Contacts of the helix formed by residues 328 - 333 (chain A) in PDB entry 3N4E
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 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 5.8 6.5 - - - +
150A ARG* 5.1 1.0 - - - +
326A ALA 3.8 0.4 + - - -
327A ASP* 1.3 80.8 - - + +
329A TRP* 1.3 66.9 + - - +
330A ASP* 3.1 37.9 + - - +
331A ARG* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG* 4.0 5.7 - - - +
153A ALA* 5.4 7.6 - - + -
154A GLU* 3.1 36.8 + - + -
302A PRO* 3.5 26.4 - - + +
325A LEU* 3.7 32.3 - - + +
326A ALA 3.4 18.8 - - - +
327A ASP 3.2 3.7 + - - -
328A ARG* 1.3 74.7 - - - +
330A ASP* 1.3 72.8 + - + +
331A ARG* 3.0 7.7 + - - +
332A GLY* 3.1 12.7 + - - -
339A PRO* 5.4 1.4 - - - +
340A ALA 3.4 18.8 - - - +
341A GLU* 3.3 40.4 - - + -
342A PRO* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 5.1 0.2 - - - -
328A ARG* 3.2 51.2 + - - -
329A TRP* 1.3 93.9 - - + +
331A ARG* 1.3 58.0 + - - +
332A GLY 3.1 6.0 + - - -
333A ARG* 3.3 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MSE 3.6 25.5 - - + +
16A GLY* 3.3 32.3 + - - +
23A PRO* 4.9 18.2 - - + +
25A SER* 4.8 7.3 + - - -
300A THR* 3.1 20.4 + - - -
301A GLN* 2.8 32.9 + - - +
302A PRO* 3.7 19.4 - - + +
327A ASP 3.3 17.0 + - - -
328A ARG* 3.0 36.0 + - + +
329A TRP* 3.0 2.8 + - - +
330A ASP* 1.3 78.5 - - - +
332A GLY* 1.3 63.7 + - - +
333A ARG 3.2 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A MSE 4.2 7.6 - - - -
302A PRO* 4.0 11.2 - - - +
329A TRP 3.1 9.3 + - - -
330A ASP 3.1 2.8 - - - -
331A ARG* 1.3 78.8 - - - +
333A ARG* 1.3 57.5 + - - +
335A VAL* 3.6 2.8 + - - +
336A PHE* 3.0 34.7 + - - +
339A PRO* 3.8 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 3.3 12.1 - - - -
330A ASP* 3.3 15.4 + - - +
331A ARG 3.2 13.9 - - - +
332A GLY* 1.3 77.4 - - - +
334A PRO* 1.4 67.4 - - + +
335A VAL 3.6 0.7 - - - -
336A PHE 3.9 6.3 + - - +
337A ARG* 3.7 31.5 + - - +
338A ASN* 5.1 0.8 - - - +
339A PRO* 3.8 23.5 - - + +
341A GLU* 4.9 17.3 - - - +
----------------------------------------------------------
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