Contacts of the helix formed by residues 245 - 254 (chain B) in PDB entry 3GUU
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 HIS 245 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.7 20.4 - - + +
153B TYR* 5.4 1.8 - + - -
241B LEU* 3.0 29.8 + - + +
242B SER 3.1 7.7 + - - +
244B ALA* 1.3 86.0 + - + +
246B PRO* 1.3 62.4 - - - +
247B ASP 3.3 2.7 - - - -
248B MET* 3.1 12.0 + - + +
249B GLU 2.9 23.7 + - - -
304B ILE* 3.4 33.8 - - + +
307B GLN* 4.0 13.0 - - - -
308B GLU* 2.8 31.4 + - + -
443B SO4 2.7 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN* 3.3 32.8 - - + +
242B SER 4.4 1.3 - - - +
243B LEU 5.7 1.8 - - - +
244B ALA 3.7 1.6 - - - +
245B HIS* 1.3 85.1 - - - +
247B ASP* 1.3 62.1 + - - +
249B GLU* 3.3 10.5 + - + +
250B SER* 3.1 30.5 + - - -
443B SO4 3.1 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 1.3 78.7 - - - +
248B MET* 1.3 63.5 + - - +
250B SER* 4.1 7.0 + - - +
251B PHE* 3.0 24.3 + - - +
300B PRO* 3.7 14.0 - - + +
443B SO4 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.0 4.7 - - - +
241B LEU* 3.8 32.5 - - + +
242B SER* 3.5 23.3 - - - +
245B HIS* 3.1 13.4 + - + +
247B ASP* 1.3 74.2 - - - +
249B GLU* 1.3 67.0 + - - +
251B PHE* 3.2 2.6 + - - +
252B ILE* 2.9 40.3 + - + +
300B PRO* 4.0 11.3 - - + +
301B ILE* 4.0 18.6 - - + -
304B ILE* 4.3 26.7 - - + -
305B LEU* 5.8 0.9 - - + -
442B 1PE 4.2 23.1 - - - +
443B SO4 2.9 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 3.0 33.4 - - - +
243B LEU* 3.8 3.4 + - - +
245B HIS 2.9 6.4 + - - +
246B PRO* 3.3 13.9 - - + +
248B MET* 1.3 76.2 - - - +
250B SER* 1.3 60.2 + - - +
252B ILE* 3.2 2.5 + - - +
253B GLU* 2.7 67.0 + - + +
264B LEU* 4.1 2.6 - - - +
268B ARG* 2.8 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO 3.1 17.1 + - - -
247B ASP* 4.1 7.7 + - - -
249B GLU* 1.3 74.2 - - - +
251B PHE* 1.3 68.6 + - - +
253B GLU* 3.4 6.4 + - - +
254B ALA* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASP 3.0 19.0 + - - +
248B MET* 3.5 4.7 - - - +
250B SER* 1.3 79.4 - - - +
252B ILE* 1.3 63.6 + - - +
254B ALA* 3.7 3.6 + - - -
255B ARG* 3.0 62.0 + - - +
295B LEU* 3.5 21.5 - - + -
298B GLU* 3.0 34.3 - - + -
299B ALA 3.4 20.4 - - - -
300B PRO* 3.6 22.0 - - + -
301B ILE* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.0 19.7 - - + -
242B SER* 3.4 24.5 - - - +
248B MET* 2.9 40.0 + - + +
249B GLU 3.8 2.9 - - - +
251B PHE* 1.3 72.3 - - - +
253B GLU* 1.3 61.7 + - + +
255B ARG* 2.8 23.4 + - - +
256B LEU* 3.0 35.3 + - + -
264B LEU* 5.3 7.6 - - + -
290B VAL* 4.5 6.7 - - + -
295B LEU* 4.0 11.7 - - + -
301B ILE* 3.7 23.1 - - + -
442B 1PE 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 2.7 64.9 + - + +
250B SER* 3.4 6.7 + - - +
252B ILE* 1.3 72.0 - - + +
254B ALA* 1.3 61.3 + - - +
255B ARG 3.1 0.9 + - - -
256B LEU* 3.4 41.1 + - + +
261B GLN* 4.9 7.3 + - - +
264B LEU* 3.6 9.5 - - + +
265B LYS* 4.8 7.3 + - - -
268B ARG* 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B SER 3.1 16.2 + - - +
251B PHE* 3.8 6.7 - - - +
253B GLU* 1.3 75.7 - - - +
255B ARG* 1.3 72.9 + - - +
256B LEU 4.8 2.2 - - - +
291B ASN* 5.1 2.8 + - - -
----------------------------------------------------------
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