Contacts of the strand formed by residues 345 - 350 (chain A) in PDB entry 2Q7N
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 TYR 345 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 3.6 1.9 - - - -
305A TRP* 3.0 57.2 + + + -
307A PRO* 3.7 25.6 - - + -
321A TYR* 5.8 0.9 - + - -
334A PHE* 4.4 20.0 - + + -
336A ARG* 3.4 29.7 + - - -
339A GLY 4.6 0.5 + - - -
340A LEU* 3.2 34.7 - - + +
341A THR* 2.5 44.8 + - - -
343A GLU* 4.1 17.7 - - + -
344A THR* 1.3 77.3 - - - +
346A ARG* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 5.2 4.8 + - - -
296A HIS* 6.1 5.1 + - - -
302A ILE* 3.7 26.1 - - + +
303A CYS 3.0 7.2 - - - +
304A SER* 3.3 27.7 + - - -
305A TRP* 3.5 5.0 - - - -
334A PHE* 5.0 5.9 - - - -
344A THR* 4.8 13.7 + - - +
345A TYR* 1.3 81.2 - - - +
347A LEU* 1.3 63.9 + - - +
348A GLY 4.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 3.6 4.9 - - - -
303A CYS* 3.1 28.7 + - - +
305A TRP* 3.8 13.7 - - + -
321A TYR 4.3 2.5 - - - +
323A LEU* 3.7 27.1 - - + +
332A ALA* 3.5 34.8 - - + +
333A VAL* 3.5 32.1 - - - +
334A PHE* 4.0 17.9 - - + +
346A ARG* 1.3 76.3 - - - +
348A GLY* 1.3 67.0 + - - +
349A VAL* 3.2 14.8 + - + +
362A LEU* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 4.4 17.2 - - - +
301A ILE 4.0 4.7 - - - -
302A ILE* 4.4 7.9 - - - -
332A ALA* 4.3 11.8 - - - +
346A ARG 4.2 1.0 + - - -
347A LEU* 1.3 76.6 - - - +
349A VAL* 1.3 60.7 + - - -
350A GLN* 4.1 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.1 6.3 - - - +
301A ILE* 2.8 42.5 + - + +
303A CYS* 5.3 0.9 - - - -
323A LEU* 3.4 38.8 - - + +
325A GLU* 4.9 3.8 - - + +
330A LYS* 4.7 15.5 - - + +
331A SER* 4.8 7.9 - - - -
332A ALA* 4.4 14.1 - - + +
347A LEU 3.6 11.9 - - - +
348A GLY* 1.3 74.0 - - - -
350A GLN* 1.3 75.3 + - - +
360A PHE* 4.4 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LYS* 4.3 19.3 + - - +
300A GLU* 4.1 17.1 - - - +
301A ILE* 4.8 1.0 - - - +
325A GLU* 5.7 0.7 - - - +
328A SER* 4.7 2.1 + - - -
330A LYS* 4.1 18.0 - - + +
348A GLY 4.1 1.2 + - - -
349A VAL* 1.3 92.5 - - - +
351A MET* 1.3 68.5 + - - +
358A HIS* 5.5 0.3 + - - -
----------------------------------------------------------
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