Contacts of the helix formed by residues 131 - 150 (chain C) in PDB entry 3LOC
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 131 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ASP 3.0 15.6 + - - -
129C LEU 3.3 0.4 - - - -
130C THR* 1.3 79.7 + - - +
132C ASP* 1.3 67.5 + - - +
133C LEU 3.4 0.7 - - - -
134C LYS 3.2 3.3 + - - -
135C ALA* 3.1 21.4 + - - +
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 4.7 15.2 + - - +
127C ASP 4.5 0.6 + - - -
128C GLU* 3.8 22.2 + - - +
131C GLY* 1.3 72.3 - - - +
133C LEU* 1.3 63.3 + - - +
135C ALA* 3.3 9.2 + - - +
136C LEU* 3.0 22.5 + - - +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 5.4 4.8 - - - +
73C LEU* 4.7 5.8 - - + -
77C LEU* 4.0 34.8 - - + -
128C GLU 3.3 18.2 + - - +
129C LEU* 3.7 23.6 - - + +
132C ASP* 1.3 77.9 - - - +
134C LYS* 1.3 65.6 + - - +
136C LEU* 3.1 6.8 + - + +
137C ILE* 2.9 44.1 + - + +
166C TRP* 4.4 9.0 - - + -
212C URA 4.4 8.3 - - + -
178D GLN* 3.6 33.0 - - + +
182D VAL* 4.8 6.1 - - + -
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Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU 3.3 10.8 + - - +
130C THR* 3.6 24.7 - - - +
131C GLY 3.2 1.6 + - - -
133C LEU* 1.3 79.6 - - - +
135C ALA* 1.3 62.2 + - - +
137C ILE* 3.3 4.7 + - - +
138C ASP* 2.9 45.4 + - - +
181D ALA 3.6 20.0 + - - +
182D VAL* 3.9 26.6 + - + -
183D THR 5.8 1.0 - - - -
184D GLY* 5.7 3.6 - - - +
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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
----------------------------------------------------------
131C GLY 3.1 12.3 + - - +
132C ASP* 3.4 14.4 - - - +
134C LYS* 1.3 77.4 - - - +
136C LEU* 1.3 65.4 + - - +
138C ASP* 3.3 7.7 + - - +
139C GLU* 3.0 22.8 + - - +
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.6 38.8 - - + -
80C LEU* 4.4 10.8 - - + -
81C LYS* 3.9 33.0 - - + -
132C ASP 3.0 10.3 + - - +
133C LEU* 3.5 8.7 - - + +
135C ALA* 1.3 79.1 - - - +
137C ILE* 1.3 61.1 + - + +
139C GLU* 3.1 13.7 + - - +
140C LYS* 2.9 50.1 + - + +
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.4 33.0 - - + -
133C LEU* 2.9 37.2 + - + +
134C LYS* 4.0 2.9 - - - +
136C LEU* 1.3 79.3 - - + +
138C ASP* 1.3 57.3 + - - +
140C LYS* 4.5 1.6 - - - +
141C SER* 2.6 47.0 + - - +
159C GLN* 4.7 8.1 - - + +
162C ILE* 4.3 17.0 - - + +
163C PHE* 5.4 2.5 - - + -
166C TRP* 4.1 20.9 - - + -
182D VAL* 4.0 28.7 - - + -
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Residues in contact with ASP 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LYS* 2.9 50.2 + - - +
135C ALA* 3.6 6.3 - - - +
137C ILE* 1.3 76.5 - - - +
139C GLU* 1.3 62.2 + - - +
141C SER* 3.6 5.7 - - - -
142C ALA* 3.1 21.5 + - - +
159C GLN* 4.7 8.4 + - - +
182D VAL* 4.5 6.6 - - - +
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Residues in contact with GLU 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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135C ALA 3.0 13.1 + - - +
136C LEU* 3.3 15.9 - - - +
138C ASP* 1.3 77.1 - - - +
140C LYS* 1.3 90.3 + - + +
142C ALA* 3.0 26.8 + - - +
143C LEU* 3.3 12.9 + - + +
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.6 44.0 - - + +
81C LYS* 3.1 25.0 + - - +
83C PHE* 3.0 28.4 + - + -
84C ARG* 3.9 8.1 - - - +
136C LEU* 2.9 29.3 + - + +
137C ILE* 4.6 1.8 - - - +
139C GLU* 1.3 102.8 + - - +
141C SER* 1.3 65.1 + - - +
143C LEU* 3.2 21.9 + - + +
144C ILE* 3.1 29.8 + - + +
162C ILE* 5.0 2.9 - - + -
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Residues in contact with SER 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ILE* 2.6 29.7 + - - +
