Contacts of the helix formed by residues 221 - 232 (chain B) in PDB entry 3GB9
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 THR 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.4 13.8 + - - +
113B VAL* 3.4 36.1 - - + -
115B ASN* 2.8 31.6 + - - +
132B ILE* 4.6 6.7 - - + -
166B TYR* 4.9 2.9 - - - +
192B TYR* 4.2 5.8 - - + -
220B SER* 1.3 85.0 + - - +
222B VAL* 1.3 64.2 + - - +
223B PRO* 3.9 0.4 - - - +
224B GLU* 3.0 30.2 + - - +
225B VAL* 3.0 28.7 + - + +
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B HIS* 3.8 35.9 - - + +
136B ILE 4.7 1.1 - - - +
137B ASN* 3.4 43.3 - - + +
166B TYR* 4.9 1.3 - - - +
192B TYR* 3.8 15.7 - - + -
194B MET* 3.8 25.1 - - + +
220B SER 2.9 7.9 + - - -
221B THR* 1.3 70.9 - - - +
223B PRO* 1.3 70.7 - - + +
225B VAL* 3.2 8.7 + - - +
226B ILE* 3.0 28.6 + - + +
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Residues in contact with PRO 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.6 31.6 - - + -
96B VAL* 4.5 4.9 - - + -
97B THR* 3.5 18.6 - - + -
137B ASN* 5.7 1.1 - - - +
146B PRO* 3.6 17.3 - - + +
194B MET* 3.7 23.3 - - + -
220B SER* 4.1 1.3 - - - -
221B THR 3.5 7.0 - - - +
222B VAL* 1.3 96.9 - - + +
224B GLU* 1.3 69.1 + - - +
226B ILE* 3.5 1.3 + - + -
227B VAL* 3.1 28.6 + - - +
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Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.9 24.3 - - + +
81B MET* 5.9 1.0 - - - +
84B ARG* 3.2 34.1 + - - +
85B PHE 4.6 1.0 + - - +
96B VAL* 4.2 25.1 - - - +
97B THR* 4.1 11.9 - - + -
100B VAL* 4.0 20.6 - - + +
111B LEU* 4.4 5.8 - - + -
113B VAL* 4.8 2.7 - - + -
220B SER* 4.8 0.6 - - - -
221B THR* 3.0 33.7 + - - +
223B PRO* 1.3 86.3 - - - +
225B VAL* 1.3 57.2 + - - +
227B VAL* 3.4 2.8 + - - +
228B ALA* 2.9 30.2 + - - +
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.8 2.2 - - - -
113B VAL* 4.3 6.5 - - + -
135B HIS* 4.0 12.6 - - + -
162B MET* 5.4 0.2 - - - -
165B ALA* 4.4 7.6 - - + -
166B TYR* 3.4 36.3 - - + +
221B THR* 3.0 33.1 + - + +
222B VAL* 3.6 6.3 - - - +
224B GLU* 1.3 75.5 - - - +
226B ILE* 1.3 58.9 + - - +
228B ALA* 3.1 6.6 + - - +
229B ARG* 2.9 39.1 + - + +
235B VAL* 4.1 22.7 - - + -
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Residues in contact with ILE 226 (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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135B HIS* 4.3 12.6 - - + +
137B ASN* 3.2 31.9 - - + +
145B ASN* 4.2 8.5 - - - +
146B PRO* 4.3 11.0 - - + -
147B LEU* 3.6 30.5 - - + -
162B MET* 3.6 29.4 - - + +
222B VAL* 3.0 25.7 + - + +
223B PRO* 3.7 3.6 - - + +
225B VAL* 1.3 77.2 - - - +
227B VAL* 1.3 66.0 + - - +
229B ARG 3.5 0.2 + - - -
230B HIS* 3.0 22.2 + - - +
199C SER* 4.3 13.5 - - - +
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Residues in contact with VAL 227 (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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97B THR* 3.5 29.4 - - - +
100B VAL* 3.8 20.6 - - + -
101B ARG* 3.8 34.5 - - + +
146B PRO* 3.7 18.6 - - + +
147B LEU* 3.9 10.5 - - + -
223B PRO 3.1 21.1 + - - +
224B GLU 3.9 3.8 - - - +
225B VAL 3.3 0.2 - - - -
226B ILE* 1.3 75.1 - - - +
228B ALA* 1.3 63.5 + - - +
230B HIS* 3.4 8.4 + - - +
231B CYS* 3.2 21.0 + - - +
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Residues in contact with ALA 228 (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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100B VAL* 3.7 13.7 - - + +
111B LEU* 3.7 22.7 - - + -
224B GLU 2.9 18.5 + - - +
225B VAL 3.1 5.6 + - - +
227B VAL* 1.3 77.6 - - - +
229B ARG* 1.3 60.1 + - - +
231B CYS* 3.1 11.6 + - - +
232B GLY 3.1 0.2 + - - -
233B LEU* 3.0 35.2 + - + +
235B VAL* 3.8 13.5 - - + -
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Residues in contact with ARG 229 (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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160B PRO* 5.1 3.1 - - - +
161B ALA 4.9 4.9 + - - +
162B MET* 3.7 27.1 - - + -
164B ASP* 3.3 31.3 + - - -
165B ALA* 3.5 39.2 + - + +
167B ASP* 5.9 0.4 + - - -
225B VAL* 2.9 19.7 + - + +
228B ALA* 1.3 73.2 - - - +
230B HIS* 1.3 66.4 + - - +
232B GLY* 3.1 16.6 + - - +
233B LEU 2.8 34.4 + - - -
234B ARG* 4.2 3.8 - - - +
235B VAL* 3.8 7.2 - - + -
291B SO4 3.1 47.0 + - - -
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.1 28.4 + - - -
147B LEU* 4.1 19.9 - - + +
151B ASN* 2.8 18.9 + - - -
152B ASP 4.1 2.9 - - - -
155B PHE* 3.1 22.6 - - + +
156B GLY* 3.3 29.3 - - - -
157B ASP 2.7 33.3 + - - -
160B PRO* 3.9 23.3 - - + -
162B MET* 4.4 1.2 - - - +
226B ILE 3.0 14.7 + - - +
227B VAL* 3.4 11.7 - - - +
229B ARG* 1.3 77.5 - - - +
231B CYS* 1.3 58.4 + - - +
232B GLY 3.5 0.3 + - - -
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Residues in contact with CYS 231 (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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100B VAL* 4.8 2.0 - - - -
101B ARG* 3.9 18.2 - - - -
104B HIS* 3.7 45.9 + - + -
155B PHE* 3.6 31.8 - - - +
227B VAL* 3.2 13.2 + - - +
228B ALA* 3.1 14.2 + - - +
230B HIS* 1.3 79.3 - - - +
232B GLY* 1.3 56.7 + - - +
233B LEU* 3.5 15.4 - - + +
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Residues in contact with GLY 232 (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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109B ASP* 4.8 1.0 - - - +
229B ARG* 3.1 22.3 + - - -
230B HIS 3.3 1.0 + - - -
231B CYS* 1.3 77.3 - - - +
233B LEU* 1.3 66.3 + - - +
234B ARG 3.7 1.2 + - - -
291B SO4 4.5 12.0 + - - -
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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