Contacts of the strand formed by residues 293 - 300 (chain A) in PDB entry 6GE3
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 PHE 293 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 4.7 1.6 - - + -
281A LEU* 4.2 9.9 - - + -
284A LEU* 3.2 35.4 - - + -
285A PHE* 3.5 40.4 - + + -
288A GLY* 4.2 8.1 - - - -
289A PRO 3.2 25.4 - - - -
290A SER 3.5 12.0 + - - +
291A ASN 3.4 2.4 - - - -
292A ALA* 1.3 84.4 - - + +
294A PHE* 1.3 71.2 + - - +
407A THR* 4.1 10.1 - - + -
410A CYS* 3.5 35.7 - - + -
430A ARG* 3.9 2.3 - - - +
431A LEU* 3.1 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER 3.3 22.0 - - - -
219A VAL* 4.1 15.5 - - + -
220A ALA 3.5 30.3 - - - -
262A LEU* 3.7 19.5 - - + -
291A ASN 3.7 20.4 - - - -
292A ALA 3.5 15.3 - - - -
293A PHE* 1.3 80.0 - - - +
295A LEU* 1.3 60.7 + - - +
409A LEU* 3.9 9.0 - - + -
410A CYS 2.9 9.5 + - - +
411A ILE* 3.4 15.6 - - + -
412A ALA 2.9 23.6 + - - -
428A ILE* 4.3 12.1 - - + -
429A TYR 3.3 17.5 - - - +
430A ARG* 4.3 8.5 - - + -
431A LEU* 3.4 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 3.7 33.2 - - + -
270A ILE* 4.1 16.6 - - + -
294A PHE* 1.3 74.8 - - - +
296A VAL* 1.3 65.0 + - - +
412A ALA* 3.3 25.8 - - + +
414A VAL* 3.8 27.8 - - + -
428A ILE* 3.7 0.5 - - - -
429A TYR* 2.8 46.8 + - + -
431A LEU* 3.8 18.1 - - + +
95L PHE* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 4.8 4.0 - - + -
226A MET* 5.9 0.2 - - + -
250A ILE* 4.1 11.9 - - + -
294A PHE* 5.3 0.4 - - + -
295A LEU* 1.3 78.8 - - - +
297A LYS* 1.3 61.9 + - - +
298A PHE* 3.8 40.8 + - + -
411A ILE* 3.7 21.3 - - + -
412A ALA 2.8 9.7 + - - +
413A TYR* 3.4 17.2 - - + +
414A VAL* 3.0 27.0 + - - +
426A HIS* 4.4 3.4 - - + -
427A HIS 3.5 7.9 - - - +
428A ILE* 4.2 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU 4.1 1.0 + - - -
296A VAL* 1.3 72.6 - - - +
298A PHE* 1.3 63.5 + - - +
299A TRP* 3.7 25.5 - - + -
414A VAL* 3.6 15.9 - - + +
415A PHE 4.2 1.1 - - - -
416A GLU* 2.7 56.5 + - - +
426A HIS* 3.1 6.8 - - - +
427A HIS* 2.9 33.7 + - + +
429A TYR* 4.2 11.6 - - + -
95L PHE* 2.9 59.6 + - + +
96L PHE* 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 4.0 15.5 - + - -
248A VAL* 3.5 40.4 - - + -
249A HIS 4.1 7.9 - - - -
250A ILE* 3.7 37.7 - - + -
296A VAL* 3.8 4.9 + - + -
297A LYS* 1.3 76.3 - - - +
299A TRP* 1.3 60.6 + - - +
413A TYR* 3.4 31.4 - + + -
414A VAL 2.9 7.1 + - - -
415A PHE* 3.5 38.4 - + + -
416A GLU 2.9 26.7 + - - +
424A ALA* 6.3 0.2 - - + -
425A GLN 3.6 5.2 - - - -
426A HIS* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 4.7 0.9 - - - +
297A LYS* 3.7 27.6 - - + -
298A PHE* 1.3 73.8 - - - +
300A ALA* 1.3 60.1 + - - +
416A GLU* 3.3 30.1 + - + -
417A VAL 3.6 18.6 - - - -
418A SER* 4.0 16.8 - - - +
419A ALA 5.4 0.7 - - - -
424A ALA* 3.2 11.1 - - - +
425A GLN* 2.9 46.1 + - + +
426A HIS 4.1 1.3 - - - -
427A HIS* 3.4 38.1 - + - -
94L SER 3.8 1.1 - - - -
95L PHE 3.3 28.3 - - - -
96L PHE 4.1 4.2 + - - -
98L PRO* 3.6 50.1 - - + +
99L PRO* 4.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE 3.4 11.0 - - - +
248A VAL* 3.9 14.6 - - + -
298A PHE 3.8 0.8 - - - -
299A TRP* 1.3 71.9 - - - +
301A ASP* 1.3 60.9 + - - +
302A LEU* 3.6 13.5 + - + +
415A PHE* 4.8 4.0 - - + -
416A GLU 2.8 16.9 + - - +
417A VAL* 3.7 5.9 - - + +
418A SER* 2.7 25.8 + - - -
501A MYR 4.1 29.4 - - + -
----------------------------------------------------------
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