Contacts of the helix formed by residues 331 - 337 (chain G) in PDB entry 3EXF
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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F LEU* 4.2 2.4 - - - +
113G LYS* 3.5 27.8 - - + +
329G GLU 3.4 5.0 - - - +
330G PRO* 1.3 86.6 - - + +
332G LEU* 1.3 64.5 + - - +
333G GLU* 3.1 23.3 - - + +
334G GLU* 3.0 42.8 + - + +
335G LEU 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ILE* 4.5 18.1 - - + +
308F LEU* 4.1 12.1 - - + -
311F ASN* 3.3 48.0 - - + +
330G PRO 3.4 2.7 + - - -
331G PRO* 1.3 71.9 - - - +
333G GLU* 1.3 69.8 + - + +
334G GLU 3.1 0.2 - - - -
335G LEU* 3.1 30.4 + - + +
357G PHE* 3.7 16.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G PRO* 3.2 19.9 - - + +
332G LEU* 1.3 94.1 + - + +
334G GLU* 1.3 57.3 + - + +
335G LEU 3.2 3.8 + - - -
336G GLY 4.0 0.9 + - - -
337G TYR* 3.2 20.7 + - - +
357G PHE* 4.7 11.1 - - - +
358G LYS* 3.9 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F LEU* 4.9 1.8 - - - -
113G LYS* 4.4 2.6 + - - -
118G LYS* 4.0 30.1 + - - +
120G LYS* 3.5 18.8 + - - -
330G PRO* 5.4 4.9 - - + -
331G PRO* 3.0 37.1 + - + +
333G GLU* 1.3 74.8 - - + +
335G LEU* 1.3 63.6 + - - +
336G GLY 3.1 2.7 - - - -
337G TYR* 3.3 52.2 + - + +
338G HIS* 4.4 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F ALA* 4.7 3.4 - - + -
300F VAL* 3.9 31.1 - - + +
303F PRO* 4.5 6.5 - - + -
308F LEU* 3.5 28.0 - - + +
311F ASN* 4.0 11.4 - - + +
312F SER* 3.4 20.0 - - - +
120G LYS* 4.7 3.6 - - - +
331G PRO 4.2 0.6 + - - -
332G LEU* 3.1 36.3 + - + +
333G GLU 3.2 0.6 - - - -
334G GLU* 1.3 78.3 - - - +
336G GLY* 1.3 62.8 + - - +
337G TYR 3.3 0.7 + - - -
348G VAL* 5.9 0.4 - - + -
357G PHE* 4.1 24.7 - - + -
102H TYR* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F VAL* 4.7 3.1 - - - -
333G GLU 4.0 1.4 + - - -
334G GLU 3.1 1.6 - - - -
335G LEU* 1.3 81.1 - - - +
337G TYR* 1.3 59.1 + - - +
339G ILE* 3.0 21.3 - - - +
348G VAL* 4.4 9.6 - - - -
357G PHE* 4.3 7.0 - - - +
358G LYS 3.4 20.0 + - - -
359G SER* 2.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G LYS* 3.4 14.9 + - - +
333G GLU* 3.2 24.7 + - - +
334G GLU* 3.3 55.6 + - + +
335G LEU 3.3 1.0 - - - -
336G GLY* 1.3 79.6 - - - +
338G HIS* 1.3 96.4 + + + +
358G LYS* 3.6 32.2 - - + +
360G VAL* 3.7 34.4 - - + +
102H TYR* 3.6 6.9 - - - -
----------------------------------------------------------
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