Contacts of the strand formed by residues 243 - 248 (chain A) in PDB entry 2GB0
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 GLY 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.8 14.1 - - - -
87A THR* 3.5 8.1 + - - -
88A GLY 3.0 15.5 + - - -
89A VAL* 3.3 3.9 - - - -
90A LEU 2.9 21.9 + - - -
146A VAL* 4.7 0.7 - - - -
242A PRO* 1.3 77.7 - - - +
244A PHE* 1.3 61.1 + - - +
255A GLY 3.4 11.7 - - - -
257A PRO* 3.9 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.9 7.5 - - - +
89A VAL* 4.2 4.5 - - - -
90A LEU* 3.2 24.7 - - + +
241A PHE* 4.1 11.7 - + - -
242A PRO* 3.6 14.1 - - + +
243A GLY* 1.3 75.5 - - - +
245A MET* 1.3 62.5 + - - +
246A VAL* 4.3 15.7 - - + -
253A TYR 4.6 0.9 - - - -
254A TYR* 3.1 10.1 - - - +
255A GLY* 2.8 64.2 + - - +
256A PHE* 3.8 3.4 - - - -
264A LEU* 4.1 9.2 - - + -
265A LYS 4.5 0.7 - - - -
266A LEU* 3.6 23.6 - - + -
297A PHE* 4.1 6.7 - + - -
302A MET* 3.5 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.7 5.6 - - + -
52A ARG* 3.9 26.5 - - - +
57A GLU* 5.7 1.3 - - - +
89A VAL* 4.5 1.9 - - + +
90A LEU 3.0 6.1 + - - -
91A VAL* 3.3 25.6 - - + +
100A PHE* 3.4 43.9 - - + -
244A PHE* 1.3 75.3 - - - +
246A VAL* 1.3 61.2 + - - +
252A ILE* 3.9 27.1 - - + -
253A TYR 3.2 6.5 - - - +
254A TYR* 4.2 11.7 - - + -
269A HIS* 4.1 22.2 - - + +
345A HIS* 6.2 3.1 - - + -
348A LYS* 6.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 4.0 4.3 - - - +
92A PHE* 3.4 55.2 - - + +
100A PHE* 4.8 3.4 - - - -
244A PHE* 4.3 10.3 - - + -
245A MET* 1.3 86.7 - - - +
247A GLU* 1.3 61.2 + - - +
248A VAL* 4.2 4.0 + - + -
251A GLY 3.8 0.3 - - - +
252A ILE* 3.1 8.3 - - - +
253A TYR* 2.7 43.7 + - + +
297A PHE* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE 3.0 9.0 + - - +
93A GLY* 3.2 22.9 - - - -
94A PRO* 3.3 7.2 - - + +
97A GLU 5.0 3.8 - - - +
98A SER* 2.5 46.6 + - - +
99A ALA 3.7 2.2 + - - -
100A PHE* 3.5 20.3 + - + +
136A TYR* 4.4 0.2 - - - -
246A VAL* 1.3 73.9 - - - +
248A VAL* 1.3 76.2 + - - +
251A GLY* 3.5 9.5 - - - +
252A ILE* 4.1 20.9 - - + +
249B PRO 5.1 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 4.6 1.6 - - + -
94A PRO* 4.7 3.6 - - - -
136A TYR* 4.0 8.3 - - + +
246A VAL* 4.6 5.8 - - + -
247A GLU* 1.3 88.6 - - - +
249A PRO* 1.3 79.3 - - + +
250A ASN* 3.0 29.2 - - - +
251A GLY 2.9 25.0 + - - +
253A TYR* 3.7 16.6 - - + -
297A PHE* 4.1 12.1 - - + -
301A TYR* 3.4 40.4 - - + +
----------------------------------------------------------
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