Contacts of the helix formed by residues 143 - 156 (chain C) in PDB entry 4UQJ
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 LEU 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C ASP* 5.2 1.0 + - - -
137C TYR* 3.6 37.9 - - + -
138C ASP 4.9 0.9 - - - +
139C SER* 4.2 21.8 - - - +
142C GLY* 1.3 74.7 - - - +
144C SER* 1.3 57.4 + - - +
145C THR 3.3 2.5 - - - -
146C LEU* 3.7 24.5 - - + +
147C GLN* 3.0 42.6 + - + +
143D LEU* 4.7 22.9 - - + -
147D GLN* 4.2 16.4 - - - +
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Residues in contact with SER 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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104C ASP* 3.3 37.1 + - - -
116C ASP* 5.5 2.4 + - - -
118C LYS* 5.5 1.5 - - - +
141C ARG 5.0 4.7 - - - -
142C GLY 3.0 6.2 - - - -
143C LEU* 1.3 79.2 - - - +
145C THR* 1.3 65.1 + - - +
147C GLN* 3.7 9.2 + - - +
148C ALA* 3.3 18.4 + - - +
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Residues in contact with THR 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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116C ASP* 5.3 2.0 - - - +
117C LEU* 5.3 6.5 - - + -
118C LYS* 4.5 26.0 - - + +
121C LEU* 5.1 11.0 - - + -
135C TYR* 3.0 9.9 + - - -
142C GLY 4.4 5.9 + - - -
144C SER* 1.3 79.0 - - - +
146C LEU* 1.3 65.7 + - - +
148C ALA* 3.2 10.0 + - - +
149C VAL* 3.1 27.4 + - - +
195C ASP* 2.7 31.1 + - - +
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Residues in contact with LEU 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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135C TYR* 3.5 37.0 - - + -
137C TYR* 3.7 30.3 - - + +
143C LEU* 3.3 36.6 + - + +
145C THR* 1.3 79.9 + - - +
147C GLN* 1.3 65.5 + - + +
149C VAL* 3.1 7.2 - - + +
150C LEU* 3.0 44.8 + - + +
162C ALA* 3.9 18.4 - - + -
195C ASP* 5.8 0.2 - - - +
143D LEU* 6.4 0.2 - - + -
146D LEU* 5.5 6.7 - - + -
147D GLN* 5.5 2.9 - - + -
150D LEU* 4.9 5.6 - - + -
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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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143C LEU* 3.0 27.6 + - + +
144C SER* 3.9 7.7 - - - +
146C LEU* 1.3 77.8 - - + +
148C ALA* 1.3 57.8 + - - +
150C LEU* 4.3 6.5 - - + -
151C ASP* 2.8 45.5 + - - +
137D TYR* 3.9 17.0 - - + +
139D SER* 4.5 8.9 - - - -
143D LEU* 4.1 28.7 - - + +
146D LEU* 5.9 2.0 - - + -
164D ASN* 3.4 25.2 + - - +
167D ASN* 4.9 5.4 + - - -
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LYS* 4.5 17.5 - - + +
122C LEU* 4.4 15.9 - - + -
144C SER 3.3 12.8 + - - +
145C THR* 3.2 15.7 + - - +
146C LEU 3.1 0.4 - - - -
147C GLN* 1.3 79.4 - - - +
149C VAL* 1.3 59.2 + - + +
151C ASP* 4.0 3.6 - - - +
152C SER* 3.0 34.3 + - - -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 4.7 10.5 - - + -
122C LEU* 3.9 22.9 - - + -
125C ILE* 4.6 11.7 - - + -
133C PHE* 5.0 11.2 - - + -
135C TYR* 4.2 35.2 - - + -
145C THR 3.1 11.6 + - - +
146C LEU* 3.1 23.8 - - + +
148C ALA* 1.3 74.0 - - + +
150C LEU* 1.3 64.9 + - + +
152C SER* 3.8 1.7 - - - -
153C ALA* 2.9 29.3 + - - +
158C TRP* 4.1 4.9 - - + -
160C VAL* 4.3 7.4 - - + +
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Residues in contact with LEU 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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146C LEU* 3.0 41.3 + - + +
147C GLN* 3.8 5.2 - - + +
148C ALA 3.3 0.2 - - - -
149C VAL* 1.3 76.7 - - + +
151C ASP* 1.3 69.2 + - - +
153C ALA* 3.2 18.4 + - + +
154C ALA* 3.5 6.1 + - - +
160C VAL* 4.4 28.3 - - + +
162C ALA* 4.7 6.5 - - + -
137D TYR* 4.7 6.1 - - - +
146D LEU* 4.6 10.1 - - + -
150D LEU* 4.0 28.5 - - + -
162D ALA* 3.9 35.9 - - + +
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Residues in contact with ASP 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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147C GLN* 2.8 32.3 + - - +
148C ALA* 4.0 3.9 - - - +
150C LEU* 1.3 78.5 - - - +
152C SER* 1.3 62.1 + - - +
154C ALA* 3.2 20.4 + - - +
155C GLU* 3.6 5.9 + - - +
137D TYR* 4.0 8.3 + - - -
162D ALA 4.5 3.2 - - - +
163D ILE* 4.6 4.7 - - - +
164D ASN* 3.9 28.8 + - - +
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Residues in contact with SER 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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122C LEU* 3.4 22.4 - - - +
148C ALA 3.0 19.2 + - - -
149C VAL 4.0 0.4 - - - -
151C ASP* 1.3 72.2 - - - +
153C ALA* 1.3 59.4 + - - +
154C ALA 3.1 2.0 - - - -
155C GLU* 3.8 6.9 - - - +
156C LYS* 2.8 35.8 + - - +
158C TRP* 3.9 23.1 - - - -
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Residues in contact with ALA 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 VAL 2.9 19.8 + - - +
150C LEU* 3.3 13.7 - - + +
151C ASP 3.2 0.4 - - - -
152C SER* 1.3 76.9 - - - +
154C ALA* 1.3 56.6 + - - +
157C LYS* 3.1 8.4 - - - -
158C TRP* 2.8 44.7 + - + +
160C VAL* 3.8 24.5 - - + -
161D THR* 6.2 0.2 - - - -
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Residues in contact with ALA 154 (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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150C LEU 3.5 5.6 + - - +
151C ASP* 3.2 13.0 + - - +
152C SER 3.1 0.6 - - - -
153C ALA* 1.3 81.6 - - - +
155C GLU* 1.3 62.3 + - - +
157C LYS* 3.8 4.2 + - - -
161D THR* 4.8 12.1 - - + -
162D ALA 5.4 0.4 - - - +
163D ILE* 4.5 22.4 - - + -
183D ASP* 4.0 33.3 - - + +
186D LEU* 4.2 10.4 - - - +
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP 3.6 6.3 + - - +
152C SER* 3.3 7.9 + - - +
154C ALA* 1.3 78.9 - - - +
156C LYS* 1.3 59.6 + - + +
157C LYS* 3.0 11.0 + - - +
183D ASP* 4.2 12.3 + - - +
186D LEU* 4.8 7.0 - - - +
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Residues in contact with LYS 156 (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 GLU* 4.8 10.1 - - + +
152C SER* 2.8 19.0 + - - +
155C GLU* 1.3 72.8 - - + +
157C LYS* 1.3 72.4 + - - +
158C TRP* 3.5 36.6 + - + +
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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