Contacts of the helix formed by residues 221 - 232 (chain C) in PDB entry 3GGS
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C ARG* 3.4 15.0 + - - +
113C VAL* 3.8 31.2 - - + -
114C THR 4.3 0.9 + - - -
115C ASN* 2.8 29.7 + - - +
132C ILE* 4.5 7.9 - - + -
166C TYR* 4.7 3.1 - - - +
192C TYR* 4.2 5.6 - - + -
220C SER* 1.3 91.0 + - - +
222C VAL* 1.3 65.8 + - - +
223C PRO 3.3 1.8 - - - -
224C GLU* 3.1 23.9 + - - +
225C VAL* 3.0 26.5 + - + +
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Residues in contact with VAL 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C HIS* 3.6 42.6 - - + +
136C ILE 4.7 0.9 - - - +
137C ASN* 3.6 35.9 - - + -
166C TYR* 4.8 1.3 - - - +
192C TYR* 3.8 13.7 - - + -
194C MET* 3.6 27.1 - - + +
220C SER 2.7 9.3 + - - -
221C THR* 1.3 70.3 - - + +
223C PRO* 1.3 70.7 - - + +
225C VAL* 3.1 8.0 + - - +
226C ILE* 2.9 26.5 + - + +
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Residues in contact with PRO 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 3.6 32.5 - - + -
96C VAL* 4.1 5.2 - - + -
97C THR* 3.4 17.7 - - + -
137C ASN* 5.4 2.7 - - - +
146C PRO* 3.6 15.9 - - + +
194C MET* 3.5 24.9 - - + -
220C SER* 3.9 3.8 - - - +
221C THR 3.5 3.1 - - - -
222C VAL* 1.3 97.6 - - + +
224C GLU* 1.3 67.2 + - - +
226C ILE* 3.6 1.5 + - + -
227C VAL* 3.1 28.9 + - - +
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Residues in contact with GLU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.8 26.3 - - + +
81C MET* 5.9 1.0 - - - +
84C ARG* 3.2 31.7 + - - +
85C PHE 4.5 5.4 + - - +
96C VAL* 4.1 24.2 - - - +
97C THR* 4.2 4.5 - - + -
100C VAL* 3.9 22.7 - - + +
111C LEU* 4.6 1.3 - - + -
113C VAL* 4.6 8.1 - - + -
220C SER* 4.9 0.3 - - - -
221C THR* 3.1 29.7 + - - +
223C PRO* 1.3 77.9 - - - +
225C VAL* 1.3 67.0 + - - +
227C VAL* 3.4 1.0 + - - +
228C ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 5.1 1.1 - - - -
113C VAL* 4.2 7.6 - - + -
135C HIS* 3.9 13.0 - - + -
162C MET* 5.4 0.2 - - - -
165C ALA* 3.9 16.6 - - + -
166C TYR* 3.3 45.1 - - + +
221C THR* 3.0 27.7 + - + +
222C VAL 3.1 6.0 + - - +
224C GLU* 1.3 75.1 - - - +
226C ILE* 1.3 59.3 + - - +
228C ALA* 3.4 5.9 + - - +
229C ARG* 2.9 34.1 + - + +
235C VAL* 3.8 16.6 - - + -
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Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A SER* 4.5 9.9 - - - +
135C HIS* 4.3 11.0 - - - +
137C ASN* 3.3 30.7 - - + +
145C ASN* 4.4 11.9 - - - +
146C PRO* 4.3 15.3 - - + -
147C LEU* 3.3 29.6 - - + -
162C MET* 3.4 29.3 - - + +
222C VAL* 2.9 28.5 + - + +
223C PRO 3.8 4.5 - - - +
225C VAL* 1.3 75.9 - - - +
227C VAL* 1.3 57.6 + - - +
229C ARG 3.4 0.2 + - - -
230C HIS* 2.9 23.9 + - - +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C THR* 3.4 33.9 - - + +
100C VAL* 3.1 33.9 - - + -
101C ARG* 4.3 18.8 - - + +
146C PRO* 3.6 15.9 - - + -
147C LEU* 4.0 13.7 - - + -
223C PRO 3.1 18.0 + - - +
224C GLU 4.0 2.0 - - - +
226C ILE* 1.3 71.5 - - - +
228C ALA* 1.3 66.1 + - - +
230C HIS* 3.2 10.8 + - - +
231C CYS* 2.9 25.5 + - - -
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C VAL* 3.5 17.5 - - + -
111C LEU* 3.9 12.3 - - + -
224C GLU 3.0 17.9 + - - +
225C VAL 3.6 4.9 - - - +
227C VAL* 1.3 78.3 - - - +
229C ARG* 1.3 56.1 + - - +
231C CYS* 3.1 5.6 + - - +
232C GLY 3.1 7.3 + - - -
233C LEU* 2.9 37.9 + - + -
235C VAL* 3.9 19.7 - - + -
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Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PRO* 5.5 0.7 - - - +
161C ALA 4.8 5.5 + - - +
162C MET* 3.8 17.3 - - + -
164C ASP* 3.6 30.4 + - - -
165C ALA* 3.4 43.7 + - + +
225C VAL* 2.9 21.2 + - + +
226C ILE 3.8 3.6 - - - +
228C ALA* 1.3 71.6 - - - +
230C HIS* 1.3 67.0 + - - +
231C CYS 3.1 1.3 - - - -
232C GLY* 2.9 16.8 + - - +
233C LEU 3.0 24.8 + - - -
234C ARG* 4.3 3.2 - - - +
235C VAL* 3.8 8.0 - - + +
294C SO4 3.3 44.2 + - - -
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Residues in contact with HIS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.3 28.1 + - - -
147C LEU* 4.2 17.6 - - + +
151C ASN* 2.9 18.7 + - - -
152C ASP 4.2 1.3 - - - -
155C PHE* 3.1 24.3 - + + +
156C GLY* 3.2 35.1 + - - -
157C ASP 2.7 38.9 + - - -
160C PRO* 3.9 23.3 - - + -
162C MET* 4.1 1.4 - - - +
226C ILE 2.9 15.3 + - - +
227C VAL* 3.3 13.2 + - - +
229C ARG* 1.3 76.5 - - - +
231C CYS* 1.3 58.2 + - - +
232C GLY 3.7 0.2 + - - -
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Residues in contact with CYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C VAL 4.8 2.2 - - - -
101C ARG* 4.3 18.2 - - - -
104C HIS* 3.6 42.5 + - - +
155C PHE* 3.7 31.1 - - - +
227C VAL 2.9 15.4 + - - +
228C ALA* 3.2 12.6 - - - +
229C ARG 3.1 0.2 - - - -
230C HIS* 1.3 78.1 - - - +
232C GLY* 1.3 57.3 + - - +
233C LEU* 3.7 15.4 + - + -
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Residues in contact with GLY 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASP* 4.6 2.3 - - - +
229C ARG* 2.9 18.8 + - - -
230C HIS 3.4 0.6 + - - -
231C CYS* 1.3 77.6 - - - +
233C LEU* 1.3 66.8 + - - +
234C ARG 3.7 1.2 + - - -
294C SO4 4.3 18.6 + - - -
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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