Contacts of the strand formed by residues 334 - 342 (chain A) in PDB entry 3EFC
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 334 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 3.4 3.4 - - - -
267A LYS* 2.7 24.4 + - - +
268A LEU 4.0 0.9 + - - -
269A SER* 3.2 29.6 - - - +
329A ASN* 2.7 48.0 + - + +
332A ASP* 3.0 32.5 - - - +
333A LYS* 1.3 75.1 - - - +
335A VAL* 1.3 57.4 + - - +
336A LYS 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 4.3 9.2 - - + -
266A TYR* 3.6 21.1 - - + +
267A LYS 3.0 8.9 + - - +
268A LEU* 3.6 9.9 - - + +
269A SER* 3.0 24.8 + - - -
296A TYR* 4.2 21.5 - - + -
326A PRO* 3.7 27.4 - - + -
327A GLU 3.5 4.3 - - - +
328A ILE* 3.3 35.0 - - + -
334A THR* 1.3 72.5 - - - +
336A LYS* 1.3 70.0 + - - +
337A LEU* 4.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER* 3.7 19.2 + - - +
270A GLY 3.8 13.0 - - - +
271A VAL 5.7 0.2 - - - -
272A GLU* 3.2 47.2 + - + +
327A GLU* 2.7 66.5 + - + +
329A ASN* 5.9 0.2 - - - +
334A THR* 4.3 1.0 - - - +
335A VAL* 1.3 73.7 - - - +
337A LEU* 1.3 64.1 + - - +
338A ARG* 3.4 7.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.3 17.9 - - + -
270A GLY 3.1 12.9 + - - +
271A VAL* 3.5 14.2 - - + +
272A GLU* 3.1 25.8 + - - +
296A TYR* 4.7 9.9 - - + +
301A VAL* 3.7 22.4 - - + -
304A MET* 3.5 32.8 - - + -
324A SER* 4.1 12.6 - - - -
325A MET 3.9 18.6 - - - +
326A PRO* 4.0 9.9 - - + -
335A VAL* 4.0 2.7 + - + -
336A LYS* 1.3 71.6 - - - +
338A ARG* 1.3 62.0 + - - +
339A VAL* 3.2 14.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLU* 4.0 28.7 + - + +
274A SER* 5.2 9.0 - - - -
323A GLN 4.2 0.9 - - - +
324A SER* 3.9 0.7 - - - -
325A MET* 3.0 63.8 + - + +
327A GLU* 2.6 43.0 + - + +
336A LYS* 3.4 10.3 + - + +
337A LEU* 1.3 71.2 - - - +
339A VAL* 1.3 61.4 + - - +
340A ASN* 3.9 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 4.0 9.2 - - + -
272A GLU 3.1 6.2 + - - +
273A VAL* 3.9 26.2 - - + -
274A SER* 3.0 26.3 + - - -
304A MET* 3.7 14.8 - - + -
305A GLU* 5.7 1.6 - - + -
308A ILE* 4.5 7.2 - - + -
322A VAL* 4.5 10.3 - - + -
323A GLN 3.8 6.1 - - - +
324A SER* 3.3 22.0 - - - +
337A LEU* 3.2 25.6 + - + -
338A ARG* 1.3 74.2 - - - +
340A ASN* 1.3 68.3 + - - +
341A VAL* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER* 3.2 19.8 + - - +
275A GLY* 4.3 9.5 - - - -
321A ARG* 4.0 3.6 + - - +
322A VAL* 3.5 4.9 - - - +
323A GLN* 3.0 39.3 + - + +
325A MET* 6.4 1.8 - - + -
338A ARG 5.0 2.2 - - - +
339A VAL* 1.3 77.9 - - - +
341A VAL* 1.3 74.3 + - - +
342A ASP* 4.0 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 3.9 9.9 - - + -
274A SER 2.9 8.1 + - - -
275A GLY* 3.4 2.8 - - - -
276A ASN 2.9 33.1 + - - +
277A LEU* 3.4 20.4 - - + -
284A ILE* 4.4 2.7 - - + -
308A ILE* 3.7 27.8 - - + -
312A LEU* 3.4 31.6 - - + -
321A ARG 3.5 4.5 - - - +
322A VAL* 3.6 19.3 - - + -
339A VAL* 4.2 3.6 - - + -
340A ASN* 1.3 80.2 + - - +
342A ASP* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLY* 6.0 0.4 - - - -
276A ASN* 3.3 25.5 + - - +
320A PRO* 3.6 0.2 - - - +
321A ARG* 2.9 59.2 + - + +
340A ASN* 4.0 7.0 + - - +
341A VAL* 1.3 72.6 - - - +
343A ALA* 1.3 77.1 + - - +
344A GLY* 4.3 0.5 - - - -
----------------------------------------------------------
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