138C ASP* 3.6 7.4 - - - -
140C LYS* 1.3 77.0 - - - +
142C ALA* 1.3 51.7 + - - +
144C ILE* 3.4 2.1 + - - -
145C ALA* 2.8 33.3 + - - +
158C PRO* 3.5 26.0 - - - +
159C GLN* 3.6 26.6 + - - +
162C ILE* 4.2 5.4 - - - +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASP 3.1 12.8 + - - +
139C GLU* 3.0 18.0 + - + +
141C SER* 1.3 73.4 - - - +
143C LEU* 1.3 66.9 + - + +
145C ALA* 3.1 9.7 + - - +
146C GLY* 3.0 18.9 + - - -
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.6 33.7 - - + +
84C ARG* 3.9 4.0 - - - +
85C GLU* 3.9 34.5 - - + +
139C GLU* 3.3 12.1 + - + +
140C LYS* 3.2 28.3 + - + +
142C ALA* 1.3 81.0 - - + +
144C ILE* 1.3 59.8 + - + +
146C GLY* 3.1 4.2 + - - -
147C TRP* 3.0 39.9 + - + +
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 5.3 1.8 - - + -
83C PHE* 5.1 18.4 - - + -
93C ILE* 5.8 4.0 - - + -
140C LYS* 3.1 18.5 + - + +
141C SER 3.7 4.3 - - - +
143C LEU* 1.3 73.8 - - + +
145C ALA* 1.3 65.4 + - - +
147C TRP* 3.3 21.1 + - + +
148C VAL* 3.2 26.0 + - + +
153C LEU* 4.2 17.0 - - + -
156C ILE* 5.1 1.6 - - + -
158C PRO* 3.6 25.6 - - + +
161C LEU* 4.4 16.6 - - + -
162C ILE* 3.8 31.9 - - + -
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Residues in contact with ALA 145 (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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141C SER 2.8 15.1 + - - +
142C ALA* 3.2 13.9 - - - +
144C ILE* 1.3 77.8 - - - +
146C GLY* 1.3 50.2 + - - +
148C VAL* 2.8 31.3 - - + +
149C LYS* 2.8 18.7 + - - +
158C PRO* 4.1 11.4 - - + +
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Residues in contact with GLY 146 (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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142C ALA 3.0 13.2 + - - -
143C LEU* 3.1 6.0 + - - -
145C ALA* 1.3 69.9 - - - +
147C TRP* 1.3 63.4 + - - +
148C VAL 3.1 1.1 - - - -
149C LYS* 4.3 7.0 - - - -
150C SER* 2.8 35.6 + - - -
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Residues in contact with TRP 147 (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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83C PHE* 4.9 15.5 - + - -
84C ARG 3.1 23.1 - - - -
85C GLU* 2.6 34.5 - - - -
86C ASP* 4.4 1.1 - - - -
87C PHE* 3.5 28.5 - - + -
89C PRO* 3.5 30.2 - - + +
92C ALA* 6.0 1.1 - - + +
93C ILE* 5.3 2.8 - - + +
143C LEU* 3.0 24.2 + - + +
144C ILE* 3.3 30.9 - - + +
146C GLY* 1.3 77.1 - - - +
148C VAL* 1.3 57.7 + - - +
150C SER* 3.6 3.7 + - - -
151C GLY 3.2 3.5 + - - -
152C LYS* 2.7 48.5 + - + +
153C LEU* 3.4 34.3 - - + -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 3.3 17.0 - - + +
145C ALA* 2.8 29.0 + - + +
146C GLY 3.1 0.6 - - - -
147C TRP* 1.3 73.0 - - - +
149C LYS* 1.3 67.9 + - + +
151C GLY* 3.1 13.7 + - - -
153C LEU* 3.8 27.7 - - + +
154C ALA 3.6 20.0 - - - +
155C PRO* 4.6 9.4 - - + -
156C ILE* 4.4 18.6 - - + +
158C PRO* 5.8 0.4 - - + -
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Residues in contact with LYS 149 (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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145C ALA 2.8 17.9 + - - +
146C GLY* 4.0 6.7 - - - +
148C VAL* 1.3 81.5 - - + +
150C SER* 1.3 58.2 + - - +
151C GLY* 3.0 5.4 + - - -
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Residues in contact with SER 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLY 2.8 23.2 + - - -
147C TRP* 3.6 6.2 + - - -
149C LYS* 1.3 71.7 - - - +
151C GLY* 1.3 58.2 + - - +
152C LYS* 3.6 30.4 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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