Contacts of the strand formed by residues 290 - 296 (chain B) in PDB entry 6GHM
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 MET 290 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER 3.5 2.8 - - - +
285B VAL* 3.7 0.2 - - - -
286B ASP* 3.0 46.3 + - - +
288B THR* 3.2 9.5 - - - +
289B LEU* 1.3 76.2 - - - +
291B CYS* 1.3 61.5 + - - +
292B SER* 4.1 2.1 + - - -
923C LYS* 3.3 34.5 - - + +
924C PHE 3.5 32.5 - - - +
925C ASN* 3.6 13.0 - - + +
926C PRO* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 4.3 5.4 - - - -
243B LEU* 4.8 0.4 - - - -
283B MET* 3.9 20.9 - - + -
284B SER 3.3 4.7 - - - +
285B VAL* 3.9 26.5 - - - -
289B LEU 3.9 11.0 - - - -
290B MET* 1.3 77.0 - - - +
292B SER* 1.3 60.4 + - - +
293B PHE* 4.9 0.7 - - - -
922C VAL* 4.0 16.4 - - - -
923C LYS 2.6 12.0 + - - -
924C PHE* 3.4 26.9 - - + -
925C ASN* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 3.4 5.0 - - - +
284B SER* 2.8 44.9 + - - -
290B MET* 4.1 3.1 + - - -
291B CYS* 1.3 75.9 - - - +
293B PHE* 1.3 70.9 + - - +
294B GLN* 5.3 2.6 - - - +
925C ASN* 4.1 22.4 - - - -
928C ALA* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TYR* 3.5 58.1 - + + -
257B PHE* 3.6 30.3 - + - -
264B VAL* 3.9 7.6 - - + -
266B LEU* 3.7 18.2 - - + -
281B ALA* 5.1 1.1 - - + -
282B MET 3.5 3.6 - - - +
283B MET* 3.6 41.1 - - + -
291B CYS 4.9 0.2 - - - -
292B SER* 1.3 82.6 - - - +
294B GLN* 1.3 63.5 + - - +
295B ILE* 4.1 10.6 + - + +
924C PHE* 4.0 14.6 - + - -
928C ALA* 4.8 10.5 - - + +
957C ASP* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 2.8 35.3 + - - +
78B TYR* 3.3 54.5 + - + +
79B GLY* 4.0 2.4 - - - -
281B ALA* 3.3 3.6 - - - -
282B MET* 2.9 57.8 + - + +
284B SER* 3.1 15.4 + - - +
292B SER* 5.3 2.9 - - - +
293B PHE* 1.3 74.6 - - - +
295B ILE* 1.3 62.2 + - - +
296B LEU* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 3.2 24.3 + - - -
253B ASP 3.8 12.6 - - - +
255B TYR* 3.9 20.4 - - + -
279B ALA* 3.8 20.9 - - + -
280B GLY 3.4 6.5 - - - +
281B ALA* 3.8 23.1 - - + -
293B PHE* 4.1 8.9 + - + +
294B GLN* 1.3 74.6 - - - +
296B LEU* 1.3 67.0 + - - +
297B LYS* 4.0 8.6 + - + +
957C ASP* 3.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASP 3.5 26.0 - - - +
74B ARG* 3.9 33.7 - - + +
75B LEU* 3.6 38.6 - - + +
78B TYR* 4.0 17.9 - - + -
268B SER 4.4 11.0 - - - +
270B PRO* 4.0 7.2 - - + +
279B ALA* 3.4 5.5 - - - +
280B GLY* 2.6 39.7 + - - +
282B MET* 5.0 0.9 - - - -
294B GLN 4.8 3.6 - - - +
295B ILE* 1.3 77.7 - - - +
297B LYS* 1.3 64.9 + - - +
----------------------------------------------------------
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