Contacts of the strand formed by residues 331 - 335 (chain D) 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 MET 331 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ALA 5.6 0.2 - - - +
330D VAL* 1.3 84.9 - - + +
332D LEU* 1.3 56.2 + - - +
333D ALA* 2.9 10.9 + - + +
340D SER* 3.4 30.1 + - - +
341D ALA* 3.9 2.5 - - - -
342D SER* 2.5 31.3 + - - -
392D MET* 5.8 7.0 - - + -
396D LEU* 4.8 3.6 - - - -
397D TYR* 3.9 44.0 - - + +
405D LYS* 5.2 4.7 - - + -
407D ILE* 4.0 32.8 - - + -
408D PRO 3.9 3.1 - - - -
409D GLN* 3.9 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ILE* 3.6 44.4 - - + +
305D ALA* 3.6 29.4 - - + -
306D LYS* 5.3 3.8 - - + +
331D MET* 1.3 65.6 - - - +
333D ALA* 1.3 60.4 + - - +
342D SER* 3.7 9.9 - - - +
343D ILE* 6.0 0.4 - - - -
360D PHE* 5.0 3.4 - - + -
407D ILE* 4.4 6.3 - - - +
408D PRO* 2.8 35.2 + - + +
409D GLN 3.4 22.7 - - - +
410D VAL* 3.5 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ILE* 4.1 9.6 - - - +
331D MET* 2.9 11.8 + - + +
332D LEU* 1.3 74.6 - - - +
334D TYR* 1.3 61.5 + - - +
341D ALA* 3.5 11.4 - - + +
342D SER* 3.7 1.1 + - - -
343D ILE* 3.4 26.1 + - - +
390D GLU 5.5 1.1 - - - +
392D MET* 3.6 42.6 - - + -
407D ILE* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D TYR* 4.4 17.4 - + + +
290D LEU* 5.0 0.2 - - + -
295D LEU* 4.0 20.0 - - + +
298D ILE* 4.1 35.9 - - + -
302D ILE* 4.7 2.5 - - + -
333D ALA* 1.3 76.4 - - - +
335D SER* 1.3 61.8 - - - +
341D ALA* 4.4 1.1 - - - -
343D ILE* 3.3 16.8 - - + +
345D ILE* 4.4 7.0 - - + -
387D HIS* 4.7 2.4 - - - -
388D PRO* 3.3 41.9 - - + +
389D GLY 2.6 20.9 + - - -
390D GLU* 3.9 8.5 - - - -
391D PRO* 3.2 38.3 - - + +
392D MET 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D TYR* 3.9 8.1 - - - -
334D TYR* 1.3 78.1 - - - +
336D ALA* 1.3 64.2 + - - +
337D ARG* 3.1 4.9 + - - +
338D ASN* 2.9 32.0 + - - +
341D ALA* 4.0 7.8 - - - +
343D ILE 3.1 6.1 + - - +
344D ARG* 3.2 11.4 - - - +
345D ILE* 2.9 25.4 + - - +
392D MET 3.7 16.6 - - - -
393D ASP* 3.6 12.4 + - - -
----------------------------------------------------------
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