Contacts of the helix formed by residues 153 - 170 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11Y ASP* 3.1 46.6 + - - +
12Y TYR* 3.6 25.8 - - + +
152Y SER* 1.3 73.9 - - - +
154Y GLU* 1.4 78.0 + - + +
156Y ALA* 3.4 21.3 + - + +
157Y VAL* 3.5 14.7 + - - +
182Y ILE* 4.5 25.7 - - + +
184Y ASP* 3.6 23.7 + - - +
186Y ASN* 5.4 1.6 + - - -
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Residues in contact with GLU 154 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152Y SER* 3.5 12.8 - - - +
153Y ARG* 1.4 96.1 - - + +
155Y ARG* 1.3 56.8 + - - +
156Y ALA 3.4 0.2 - - - -
157Y VAL* 3.8 16.6 - - - +
158Y GLU* 4.1 12.5 - - - +
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Residues in contact with ARG 155 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146Y TYR* 5.7 6.5 - - - -
151Y ILE* 3.4 23.8 - - + -
152Y SER* 3.1 20.0 + - - +
154Y GLU* 1.3 75.6 - - - +
156Y ALA* 1.3 59.0 + - - +
157Y VAL 3.2 2.5 - - - -
158Y GLU* 3.0 57.1 + - - +
159Y LEU* 3.0 15.7 + - + +
162Y LYS* 5.3 9.7 - - - +
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Residues in contact with ALA 156 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y ILE* 4.6 0.8 - - + +
12Y TYR* 3.2 32.8 - - + +
14Y LEU* 3.5 25.0 - - + +
151Y ILE* 4.3 3.4 - - - -
152Y SER 2.8 6.0 + - - +
153Y ARG* 3.4 12.8 - - - +
155Y ARG* 1.3 76.7 - - - +
157Y VAL* 1.4 55.9 + - + +
159Y LEU* 3.5 10.6 + - - +
160Y LEU* 3.0 30.8 + - - +
182Y ILE* 6.2 1.3 - - + -
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Residues in contact with VAL 157 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y LEU* 5.3 2.7 - - + -
153Y ARG 3.5 14.8 - - - +
154Y GLU* 3.8 13.0 - - - +
156Y ALA* 1.4 75.6 - - + +
158Y GLU* 1.4 63.1 + - + +
160Y LEU* 3.6 6.6 + - - +
161Y ARG* 3.0 50.6 + - - +
180Y VAL* 5.9 4.3 - - + -
191Y LEU* 5.2 17.3 - - + -
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Residues in contact with GLU 158 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Y GLU 4.1 15.5 - - - +
155Y ARG* 3.0 51.0 + - - +
157Y VAL* 1.4 78.1 - - + +
159Y LEU* 1.3 66.2 + - - +
161Y ARG* 3.6 9.7 - - - +
162Y LYS* 3.0 34.1 + - + +
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Residues in contact with LEU 159 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y ILE* 3.9 11.6 - - + +
142Y ILE* 5.2 2.0 - - + +
143Y LEU* 3.8 24.7 - - + -
146Y TYR* 3.7 33.0 - - + -
147Y TYR* 2.9 43.5 - - + +
151Y ILE* 4.0 12.3 - - + -
155Y ARG* 3.0 18.5 + - + +
156Y ALA* 3.7 6.3 - - - +
157Y VAL 3.4 0.2 - - - -
158Y GLU* 1.3 76.0 - - - +
160Y LEU* 1.3 59.1 + - - +
162Y LYS* 3.9 9.1 + - + +
163Y CYS* 3.6 21.8 + - - -
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Residues in contact with LEU 160 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y ILE* 3.6 41.1 - - + -
7Y ILE* 4.6 9.4 - - + -
14Y LEU* 4.0 16.2 - - + -
16Y ALA* 3.7 9.0 - - + -
156Y ALA 3.0 17.3 + - - +
157Y VAL* 3.9 5.6 - - - +
159Y LEU* 1.3 75.6 - - - +
161Y ARG* 1.4 62.5 + - - +
162Y LYS 3.3 0.4 - - - -
163Y CYS* 3.1 17.5 + - + +
164Y LEU* 3.2 24.4 + - + +
180Y VAL* 3.4 46.4 - - + -
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Residues in contact with ARG 161 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Y VAL* 3.0 41.0 + - - +
158Y GLU* 3.6 11.0 - - - +
160Y LEU* 1.4 75.4 - - - +
162Y LYS* 1.3 62.2 + - + +
164Y LEU* 3.3 33.0 + - + +
165Y GLU* 3.8 13.4 + - + +
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Residues in contact with LYS 162 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ARG* 3.0 54.7 + - - +
142Y ILE* 5.0 4.7 - - + -
146Y TYR* 3.6 42.8 + - + -
155Y ARG* 5.3 10.1 - - - +
158Y GLU* 3.0 21.1 + - + +
159Y LEU* 4.0 10.3 - - + +
