Contacts of the helix formed by residues 331 - 337 (chain I) in PDB entry 3EXG
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 PRO 331 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I LYS* 4.7 16.2 - - + -
329I GLU 3.4 4.2 - - - +
330I PRO* 1.3 87.8 - - + +
332I LEU* 1.3 67.8 + - - +
333I GLU* 3.2 19.7 - - + +
334I GLU* 3.1 48.9 + - + +
308L LEU* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I PRO 3.5 2.8 + - - -
331I PRO* 1.3 72.0 - - - +
333I GLU* 1.3 60.1 + - + +
334I GLU 3.0 0.2 - - - -
335I LEU* 2.9 29.0 + - + +
357I PHE* 3.8 18.9 - - + -
307L ILE* 4.6 17.7 - - + +
308L LEU* 3.9 18.2 - - + -
311L ASN* 3.3 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I PRO* 3.9 19.4 - - + +
332I LEU* 1.3 81.2 + - - +
334I GLU* 1.3 69.3 + - + +
335I LEU 3.2 3.5 + - - -
336I GLY 4.3 1.0 + - - -
337I TYR* 4.1 14.3 + - - +
357I PHE* 4.4 11.8 - - - -
358I LYS* 4.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I LYS* 4.5 17.3 - - - +
120I LYS* 3.5 14.1 + - - +
330I PRO* 5.8 1.8 - - + -
331I PRO* 3.1 38.5 + - + +
332I LEU 3.0 1.8 + - - -
333I GLU* 1.3 84.7 - - + +
335I LEU* 1.3 63.8 + - - +
336I GLY 3.1 3.7 + - - -
337I TYR* 3.2 57.0 + - + +
338I HIS* 5.1 1.6 + - - -
308L LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I LYS* 3.9 1.0 + - - -
331I PRO 4.3 0.4 + - - -
332I LEU 2.9 16.1 + - - +
333I GLU 3.2 1.6 - - - -
334I GLU* 1.3 77.9 - - - +
336I GLY* 1.3 61.2 + - - +
337I TYR 3.5 0.9 + - - -
348I VAL* 5.6 0.7 - - + -
357I PHE* 3.7 24.2 - - + -
102J TYR* 2.8 24.3 + - - +
298L ALA* 4.9 4.5 - - + -
300L VAL* 3.7 33.0 - - + -
308L LEU* 3.5 36.8 - - + +
311L ASN* 3.8 25.8 - - + +
312L SER* 3.5 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I GLU 4.3 1.2 + - - -
334I GLU 3.1 1.0 - - - -
335I LEU* 1.3 84.3 - - - +
337I TYR* 1.3 61.2 + - - +
339I ILE* 3.2 17.6 - - - +
348I VAL* 5.1 2.0 - - - -
357I PHE* 4.5 9.9 - - - +
358I LYS 3.6 22.5 + - - -
359I SER* 3.0 24.9 + - - -
102J TYR* 4.7 0.2 - - - -
300L VAL* 4.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 337 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I LYS* 3.2 16.2 + - - +
333I GLU* 4.1 8.9 + - - +
334I GLU* 3.2 60.1 + - + +
335I LEU 3.4 1.0 - - - -
336I GLY* 1.3 78.0 - - - +
338I HIS* 1.3 92.1 + + + +
358I LYS* 3.6 31.6 - - + +
360I VAL* 3.3 41.1 - - + +
102J TYR* 3.7 6.1 - - - -
----------------------------------------------------------
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