Contacts of the helix formed by residues 147 - 166 (chain Y) in PDB entry 3SDI
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 SER 147 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8Y PHE* 4.1 0.7 - - - -
9Y GLN* 4.1 4.9 - - - +
145Y ASP 3.3 3.4 + - - -
146Y LEU* 1.3 73.7 - - - +
148Y VAL* 1.3 66.8 + - - +
149Y GLU* 3.5 8.9 + - - +
150Y ASP* 2.9 32.6 + - - +
151Y ALA* 2.8 21.3 + - - +
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Residues in contact with VAL 148 (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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8Y PHE* 3.9 15.7 - - + -
9Y GLN* 4.2 5.8 - - - +
10Y GLY* 4.3 12.1 - - - +
13Y ILE* 4.6 0.9 - - - +
146Y LEU 3.7 2.0 + - - -
147Y SER* 1.3 71.4 - - - +
149Y GLU* 1.3 59.8 + - + +
151Y ALA* 3.3 1.9 + - - +
152Y LEU* 3.0 41.7 + - + +
177Y HIS* 3.6 40.4 - - + +
187Y HIS* 5.6 1.3 - - + +
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Residues in contact with GLU 149 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Y SER* 3.1 7.8 + - - +
148Y VAL* 1.3 82.3 - - + +
150Y ASP* 1.3 71.6 + - - +
152Y LEU* 3.7 9.3 + - + +
153Y TYR* 3.4 20.8 + - - +
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Residues in contact with ASP 150 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146Y LEU* 4.5 14.3 - - + +
147Y SER* 2.9 29.9 + - - +
149Y GLU* 1.3 84.4 - - - +
151Y ALA* 1.3 59.8 + - - +
153Y TYR* 3.5 7.6 + - - +
154Y LEU* 2.9 28.1 + - - +
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Residues in contact with ALA 151 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Y PHE* 3.4 20.3 - - + -
8Y PHE* 3.4 43.7 - - + -
13Y ILE* 3.7 12.5 - - + +
146Y LEU* 4.1 10.2 - - + +
147Y SER 2.8 11.9 + - - +
148Y VAL 3.7 0.7 - - - +
150Y ASP* 1.3 71.0 - - - +
152Y LEU* 1.3 64.8 + - - +
154Y LEU* 3.4 3.7 + - - -
155Y GLY 3.1 19.1 + - - -
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Residues in contact with LEU 152 (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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13Y ILE* 3.8 20.1 - - + +
148Y VAL* 3.0 32.6 + - + +
149Y GLU* 3.9 10.1 - - + +
150Y ASP 3.4 0.2 - - - -
151Y ALA* 1.3 76.6 - - - +
153Y TYR* 1.3 62.3 + - - +
155Y GLY 3.5 0.5 + - - -
156Y LYS* 3.0 22.7 + - - +
175Y LEU* 3.6 39.0 - - + +
176Y TYR 4.5 2.0 - - - +
177Y HIS* 4.4 3.6 - - + -
187Y HIS* 3.6 52.9 - - + +
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Residues in contact with TYR 153 (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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140J HIS* 5.3 0.9 - + - -
149Y GLU 3.4 11.7 + - - +
150Y ASP* 3.7 11.0 - - - +
151Y ALA 3.3 0.2 - - - -
152Y LEU* 1.3 76.2 - - - +
154Y LEU* 1.3 60.0 + - + +
156Y LYS* 3.1 30.2 + - + +
157Y ARG* 2.7 53.2 + - + +
199Y VAL* 3.8 22.8 - - + +
203Y GLU* 2.9 42.4 + - - +
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Residues in contact with LEU 154 (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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140J HIS* 5.7 1.6 - - - +
6Y PHE* 4.7 2.2 - - + -
137Y VAL* 4.3 12.6 - - + +
138Y LEU* 3.8 24.5 - - + +
141Y ASN* 3.6 52.9 - - + +
142Y TYR* 3.9 3.4 - - + +
146Y LEU* 3.8 17.3 - - + -
