Contacts of the helix formed by residues 132 - 143 (chain C) in PDB entry 1GSD
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 TYR 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C GLY* 3.4 29.4 - - - -
101C ASP* 3.8 15.6 + - - +
102C LEU* 3.8 39.7 - - + -
105C MET* 4.5 5.9 - - + +
127C LYS* 3.0 37.9 + - + +
128C ILE 4.5 0.9 - - - +
131C ARG* 1.3 102.5 + - + +
133C PHE* 1.3 68.4 + - + +
135C ALA* 3.0 13.5 + - - +
136C PHE* 3.0 29.7 + + + -
52D PHE* 3.4 36.6 - + + -
54D GLN* 4.0 7.8 + - - -
67D GLN* 5.3 0.2 - - - -
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Residues in contact with PHE 133 (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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102C LEU* 4.8 2.7 - - + -
128C ILE* 3.0 45.1 + - + +
132C TYR* 1.3 75.4 - - + +
134C PRO* 1.3 67.4 - - + +
136C PHE* 3.3 4.5 + + - -
137C GLU* 2.9 26.3 + - - +
160C LEU* 5.4 2.0 - - + -
163C LEU* 4.6 14.8 - - + -
164C LEU* 3.5 30.1 - - + -
167C VAL* 3.7 31.2 - - + -
174C LEU 4.1 2.5 - - - -
175C ILE* 4.1 17.9 - - + -
178C PHE* 3.6 36.8 - + + -
181C LEU* 3.7 17.6 - - + +
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Residues in contact with PRO 134 (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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128C ILE 3.4 4.3 - - - +
129C LYS 2.9 30.5 - - - +
130C ASN* 3.8 12.6 - - - +
131C ARG 3.7 10.3 - - - +
132C TYR 3.5 3.8 - - - -
133C PHE* 1.3 91.6 - - + +
135C ALA* 1.3 55.3 + - - +
137C GLU* 3.7 2.8 - - + +
138C LYS* 3.0 31.4 + - - +
178C PHE* 3.9 15.3 - - + -
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Residues in contact with ALA 135 (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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131C ARG 3.3 14.1 + - - +
132C TYR 3.0 9.6 + - - +
134C PRO* 1.3 80.6 - - - +
136C PHE* 1.3 61.2 + - - +
138C LYS* 3.5 8.0 + - - +
139C VAL* 3.3 25.8 + - - +
51D MET* 3.8 29.3 - - + +
52D PHE* 3.8 17.7 - - + -
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Residues in contact with PHE 136 (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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95C TYR* 3.4 46.9 - + + -
99C ILE* 3.5 24.9 - - + -
132C TYR* 3.0 38.6 + + + +
133C PHE* 4.1 5.4 - + - +
135C ALA* 1.3 72.8 - - - +
137C GLU* 1.3 66.1 + - - +
139C VAL* 3.2 7.5 + - + +
140C LEU* 3.1 26.0 + - - +
148C LEU* 4.4 11.8 - - + +
160C LEU* 4.0 23.6 - - + -
163C LEU* 5.5 2.7 - - + -
181C LEU* 3.9 21.3 - - + -
51D MET* 4.0 12.3 - - + -
52D PHE* 3.6 18.6 - + - -
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Residues in contact with GLU 137 (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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133C PHE 2.9 18.9 + - - +
134C PRO* 3.7 4.7 - - + +
136C PHE* 1.3 76.6 - - - +
138C LYS* 1.3 56.7 + - - +
140C LEU* 3.3 5.3 + - - +
141C LYS* 2.8 33.1 + - + +
177C SER 5.3 0.9 - - - +
178C PHE* 3.2 30.9 - - + +
179C PRO* 3.4 13.9 - - - +
180C LEU* 2.9 38.3 + - + +
181C LEU* 3.0 30.5 + - - +
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Residues in contact with LYS 138 (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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134C PRO 3.0 18.1 + - - +
135C ALA* 3.6 8.1 - - - +
136C PHE 3.2 0.2 - - - -
137C GLU* 1.3 78.5 - - - +
139C VAL* 1.3 57.3 + - + +
141C LYS* 3.6 25.8 - - - +
142C SER* 2.8 32.3 + - - -
48D GLY* 5.1 15.8 + - - -
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Residues in contact with VAL 139 (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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95C TYR* 3.5 42.8 - - + +
135C ALA 3.3 14.8 + - - +
136C PHE* 3.2 10.2 + - + +
138C LYS* 1.3 76.7 - - + +
140C LEU* 1.3 62.5 + - - +
142C SER* 2.8 24.0 + - - +
143C HIS* 3.4 26.5 + - + +
148C LEU* 3.9 20.9 - - + +
51D MET* 4.1 8.5 - - + -
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Residues in contact with LEU 140 (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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136C PHE 3.1 12.5 + - - +
137C GLU* 3.7 6.1 - - - +
139C VAL* 1.3 75.1 - - - +
141C LYS* 1.3 58.4 + - - +
143C HIS* 3.5 11.1 + - + -
144C GLY* 2.9 31.4 + - - -
145C GLN 4.0 18.2 + - - +
146C ASP 4.6 5.4 - - - +
147C TYR 4.2 9.0 - - - +
148C LEU* 4.0 21.1 - - + +
180C LEU* 3.5 41.0 - - + +
181C LEU* 3.6 28.5 - - + -
184C LEU* 4.2 15.0 - - + -
187C ARG* 5.1 2.2 - - - +
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Residues in contact with LYS 141 (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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137C GLU* 2.8 20.6 + - + +
138C LYS* 3.6 27.1 - - - +
140C LEU* 1.3 79.3 - - - +
142C SER* 1.3 64.4 + - - +
143C HIS 3.5 0.2 + - - -
144C GLY* 3.7 6.7 + - - -
180C LEU* 3.5 19.2 - - + +
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Residues in contact with SER 142 (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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138C LYS* 2.8 20.0 + - - -
139C VAL* 2.8 22.3 + - - +
141C LYS* 1.3 83.0 - - - +
143C HIS* 1.3 63.9 + - - +
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Residues in contact with HIS 143 (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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139C VAL* 3.4 26.1 + - + +
140C LEU* 3.7 11.9 - - + -
142C SER* 1.3 81.9 + - - +
144C GLY* 1.3 67.4 + - - +
145C GLN* 2.9 60.5 + - + +
147C TYR 3.0 20.6 + - - -
148C LEU 2.9 27.8 + - - -
149C VAL* 5.7 0.2 - - - -
150C GLY 6.0 1.6 - - - -
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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