Contacts of the helix formed by residues 153 - 170 (chain K) in PDB entry 5A0Q
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 153 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ASP* 3.1 47.0 + - - +
12K TYR* 3.6 24.6 - - + +
152K SER* 1.3 73.5 - - - +
154K GLU* 1.4 78.6 + - + +
156K ALA* 3.4 20.6 + - + +
157K VAL* 3.5 15.2 + - - +
182K ILE* 4.5 25.5 - - + +
184K ASP* 3.6 23.7 + - - +
186K ASN* 5.4 1.4 + - - -
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Residues in contact with GLU 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K SER* 3.5 12.8 - - - +
153K ARG* 1.4 96.3 - - + +
155K ARG* 1.3 58.5 + - - +
157K VAL* 3.8 16.6 - - - +
158K GLU* 4.1 12.1 - - - +
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Residues in contact with ARG 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K TYR* 5.7 6.7 - - - -
151K ILE* 3.4 23.8 - - + -
152K SER* 3.1 20.5 + - - +
154K GLU* 1.3 76.1 - - - +
156K ALA* 1.3 59.5 + - - +
157K VAL 3.2 2.2 - - - -
158K GLU* 3.0 57.4 + - - +
159K LEU* 3.0 15.4 + - + +
162K LYS* 5.3 9.9 - - - +
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Residues in contact with ALA 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ILE* 4.6 1.2 - - + +
12K TYR* 3.2 31.0 - - + +
14K LEU* 3.5 25.3 - - + +
151K ILE* 4.3 3.1 - - - -
152K SER 2.8 7.1 + - - +
153K ARG* 3.4 13.0 - - - +
154K GLU 3.4 0.2 - - - -
155K ARG* 1.3 77.1 - - - +
157K VAL* 1.4 57.2 + - + +
159K LEU* 3.5 9.9 + - - +
160K LEU* 3.0 30.0 + - - +
182K ILE* 6.2 1.1 - - + -
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Residues in contact with VAL 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LEU* 5.3 2.2 - - + -
153K ARG 3.5 14.4 - - - +
154K GLU* 3.8 13.7 - - - +
156K ALA* 1.4 76.7 - - + +
158K GLU* 1.4 62.9 + - + +
160K LEU* 3.9 5.6 - - - +
161K ARG* 3.0 49.4 + - - +
180K VAL* 5.9 3.8 - - + -
191K LEU* 5.2 17.3 - - + +
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Residues in contact with GLU 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K GLU 4.1 14.9 - - - +
155K ARG* 3.0 52.3 + - - +
157K VAL* 1.4 77.6 - - + +
159K LEU* 1.3 64.7 + - - +
161K ARG* 3.3 9.9 + - - +
162K LYS* 3.0 34.2 + - + +
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Residues in contact with LEU 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ILE* 3.9 11.4 - - + -
142K ILE* 5.6 1.5 - - + +
143K LEU* 3.8 24.9 - - + -
146K TYR* 3.7 33.0 - - + -
147K TYR* 2.9 43.3 - - + +
151K ILE* 4.0 13.7 - - + -
155K ARG* 3.0 17.8 + - + +
156K ALA* 3.7 6.1 - - - +
158K GLU* 1.3 76.4 - - - +
160K LEU* 1.3 59.1 + - - +
162K LYS* 3.9 10.0 + - + +
163K CYS* 3.6 22.2 + - - -
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Residues in contact with LEU 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ILE* 3.6 40.8 - - + -
7K ILE* 4.6 9.4 - - + -
14K LEU* 4.0 16.6 - - + -
16K ALA* 3.7 10.1 - - + -
156K ALA 3.0 17.0 + - - +
157K VAL* 3.9 5.6 - - - +
159K LEU* 1.3 77.0 - - - +
161K ARG* 1.4 62.3 + - - +
162K LYS 3.3 0.2 - - - -
163K CYS* 3.1 17.7 + - + +
164K LEU* 3.2 22.2 + - + +
180K VAL* 3.4 45.8 - - + -
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Residues in contact with ARG 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K VAL* 3.0 41.6 + - - +
158K GLU* 3.3 10.2 + - - +
160K LEU* 1.4 75.7 - - - +
162K LYS* 1.3 61.3 + - + +
164K LEU* 3.3 34.5 + - + +
165K GLU* 3.8 13.7 + - + +
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Residues in contact with LYS 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K ILE* 5.0 4.7 - - + -
146K TYR* 3.6 43.2 + - + -
155K ARG* 5.3 10.1 - - - +
158K GLU* 3.0 21.7 + - + +
159K LEU* 4.0 10.3 - - + +
160K LEU 3.3 0.2 - - - -
161K ARG* 1.3 74.6 - - + +