150Y ASP 2.9 18.5 + - - +
151Y ALA* 3.7 7.2 - - - +
152Y LEU 3.3 0.2 - - - -
153Y TYR* 1.3 78.8 - - + +
155Y GLY* 1.3 57.9 + - - +
157Y ARG* 3.2 6.0 + - + -
158Y SER* 2.8 42.1 + - - +
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Residues in contact with GLY 155 (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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4Y LEU* 3.7 15.1 - - - +
6Y PHE* 4.0 17.5 - - - -
13Y ILE* 4.3 6.3 - - - -
15Y ALA* 4.1 7.6 - - - -
151Y ALA 3.1 13.7 + - - -
152Y LEU 3.8 2.7 - - - -
154Y LEU* 1.3 75.9 - - - +
156Y LYS* 1.3 63.1 + - - +
158Y SER* 3.2 4.0 + - - -
159Y ILE* 3.0 26.0 + - - +
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Residues in contact with LYS 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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152Y LEU 3.0 13.8 + - - +
153Y TYR* 3.1 34.9 + - + +
155Y GLY* 1.3 75.0 - - - +
157Y ARG* 1.3 59.8 + - - +
159Y ILE* 3.1 4.5 + - - +
160Y LEU* 2.9 25.6 + - - +
173Y VAL* 4.1 22.1 - - + +
175Y LEU* 4.2 17.0 - - + +
190Y HIS* 4.1 31.7 - - + -
195Y LEU* 3.7 37.6 - - + +
198Y LYS* 6.2 2.0 - - - +
199Y VAL* 5.6 0.9 - - + -
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Residues in contact with ARG 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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136J SER 5.2 0.6 + - - -
139J ASP 3.8 2.2 + - - -
140J HIS* 3.1 51.7 + - + +
137Y VAL* 4.2 12.7 - - + +
153Y TYR* 2.7 38.8 + - + +
154Y LEU* 3.7 6.3 - - + +
156Y LYS* 1.3 74.7 - - - +
158Y SER* 1.3 56.9 + - - +
160Y LEU* 3.2 12.0 + - - +
161Y ALA* 2.8 44.3 + - - +
199Y VAL* 3.7 19.9 - - - +
203Y GLU* 2.9 19.5 + - - -
205Y SER* 3.5 11.9 + - - -
206Y PHE* 3.6 26.8 - - - -
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Residues in contact with SER 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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4Y LEU* 4.1 13.0 - - - -
134Y ALA* 3.8 25.9 - - - +
137Y VAL* 3.4 24.6 - - - +
138Y LEU* 3.4 23.4 + - - +
154Y LEU* 2.8 24.2 + - - +
155Y GLY* 3.6 4.7 - - - -
157Y ARG* 1.3 71.0 - - - +
159Y ILE* 1.3 64.7 + - - +
161Y ALA* 3.4 4.9 + - - +
162Y ALA* 3.3 15.4 + - - +
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Residues in contact with ILE 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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2Y THR* 3.6 39.9 - - + +
4Y LEU* 3.2 31.0 - - + -
15Y ALA* 3.7 23.3 - - + +
16Y VAL 4.0 8.5 - - - +
17Y ASP* 4.1 16.8 - - + +
155Y GLY 3.0 10.6 + - - +
156Y LYS 3.5 7.0 - - - +
158Y SER* 1.3 73.6 - - - +
160Y LEU* 1.3 65.7 + - - +
162Y ALA* 3.0 5.3 + - - +
163Y ALA* 2.8 24.1 + - + +
172Y SER 4.7 0.2 - - - +
173Y VAL* 3.6 26.2 - - + -
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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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156Y LYS 2.9 13.0 + - - +
157Y ARG* 3.4 15.7 - - - +
159Y ILE* 1.3 76.2 - - - +
161Y ALA* 1.3 64.3 + - - +
163Y ALA* 3.1 5.6 + - - +
164Y HIS* 3.0 24.6 + - + +
173Y VAL* 4.6 2.4 - - - +
192Y VAL* 3.8 30.3 - - + -
195Y LEU* 4.1 21.1 - - + -
196Y PHE* 4.1 20.0 - - + -
199Y VAL* 4.0 31.9 - - + -
206Y PHE* 3.8 27.6 - - + -
