Contacts of the strand formed by residues 243 - 248 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 3.9 13.7 - - - -
87B THR* 3.6 7.7 + - - -
88B GLY 3.1 14.0 + - - -
89B VAL* 3.4 4.7 - - - -
90B LEU 2.8 22.2 + - - -
146B VAL* 4.9 0.4 - - - -
242B PRO* 1.3 80.0 - - - +
244B PHE* 1.3 61.4 + - - +
255B GLY 3.4 11.4 - - - -
257B PRO* 3.9 10.2 - - - +
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.9 6.8 - - - +
89B VAL* 4.2 4.3 - - - -
90B LEU* 3.2 23.1 - - + +
92B PHE* 5.7 0.2 - - + -
130B ILE* 6.3 0.4 - - + -
241B PHE* 4.1 10.8 - + - -
242B PRO* 3.6 14.1 - - + +
243B GLY* 1.3 75.5 - - - +
245B MET* 1.3 63.0 + - - +
246B VAL* 4.2 16.4 - - + -
253B TYR 4.5 1.3 - - - -
254B TYR* 3.1 10.8 - - - +
255B GLY* 2.9 65.4 + - - +
256B PHE* 3.8 3.1 - - - -
264B LEU* 4.3 7.6 - - + -
265B LYS 4.5 1.6 - - - -
266B LEU* 3.6 23.8 - - + -
297B PHE* 4.1 7.9 - + - -
302B MET* 3.6 44.0 - - + -
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 5.8 6.1 - - + -
52B ARG* 4.5 13.9 - - - -
57B GLU* 3.7 19.1 - - + +
89B VAL* 4.5 1.9 - - + +
90B LEU 3.1 5.3 + - - -
91B VAL* 3.3 29.0 - - + +
100B PHE* 3.5 45.0 - - + -
244B PHE* 1.3 75.1 - - - +
246B VAL* 1.3 63.5 + - - +
252B ILE* 3.7 30.3 - - + -
253B TYR 3.2 6.5 - - - +
254B TYR* 4.1 11.9 - - + +
269B HIS* 4.0 20.9 - - + +
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU 4.1 4.0 - - - +
92B PHE* 3.5 54.7 - - + +
100B PHE* 4.9 2.5 - - - -
244B PHE* 4.2 9.9 - - + -
245B MET* 1.3 86.9 - - - +
247B GLU* 1.3 60.7 + - - +
248B VAL* 4.6 3.8 - - + -
251B GLY 3.8 0.5 - - - +
252B ILE* 3.1 9.7 - - - +
253B TYR* 2.8 42.6 + - + +
297B PHE* 3.7 35.4 - - + -
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU 5.4 3.3 - - - +
249A PRO 5.6 2.1 - - - +
92B PHE 3.0 9.7 + - - +
93B GLY* 3.2 22.3 - - - -
94B PRO* 3.3 6.2 - - + +
97B GLU 5.0 3.4 - - - +
98B SER* 2.5 46.6 + - - +
99B ALA 3.9 1.4 + - - -
100B PHE* 3.5 19.8 + - + +
136B TYR* 4.3 0.5 - - - -
246B VAL* 1.3 74.1 - - - +
248B VAL* 1.3 77.1 + - - +
251B GLY* 3.5 8.7 - - - +
252B ILE* 4.1 18.9 - - + +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 4.6 1.8 - - + -
94B PRO* 4.8 4.0 - - - -
136B TYR* 4.0 8.5 - - + +
246B VAL* 4.6 6.7 - - + -
247B GLU* 1.3 86.4 - - - +
249B PRO* 1.3 79.4 - - + +
250B ASN* 3.0 29.2 - - - +
251B GLY 2.9 26.6 + - - +
253B TYR* 3.7 16.2 - - + -
297B PHE* 4.1 11.9 - - + -
301B TYR* 3.3 40.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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