Contacts of the strand formed by residues 331 - 339 (chain A) in PDB entry 1QZZ
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 LEU 331 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.8 19.3 - - + -
274A VAL* 3.5 32.5 - - + -
277A LEU* 4.7 4.0 - - + -
283A LEU* 3.8 31.0 - - + -
323A VAL 4.9 0.5 - - - +
326A ALA* 3.0 27.5 + - + +
327A GLY* 3.2 23.4 + - - -
329A ALA* 4.1 3.6 - - + -
330A GLY* 1.3 79.6 - - - +
332A ALA* 1.3 58.8 + - - +
353A PHE* 3.9 18.1 - - + -
354A THR 3.3 20.0 - - - +
355A ALA* 4.2 3.1 - - - +
356A VAL* 3.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 1.3 74.0 - - - +
333A LEU* 1.3 68.2 + - - +
334A ALA 3.3 0.3 + - - -
353A PHE* 3.3 6.4 - - - -
354A THR* 3.0 37.6 + - - +
356A VAL* 3.1 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 3.7 28.5 - - + +
332A ALA* 1.3 74.0 - - - +
334A ALA* 1.3 59.2 + - - +
335A SER* 3.6 27.4 - - - +
336A GLU* 4.7 12.3 - - + +
351A LEU* 4.0 13.5 - - + -
352A GLU 3.6 6.1 - - - +
353A PHE* 3.5 33.1 - - + -
354A THR* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 4.6 3.8 - - - +
332A ALA 3.3 1.2 + - - +
333A LEU* 1.3 75.0 - - - +
335A SER* 1.3 62.3 + - - +
352A GLU* 2.6 36.4 + - + +
353A PHE* 4.4 0.7 - - - -
354A THR* 4.1 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.6 8.0 - - - +
334A ALA* 1.3 80.5 - - - +
336A GLU* 1.3 62.6 + - - +
337A ARG* 3.6 24.0 + - - +
350A ILE 3.8 0.2 - - - +
352A GLU* 2.8 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 2.8 48.6 + - - +
333A LEU* 4.7 11.8 - - + +
335A SER* 1.3 76.4 + - - +
337A ARG* 1.3 75.6 + - - +
338A THR* 3.3 25.3 + - - +
349A SER* 4.9 2.7 - - - +
350A ILE 3.5 7.6 - - - +
351A LEU* 3.5 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA* 2.5 47.0 + - + -
178A TYR* 3.5 36.3 - - - +
179A ASP* 4.4 3.4 - - - +
335A SER* 3.6 21.7 + - - +
336A GLU* 1.3 86.3 - - - +
338A THR* 1.3 64.4 + - - +
339A SER* 5.6 1.1 - - - -
348A PHE* 5.1 3.4 - - + -
349A SER* 3.1 2.0 - - - -
350A ILE* 2.8 50.6 + - + +
352A GLU* 4.4 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 5.8 4.3 - - - +
319A ARG* 3.1 36.3 + - - +
336A GLU* 3.3 17.0 + - - +
337A ARG* 1.3 72.8 - - - +
339A SER* 1.3 63.2 + - - +
347A ASP* 5.4 5.9 - - - +
348A PHE 3.1 13.0 - - - -
349A SER* 3.4 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA* 5.6 0.7 - - - +
177A ALA* 5.4 5.4 - - - -
337A ARG* 5.6 1.1 - - - -
338A THR* 1.3 76.7 - - - +
340A GLY* 1.3 74.1 + - - +
347A ASP* 3.4 8.5 - - - +
348A PHE* 2.8 55.4 + - - +
----------------------------------------------------------
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