Contacts of the strand formed by residues 341 - 346 (chain A) in PDB entry 3F9C
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 ARG 341 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR 5.2 1.6 + - - -
310A ILE* 2.7 46.9 + - - +
312A GLN 2.8 25.1 + - - -
313A PRO* 4.1 0.2 - - - +
314A LEU* 3.3 27.3 - - + +
316A PHE* 4.3 11.9 - - + -
334A CYS* 2.5 36.5 + - + +
335A TYR* 3.6 42.6 + - + +
339A LYS* 3.6 28.8 + - - +
340A GLU* 1.3 89.7 + - - +
342A LYS* 1.3 72.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU 3.1 5.9 + - - -
315A PHE* 3.5 20.4 - - + -
316A PHE* 2.9 29.8 + - - -
335A TYR* 3.6 3.4 - - - -
340A GLU* 3.4 28.3 - - - +
341A ARG* 1.3 82.4 - - - +
343A MET* 1.3 62.0 + - - +
391A PHE* 4.2 9.0 - - + -
409A ILE* 3.6 29.2 - - + +
410A GLU* 3.3 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 4.6 0.2 - - - -
316A PHE* 3.2 20.9 - - + +
318A ASN* 3.8 12.8 - - - +
328A ILE* 4.8 3.8 - - + -
331A MET* 3.8 36.8 - - + -
332A LYS* 5.1 9.0 - - + +
335A TYR* 3.4 27.4 + - + +
342A LYS* 1.3 76.3 - - - +
344A ILE* 1.3 68.0 + - - +
409A ILE 4.5 1.9 - - - +
410A GLU 5.5 0.3 - - - -
418A PRO* 4.2 0.7 - - - +
419A GLY* 2.8 38.6 + - - +
420A THR* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 3.9 11.9 - - + -
316A PHE 3.0 7.9 + - - +
317A ILE* 3.8 26.7 - - + -
318A ASN* 3.1 26.0 + - - +
343A MET* 1.3 75.4 - - - +
345A THR* 1.3 68.0 + - - +
346A ILE* 5.0 0.7 - - + -
383A LEU 5.0 2.2 - - - +
387A ALA* 4.1 17.7 - - + -
408A LEU 3.4 22.0 - - - +
409A ILE 3.3 26.9 - - - +
410A GLU 4.2 0.4 - - - -
411A GLY* 3.5 17.7 - - - +
416A LEU* 4.0 22.4 - - + -
417A ILE 3.4 7.0 - - - +
419A GLY 3.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 3.6 11.7 - - + +
319A SER 3.8 5.8 - - - +
320A GLU* 3.5 35.9 - - + +
344A ILE* 1.3 76.4 + - - +
346A ILE* 1.3 64.6 + - - +
416A LEU* 3.3 8.0 - - - +
417A ILE* 2.7 48.2 + - + +
419A GLY 2.6 22.2 + - - -
420A THR* 3.5 10.8 + - - -
421A ASN* 3.5 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 4.0 14.1 - - + -
318A ASN 3.0 11.8 + - - +
320A GLU* 3.0 17.2 + - - +
344A ILE* 5.0 0.2 - - + -
345A THR* 1.3 69.5 - - - +
347A ARG* 1.3 63.4 + - - +
349A SER* 2.8 35.2 + - - +
353A ASN* 6.3 0.7 - - + -
354A PHE* 4.0 31.9 - - + -
375A ILE* 3.5 28.7 - - + -
380A ALA* 3.9 28.5 - - + +
383A LEU* 4.5 5.6 - - + -
384A SER* 4.2 6.7 - - - +
415A ASN 3.6 6.1 - - - +
416A LEU* 3.8 15.7 - - + -
----------------------------------------------------------
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