* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F PRO* 3.6 7.8 - - - +
313F ASN* 3.6 21.3 - - - -
314F PRO 3.9 0.2 - - - -
315F THR* 2.6 41.6 + - - -
317F ASN* 1.3 77.4 - - - +
319F TYR* 1.3 57.7 + - - +
321F ARG* 3.2 19.8 + - - +
322F LEU* 3.3 16.2 + - - +
362F ASP* 2.7 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F ASN* 3.5 8.8 + - + +
313F ASN* 2.8 27.5 + - + +
315F THR 3.2 21.8 - - - -
316F THR* 3.6 10.5 - - - +
317F ASN 3.1 1.0 - - - -
318F SER* 1.3 74.1 - - - +
320F LYS* 1.3 61.4 + - + +
321F ARG 3.3 1.3 - - - -
322F LEU* 3.4 41.4 - - + +
323F VAL* 4.2 7.3 - - - +
411F ALA* 3.5 30.1 - - + -
412F GLY 4.0 13.6 - - - +
413F SER* 3.7 21.8 - - - -
414F LEU* 3.3 28.3 - - + -
417F ALA* 3.3 22.0 - - - +
454L ARG* 4.7 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F LYS* 3.4 30.0 - - + -
316F THR* 3.7 10.4 + - - +
317F ASN* 2.9 13.4 + - - +
319F TYR* 1.3 79.0 - - - +
321F ARG* 1.3 58.9 - - - +
323F VAL* 4.0 16.0 - - - +
453F VAL* 5.0 5.5 - - - +
458F HIS* 5.2 0.4 - - - -
453L VAL 4.1 4.0 + - - -
454L ARG* 3.1 30.0 + - - +
455L MET* 3.9 13.2 - - - +
456L THR 3.3 22.9 - - - +
457L PRO* 3.7 14.1 - - + -
458L HIS* 4.4 4.0 - - - +
461L GLU* 2.7 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F PRO* 4.1 20.9 - - + +
258F LYS* 4.1 14.2 + - + +
265F GLY* 4.4 9.2 - - - +
266F SER 3.4 25.7 + - - +
267F GLY* 3.4 23.5 - - - +
269F HIS* 4.5 6.7 + - - -
313F ASN* 4.1 1.6 + - - -
317F ASN 3.8 1.0 + - - -
318F SER 3.2 10.7 + - - +
320F LYS* 1.3 78.2 - - - +
322F LEU* 1.3 70.7 + - + +
323F VAL* 2.9 15.0 + - - +
328F ALA* 4.0 12.6 - - - +
329F PRO* 4.2 13.5 - - + +
359F ARG 3.3 22.4 + - - -
360F PHE 2.9 25.9 + - - -
361F PRO 3.5 5.5 + - - -
362F ASP* 3.9 7.4 + - - +
----------------------------------------------------------
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