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Residues in contact with ALA 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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136J SER* 4.0 14.1 - - - +
139J ASP* 5.3 0.8 - - + +
133Y PHE* 4.1 5.0 - - - +
137Y VAL* 3.4 33.0 - - + -
157Y ARG* 2.8 24.0 + - - +
158Y SER 3.4 9.6 - - - +
160Y LEU* 1.3 73.5 - - - +
162Y ALA* 1.3 61.8 + - - +
164Y HIS* 3.4 3.8 + - - +
165Y ARG* 3.2 25.3 + - - +
206Y PHE* 4.6 7.9 - - + -
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Residues in contact with ALA 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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2Y THR* 3.1 33.9 - - + +
130Y GLY* 3.7 19.1 - - - +
133Y PHE* 3.7 14.1 - - + -
134Y ALA 4.3 0.9 - - - +
158Y SER 3.3 5.9 + - - +
159Y ILE 3.0 7.6 + - - +
161Y ALA* 1.3 75.7 - - - +
163Y ALA* 1.3 68.3 + - - +
164Y HIS 3.1 1.6 - - - -
166Y ASP* 2.9 28.4 + - - +
169Y SER* 4.1 2.2 - - - -
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Residues in contact with ALA 163 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194I ASP* 3.5 10.9 - - + +
2Y THR* 5.7 0.2 - - - -
17Y ASP* 5.5 1.3 - - + -
159Y ILE* 2.8 16.1 + - + +
160Y LEU* 3.5 9.4 - - - +
162Y ALA* 1.3 76.7 - - - +
164Y HIS* 1.3 59.4 + - - +
169Y SER* 3.9 13.2 - - - -
170Y GLY* 3.8 20.0 - - - +
192Y VAL* 4.1 22.0 - - + -
301Y MG 2.4 31.0 - - - -
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Residues in contact with HIS 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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29I ASN* 4.4 1.1 - - - -
171I TRP* 2.9 55.6 + + - -
193I GLN* 2.8 33.8 + - + +
194I ASP* 4.6 1.6 - - - -
139J ASP* 3.4 24.0 - - - -
160Y LEU* 3.0 16.2 + - + +
161Y ALA 3.6 4.0 - - - +
163Y ALA* 1.3 81.1 - - - +
165Y ARG* 1.3 61.6 + - - +
166Y ASP 4.9 0.3 - - - +
192Y VAL* 6.2 0.4 - - - -
196Y PHE* 3.7 13.2 - + + -
206Y PHE* 3.7 20.4 - + + -
208Y ASN* 3.1 21.0 + - - -
209Y VAL* 3.7 23.5 - - + +
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Residues in contact with ARG 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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19I ARG* 5.2 0.2 + - - -
24I SER 3.1 5.5 - - - +
25I LEU* 3.8 4.3 - - + -
26I GLY* 2.8 61.1 + - - -
27I VAL* 3.5 19.2 + - - +
29I ASN* 4.5 1.4 + - - -
171I TRP* 3.9 14.2 - - - -
124J TYR* 4.0 9.9 - - - -
135J PHE* 3.5 35.3 - - + +
136J SER* 4.7 4.0 - - - +
139J ASP* 2.7 44.3 + - - +
133Y PHE* 3.5 29.8 - - + -
161Y ALA 3.2 11.9 + - - +
164Y HIS* 1.3 79.7 - - + +
166Y ASP* 1.3 60.2 + - - +
167Y ALA 3.8 0.3 + - - -
208Y ASN* 3.2 22.0 + - - +
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Residues in contact with ASP 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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24I SER* 3.6 21.3 - - - -
129Y SER* 2.7 31.7 + - - -
130Y GLY* 3.1 9.7 + - - -
133Y PHE* 3.7 19.5 - - + -
162Y ALA 2.9 20.4 + - - +
163Y ALA 3.4 1.2 - - - +
164Y HIS 5.1 0.2 - - - -
165Y ARG* 1.3 72.5 - - - +
167Y ALA* 1.3 64.7 + - - +
168Y TYR* 3.1 10.9 + - - +
169Y SER* 2.7 26.9 + - - +
301Y MG 2.3 27.8 - - - -
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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