Contacts of the helix formed by residues 154 - 164 (chain A) in PDB entry 6Q2N
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ALA* 2.8 10.9 + - - +
153A GLU* 1.3 75.5 - - - +
155A THR* 1.3 71.4 + - - +
156A TYR* 3.4 18.3 + - + +
157A ASP* 3.4 32.5 + - - +
158A LYS* 3.3 17.3 + - - +
180B ARG* 5.9 2.7 - - - +
184B PHE* 6.1 0.5 - - - -
202B LYS 5.1 6.4 + - - -
203B HIS* 5.7 2.4 + - - -
591F VAL* 5.4 8.3 - - - -
621F GLU* 5.6 0.8 + - - -
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Residues in contact with THR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 1.3 76.7 + - - +
156A TYR* 1.3 59.4 + - - +
158A LYS* 3.0 11.7 + - + +
159A ILE* 2.9 34.6 + - + +
130B LEU* 3.7 46.0 - - + +
132B LEU* 3.9 24.8 - - + +
203B HIS 6.1 1.1 - - - -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 3.2 14.7 + - + +
155A THR* 1.3 79.9 - - - +
157A ASP* 1.3 66.7 + - - +
159A ILE* 3.2 8.1 + - + +
160A LEU* 2.9 64.5 + - + +
142B PHE* 3.7 35.0 - + + -
144B TYR* 3.6 31.1 - + + -
145B CYS* 3.0 27.9 + - + -
146B SER* 4.7 2.4 - - - -
179B CYS 5.6 5.4 - - - -
180B ARG* 6.3 1.1 - - - -
203B HIS 5.6 1.3 - - - +
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Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 5.5 0.3 - - - -
152A ALA* 2.9 32.4 - - - +
154A THR* 3.4 12.7 + - - +
155A THR 3.2 0.6 - - - -
156A TYR* 1.3 83.0 - - - +
158A LYS* 1.3 60.9 + - - +
160A LEU* 3.3 25.2 - - - +
161A LYS* 2.9 28.4 + - - +
176A GLN* 3.6 26.3 + - - +
177A ALA* 5.6 5.9 + - - +
180B ARG* 4.1 17.0 + - - -
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA* 5.2 7.5 - - + +
154A THR 3.3 10.1 + - - +
155A THR* 3.0 14.6 + - + +
157A ASP* 1.3 78.0 - - - +
159A ILE* 1.3 59.3 + - + +
161A LYS* 3.3 9.5 + - + +
162A ASN* 2.9 43.4 + - - +
130B LEU 5.1 10.1 - - - +
131B GLY* 4.0 18.4 + - - +
606F TYR* 4.7 8.7 + - - -
621F GLU* 6.5 0.9 - - + -
622F PRO* 4.2 25.8 - - + +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 2.9 23.6 + - + +
156A TYR* 3.2 11.0 + - + +
158A LYS* 1.3 78.4 - - + +
160A LEU* 1.3 60.7 + - - +
162A ASN* 3.2 24.5 + - + +
163A LEU* 2.9 30.9 + - + +
125B LEU* 4.7 20.6 - - + -
129B ASP 3.4 24.5 - - - +
130B LEU* 4.1 11.9 - - + +
142B PHE* 6.2 3.8 - - + -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TYR* 2.9 51.2 + - + +
157A ASP* 3.3 29.8 - - - +
158A LYS 3.3 0.2 - - - -
159A ILE* 1.3 77.2 - - - +
161A LYS* 1.3 60.9 + - - +
163A LEU* 3.3 9.4 + - + +
164A SER* 3.3 26.5 + - - -
175A GLY 6.1 2.0 - - - +
176A GLN* 4.5 11.7 - - - +
144B TYR* 5.6 5.2 - - + -
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA 5.9 1.3 - - - +
157A ASP 2.9 17.1 + - - +
158A LYS* 3.3 9.2 + - + +
160A LEU* 1.3 76.8 - - - +
162A ASN* 1.3 62.1 + - - +
163A LEU 3.6 0.2 + - - -
164A SER* 4.1 10.9 + - - -
176A GLN* 4.7 17.2 + - + +
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Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS* 2.9 33.1 + - - +
159A ILE* 3.5 31.0 - - + +
160A LEU 3.2 0.2 - - - -
161A LYS* 1.3 79.2 - - - +
163A LEU* 1.3 62.6 + - - +
164A SER 4.6 2.4 - - - +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 2.9 18.1 + - + +
160A LEU* 3.3 11.6 + - + +
162A ASN* 1.3 79.5 - - - +
164A SER* 1.3 65.7 + - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU 3.3 13.8 + - - -
161A LYS* 4.5 9.9 - - - -
162A ASN 3.6 2.7 - - - +
163A LEU* 1.3 84.7 - - - +
173A LYS* 4.9 10.7 + - - -
174A VAL 4.8 11.0 + - - -
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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