161Y ARG* 1.3 75.9 - - + +
163Y CYS* 1.3 61.2 + - - +
165Y GLU* 3.4 24.5 + - - +
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Residues in contact with CYS 163 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y TYR* 4.7 6.5 - - + +
5Y ILE* 5.1 9.0 - - + -
7Y ILE* 6.2 0.4 - - - -
139Y THR* 3.9 21.4 - - + +
142Y ILE* 4.1 31.0 - - - -
143Y LEU* 4.3 22.4 - - - -
159Y LEU* 3.6 14.1 + - - +
160Y LEU* 3.1 19.5 + - + +
162Y LYS* 1.3 75.7 - - - +
164Y LEU* 1.4 65.5 + - + +
166Y GLU* 3.3 18.4 + - - +
167Y LEU* 4.1 5.6 - - - +
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Residues in contact with LEU 164 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y TYR* 5.9 1.1 - - + -
5Y ILE* 5.8 2.5 - - + -
16Y ALA* 5.9 0.7 - - + -
160Y LEU* 3.2 29.5 + - + +
161Y ARG* 3.4 26.7 - - + +
162Y LYS 3.2 0.8 - - - -
163Y CYS* 1.4 79.0 - - + +
165Y GLU* 1.3 61.6 + - + +
166Y GLU 3.4 0.2 + - - -
167Y LEU* 3.4 22.4 + - + +
168Y GLN* 3.9 15.0 + - - +
178Y PHE* 3.4 57.0 - - + -
180Y VAL* 5.4 6.1 - - + -
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Residues in contact with GLU 165 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ARG* 3.3 32.6 + - - +
161Y ARG* 3.8 11.8 - - - +
162Y LYS* 3.4 28.1 + - - +
163Y CYS 3.2 0.2 - - - -
164Y LEU* 1.3 77.8 - - + +
166Y GLU* 1.3 56.8 + - - +
168Y GLN* 3.3 5.9 + - - +
169Y LYS* 2.9 46.8 + - + +
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Residues in contact with GLU 166 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L TYR* 4.2 2.1 - - - +
137L GLY* 3.7 29.7 + - - -
140L ASP* 3.8 2.8 - - - +
141L ARG* 3.2 19.7 + - - +
138Y LEU* 3.5 39.8 - - + +
139Y THR* 3.9 7.6 - - + -
142Y ILE* 3.7 11.0 - - + -
163Y CYS 3.3 11.6 + - - +
164Y LEU 3.2 0.6 - - - -
165Y GLU* 1.3 79.8 - - - +
167Y LEU* 1.3 56.0 + - + +
170Y ARG* 3.1 37.1 + - - +
171Y PHE* 3.1 25.8 + - - +
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Residues in contact with LEU 167 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y TYR* 3.4 47.1 - - + -
135Y GLY* 4.1 19.5 - - - +
138Y LEU* 5.4 1.3 - - + -
139Y THR* 4.1 10.8 - - + -
163Y CYS 4.1 14.4 - - - +
164Y LEU* 3.8 10.1 - - + +
165Y GLU 3.3 1.0 - - - -
166Y GLU* 1.3 75.4 - - - +
168Y GLN* 1.4 61.2 + - + +
171Y PHE* 3.4 21.7 - - + +
173Y LEU 3.0 23.4 - - - +
175Y LEU* 4.2 14.5 + - + -
178Y PHE* 3.4 31.9 - - + -
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Residues in contact with GLN 168 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K GLN* 3.5 6.8 + - - -
174K ASN* 4.2 24.7 + - - +
164Y LEU* 4.1 13.3 - - - +
165Y GLU* 3.3 6.8 + - - +
166Y GLU 3.2 0.2 - - - -
167Y LEU* 1.4 83.9 - - + +
169Y LYS* 1.4 62.9 + - + +
170Y ARG 3.4 1.3 - - - -
171Y PHE 3.4 12.7 - - - +
173Y LEU 4.8 1.1 - - - -
174Y ASN* 3.4 25.1 + - - +
175Y LEU 4.2 11.2 - - - +
176Y PRO* 4.4 17.0 + - - +
178Y PHE* 5.4 2.9 - - + -
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Residues in contact with LYS 169 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K GLN* 3.6 10.2 + - - +
30K ASP* 4.2 9.0 - - - +
140L ASP* 5.1 15.4 - - + +
141L ARG* 5.4 5.4 - - - +
165Y GLU* 2.9 31.3 + - + +
168Y GLN* 1.4 79.1 - - + +
170Y ARG* 1.3 68.2 + - + +
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Residues in contact with ARG 170 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K VAL* 2.9 31.8 - - + +
27K GLN* 3.0 32.4 + - - +
28K MET* 5.3 4.2 + - - +
125L THR* 4.6 11.7 + - - +
136L TYR* 2.1 71.5 - - - +
140L ASP* 2.1 40.1 + - - +
141L ARG* 5.9 0.2 - - - +
166Y GLU* 3.1 35.1 + - - +
169Y LYS* 1.3 86.7 + - + +
171Y PHE* 1.3 62.3 + - - +
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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