163K CYS* 1.3 60.7 + - - +
165K GLU* 3.4 24.6 + - - +
141Z ARG* 3.0 53.8 + - - +
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Residues in contact with CYS 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K TYR* 4.7 7.0 - - + +
5K ILE* 5.1 8.3 - - + -
7K ILE* 6.2 0.7 - - - -
139K THR* 3.9 21.7 - - + +
142K ILE* 4.1 31.4 - - - -
143K LEU* 4.3 22.4 - - - -
159K LEU* 3.6 14.0 + - - +
160K LEU* 3.1 20.3 + - + +
162K LYS* 1.3 75.1 - - - +
164K LEU* 1.4 64.4 + - + +
166K GLU* 3.3 18.7 + - - +
167K LEU* 4.1 5.2 - - - +
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Residues in contact with LEU 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 5.9 1.6 - - + -
5K ILE* 5.8 2.0 - - + -
16K ALA* 5.9 0.4 - - + -
160K LEU* 3.2 30.0 + - + +
161K ARG* 3.4 25.8 - - + +
162K LYS 3.2 1.2 - - - -
163K CYS* 1.4 78.5 - - + +
165K GLU* 1.3 62.5 + - + +
166K GLU 3.4 0.2 + - - -
167K LEU* 3.4 21.8 + - + +
168K GLN* 3.9 15.5 + - - +
178K PHE* 3.4 57.5 - - + -
180K VAL* 5.4 5.6 - - + -
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Residues in contact with GLU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K ARG* 3.8 12.2 - - + +
162K LYS* 3.4 27.8 + - - +
163K CYS 3.2 0.2 - - - -
164K LEU* 1.3 77.6 - - + +
166K GLU* 1.3 55.5 + - - +
168K GLN* 3.3 5.4 + - - +
169K LYS* 2.9 47.4 + - + +
141Z ARG* 3.3 34.3 + - - +
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Residues in contact with GLU 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K LEU* 3.5 39.4 - - + +
139K THR* 3.9 8.7 - - + -
142K ILE* 3.7 12.6 - - + -
163K CYS 3.3 12.1 + - - +
164K LEU 3.2 1.2 - - - -
165K GLU* 1.3 79.5 - - - +
167K LEU* 1.3 56.7 + - - +
168K GLN 3.2 0.2 - - - -
170K ARG* 3.1 36.6 + - - +
171K PHE* 3.1 25.6 + - - +
136Z TYR* 4.2 2.3 - - - +
137Z GLY* 3.7 28.4 + - - -
140Z ASP* 3.8 3.1 - - - +
141Z ARG* 3.2 18.9 + - - +
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Residues in contact with LEU 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K TYR* 3.4 44.9 - - + -
135K GLY* 4.1 20.0 - - - -
138K LEU* 5.4 1.3 - - + -
139K THR* 4.1 10.8 - - + -
163K CYS 4.1 14.1 - - - +
164K LEU* 3.4 10.3 + - + +
165K GLU 3.3 0.8 - - - -
166K GLU* 1.3 76.5 - - + +
168K GLN* 1.4 60.2 + - + +
171K PHE* 3.4 20.9 - - + +
173K LEU 3.0 24.4 - - - +
175K LEU* 4.2 14.0 + - + -
178K PHE* 3.4 33.0 - - + -
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Residues in contact with GLN 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K LEU* 3.9 13.8 + - - +
165K GLU* 3.3 6.9 + - - +
167K LEU* 1.4 82.4 - - + +
169K LYS* 1.4 63.4 + - + +
170K ARG 3.4 0.7 - - - -
171K PHE 3.4 13.2 - - - +
173K LEU 4.8 1.3 - - - -
174K ASN* 3.4 25.0 + - - +
175K LEU 4.2 10.1 - - - +
176K PRO* 4.4 17.2 + - - +
178K PHE* 5.4 2.7 - - + -
27Y GLN* 3.5 6.6 + - - -
174Y ASN* 4.2 23.3 + - - +
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Residues in contact with LYS 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K GLU* 2.9 31.5 + - + +
168K GLN* 1.4 78.1 - - + +
170K ARG* 1.3 70.4 + - + +
27Y GLN* 3.6 9.6 + - - +
30Y ASP* 4.2 9.4 - - - +
140Z ASP* 5.1 16.0 - - + +
141Z ARG* 5.4 5.6 - - - +
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Residues in contact with ARG 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K GLU* 3.1 34.1 + - - +
169K LYS* 1.3 86.9 + - + +
171K PHE* 1.3 62.5 + - - +
26Y VAL* 2.9 31.2 - - + +
27Y GLN* 3.0 34.2 + - - +
28Y MET* 5.3 4.4 + - - +
125Z THR* 4.6 11.5 + - - +
136Z TYR* 2.1 71.8 - - - +
140Z ASP* 2.1 40.6 + - - +
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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
------------------------------------------------------------
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