Contacts of the helix formed by residues 139 - 153 (chain C) in PDB entry 3Q37
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 ARG 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C GLU* 2.9 19.8 + - - +
137C ALA* 3.9 20.6 - - - +
138C GLY* 1.3 81.4 - - - +
140C THR* 1.3 65.4 + - - +
141C ALA 3.4 2.2 - - - -
142C ALA* 3.9 28.1 - - + +
143C VAL* 2.9 40.8 + - + +
146C THR* 5.6 2.4 + - - -
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Residues in contact with THR 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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130C GLU* 2.7 43.1 + - - +
134C GLU 4.0 1.4 + - - -
135C ARG* 3.6 21.5 + - - +
138C GLY 3.5 4.2 + - - -
139C ARG* 1.3 76.5 - - - +
141C ALA* 1.3 66.8 + - - +
143C VAL* 3.8 0.5 - - - +
144C VAL* 3.0 26.9 + - + +
187C VAL* 4.0 27.8 - - + -
190C LEU* 4.5 7.6 - - + -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLY 5.3 0.6 + - - -
139C ARG 3.4 0.4 - - - -
140C THR* 1.3 79.7 - - - +
142C ALA* 1.3 65.1 + - - +
144C VAL* 4.3 0.4 - - - -
145C LEU* 3.0 37.9 + - + +
190C LEU* 3.8 31.0 - - + -
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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
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139C ARG* 3.4 40.6 + - + +
140C THR 3.3 0.4 - - - -
141C ALA* 1.3 80.3 - - - +
143C VAL* 1.3 55.1 + - - +
145C LEU* 3.9 2.3 - - - +
146C THR* 2.7 39.0 + - - +
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Residues in contact with VAL 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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129C GLY 4.1 0.9 - - - +
130C GLU* 3.9 16.4 - - + -
134C GLU* 3.5 44.9 - - + +
139C ARG* 2.9 39.2 + - + +
140C THR 3.8 2.2 - - - +
142C ALA* 1.3 77.6 - - - +
144C VAL* 1.3 58.4 + - - +
146C THR* 3.2 6.7 + - - -
147C GLN* 3.0 44.9 + - + +
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Residues in contact with VAL 144 (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 VAL* 4.4 6.0 - - + +
129C GLY* 3.8 35.9 - - - +
130C GLU* 4.0 11.9 - - + +
140C THR* 3.0 21.1 + - + +
141C ALA* 3.9 4.5 - - - +
143C VAL* 1.3 74.3 - - - +
145C LEU* 1.3 60.5 + - - +
147C GLN* 3.4 11.6 + - - +
148C LEU* 3.0 27.5 + - - +
167C TYR* 4.2 9.2 - - + -
187C VAL* 4.4 9.2 - - + -
190C LEU* 4.1 16.2 - - + -
191C LEU* 4.0 24.0 - - + +
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Residues in contact with LEU 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 ALA* 3.0 28.5 + - + +
142C ALA* 4.2 2.5 - - - +
144C VAL* 1.3 74.6 - - - +
146C THR* 1.3 60.9 + - - +
148C LEU* 4.1 4.2 - - + +
149C ALA* 2.9 31.0 + - - +
190C LEU* 3.6 32.8 - - + +
191C LEU* 4.2 15.9 - - + -
194C TRP* 3.6 49.3 + - + +
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Residues in contact with THR 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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107C ASN* 3.7 18.1 + - - +
139C ARG* 5.6 2.6 + - - -
142C ALA 2.7 24.6 + - - -
143C VAL* 3.6 5.8 - - - -
145C LEU* 1.3 74.8 - - - +
147C GLN* 1.3 64.4 + - - +
149C ALA* 3.9 4.2 - - - +
150C ALA* 3.1 23.0 + - - +
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Residues in contact with GLN 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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100C ARG* 3.9 32.1 + - - +
107C ASN* 3.6 27.4 + - - +
128C VAL* 3.2 20.2 - - + +
129C GLY 2.8 43.6 + - - +
143C VAL* 3.0 21.8 + - + +
144C VAL* 3.6 11.4 - - - +
145C LEU 3.3 0.2 - - - -
146C THR* 1.3 77.5 - - - +
148C LEU* 1.3 60.9 + - - +
150C ALA* 3.6 4.0 + - - +
151C VAL* 3.5 23.4 + - - +
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Residues in contact with LEU 148 (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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126C VAL* 5.5 4.0 - - + -
128C VAL* 4.5 11.2 - - + +
144C VAL 3.0 16.8 + - - +
145C LEU* 4.1 5.8 - - + +
147C GLN* 1.3 75.2 - - - +
149C ALA* 1.3 60.8 + - - +
151C VAL* 3.2 12.4 + - + +
152C ALA* 2.8 26.3 + - - +
160C TRP* 4.1 15.9 - - + -
163C VAL* 6.1 0.9 - - + -
165C ILE* 3.6 36.8 - - + -
191C LEU* 4.0 20.6 - - + +
194C TRP* 3.6 31.4 - - + -
195C VAL* 4.0 9.2 - - + -
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Residues in contact with ALA 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 LEU 2.9 21.0 + - - +
146C THR* 3.9 5.8 - - - +
147C GLN 3.4 0.2 - - - -
148C LEU* 1.3 74.0 - - - +
150C ALA* 1.3 66.1 + - - +
152C ALA* 3.7 0.9 - - - +
153C GLN* 3.0 27.2 + - - +
194C TRP* 3.9 26.7 - - + +
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Residues in contact with ALA 150 (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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107C ASN* 3.9 32.8 - - + +
108C GLU* 4.8 6.5 - - - +
111C ALA* 3.3 14.5 - - + +
146C THR 3.1 16.6 + - - +
147C GLN 3.7 6.3 - - - +
148C LEU 3.2 0.2 - - - -
149C ALA* 1.3 79.4 - - - +
151C VAL* 1.3 61.6 + - - +
153C GLN* 3.6 16.3 + - - +
154C LYS* 3.9 6.8 - - - +
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Residues in contact with VAL 151 (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 ARG* 5.6 1.3 - - - +
107C ASN 5.3 0.7 - - - +
110C VAL* 4.5 5.8 - - + -
111C ALA* 3.7 24.0 - - + +
114C VAL* 3.7 32.3 - - + -
126C VAL* 4.0 27.4 - - + -
128C VAL* 6.1 0.2 - - + -
147C GLN 3.5 14.6 + - - +
148C LEU* 3.2 15.2 + - + +
149C ALA 3.2 0.4 - - - -
150C ALA* 1.3 74.6 - - + +
152C ALA* 1.3 67.8 + - - +
154C LYS* 3.1 14.6 + - - +
155C LEU* 3.3 23.0 - - + +
160C TRP* 5.7 2.2 - - + -
163C VAL* 5.9 1.8 - - + -
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Residues in contact with ALA 152 (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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148C LEU 2.8 17.2 + - - +
149C ALA 3.7 3.1 - - - +
151C VAL* 1.3 76.6 - - - +
153C GLN* 1.3 62.5 + - - +
155C LEU* 3.1 23.5 + - - +
160C TRP* 4.0 24.0 + - + +
194C TRP* 3.5 30.3 - - + -
199C LEU* 5.3 2.7 - - + -
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Residues in contact with GLN 153 (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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149C ALA 3.0 17.0 + - - +
150C ALA* 3.9 10.7 - - - +
151C VAL 3.2 0.4 - - - -
152C ALA* 1.3 77.6 - - - +
154C LYS* 1.3 73.3 + - + +
155C LEU 3.8 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