Contacts of the helix formed by residues 154 - 169 (chain X) in PDB entry 1SHT
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 154 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152X ASP 3.3 0.4 + - - -
153X GLY* 1.3 75.6 - - - +
155X VAL* 1.3 65.2 + - - +
156X PRO* 3.3 2.0 - - - -
157X SER* 2.9 35.6 + - - +
158X TYR* 3.1 43.3 + - + +
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Residues in contact with VAL 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X THR 3.5 21.1 - - - +
119X TYR* 4.1 20.0 - - + -
120X ILE* 4.1 6.7 - - + -
121X HIS* 3.8 29.4 - - + +
151X LEU* 4.0 17.3 - - + -
152X ASP 3.0 20.9 + - - +
154X LEU* 1.3 79.0 - - - +
156X PRO* 1.3 66.0 - - + +
158X TYR* 3.2 11.2 + - + +
159X ALA* 2.8 22.2 + - - +
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Residues in contact with PRO 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X LEU* 3.9 27.6 - - + +
152X ASP 3.6 10.1 - - - +
153X GLY 3.4 17.3 - - - +
154X LEU 3.5 0.9 - - - -
155X VAL* 1.3 90.4 - - + +
157X SER* 1.3 60.9 + - - +
159X ALA* 3.8 0.6 - - + +
160X GLU* 3.0 38.7 + - - +
185X GLN* 3.4 24.2 - - - +
188X ARG* 5.3 1.8 - - - +
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Residues in contact with SER 157 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X LEU* 2.9 31.2 + - - +
156X PRO* 1.3 78.8 - - - +
158X TYR* 1.3 72.0 + - - +
160X GLU* 3.5 6.1 + - - +
161X LYS* 3.1 26.3 + - - +
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Residues in contact with TYR 158 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X HIS* 3.5 45.5 - + + +
154X LEU* 3.1 45.9 + - + +
155X VAL* 3.6 7.2 - - + +
157X SER* 1.3 93.1 + - - +
159X ALA* 1.3 58.0 + - - +
161X LYS* 3.7 12.6 - - + +
162X GLU* 3.0 29.8 + - - +
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Residues in contact with ALA 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X ILE* 3.5 28.5 - - + -
121X HIS* 3.7 11.1 - - - +
124X LEU* 3.8 8.7 - - + +
151X LEU* 4.1 4.5 - - + -
155X VAL 2.8 19.8 + - - +
156X PRO* 3.8 3.1 - - + +
158X TYR* 1.3 70.4 - - - +
160X GLU* 1.3 65.6 + - - +
162X GLU* 3.3 0.6 + - - -
163X ALA* 3.0 25.3 + - - +
189X ILE* 4.0 20.0 - - + -
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Residues in contact with GLU 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156X PRO* 3.0 25.1 + - - +
157X SER* 4.1 5.2 - - - +
159X ALA* 1.3 74.9 - - - +
161X LYS* 1.3 62.8 + - - +
163X ALA* 3.4 3.4 + - - +
164X LYS* 3.1 36.0 + - - +
167X ARG* 4.8 1.2 + - - -
185X GLN* 2.8 31.3 + - - +
188X ARG* 3.0 55.1 + - - +
189X ILE* 4.5 2.0 - - + -
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Residues in contact with LYS 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X SER 3.1 19.5 + - - +
158X TYR* 3.7 11.7 - - + +
160X GLU* 1.3 77.9 - - - +
162X GLU* 1.3 64.2 + - - +
164X LYS* 3.3 11.7 + - + +
165X ILE* 3.0 37.5 + - + +
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Residues in contact with GLU 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X HIS* 3.8 9.5 - - + +
124X LEU* 3.6 25.8 - - + -
125X LYS* 3.7 32.9 - - - +
128X ASN* 2.7 40.9 + - - +
158X TYR 3.0 18.9 + - - +
159X ALA* 3.3 3.6 + - - +
161X LYS* 1.3 78.4 - - - +
163X ALA* 1.3 57.2 + - - +
165X ILE* 3.3 22.1 + - - +
166X SER* 2.9 23.0 + - - -
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Residues in contact with ALA 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X LEU* 4.5 6.7 - - + +
159X ALA 3.0 16.1 + - - +
160X GLU 3.9 4.3 - - - +
161X LYS 3.2 0.2 - - - -
162X GLU* 1.3 74.1 - - - +
164X LYS* 1.3 60.8 + - - +
166X SER* 3.2 10.6 + - - -
167X ARG* 3.0 37.3 + - - +
173X VAL* 4.5 5.4 - - + -
189X ILE* 3.3 41.5 - - + +
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Residues in contact with LYS 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X GLU* 3.1 25.6 + - - +
161X LYS* 3.3 11.9 + - - +
163X ALA* 1.3 74.9 - - - +
165X ILE* 1.3 64.4 + - - +
167X ARG* 3.3 23.5 + - - +
168X SER* 3.0 22.2 + - - -
188X ARG 5.8 2.5 - - - -
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Residues in contact with ILE 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ASN* 3.8 14.1 - - + +
132X GLN* 5.6 2.7 - - - +
161X LYS* 3.0 36.3 + - + +
162X GLU* 3.3 29.6 + - - +
164X LYS* 1.3 72.0 - - - +
166X SER* 1.4 67.7 + - - +
168X SER* 2.6 27.3 + - - +
169X LEU* 3.1 21.7 + - + +
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Residues in contact with SER 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X LEU* 4.9 4.0 + - - +
128X ASN* 2.5 33.4 + - - -
143X ILE* 3.3 23.7 - - - +
162X GLU 2.9 13.3 + - - -
163X ALA* 3.2 12.1 + - - -
165X ILE* 1.4 72.0 - - - +
167X ARG* 1.3 64.4 + - - +
169X LEU* 3.0 15.3 + - - +
170X GLY 3.4 0.2 + - - -
171X ALA* 3.1 23.0 + - - +
173X VAL* 3.8 11.4 - - - +
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Residues in contact with ARG 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X LEU* 5.3 0.5 - - - +
160X GLU 4.8 0.2 + - - -
163X ALA* 3.0 23.6 + - - +
164X LYS* 3.7 25.8 - - - +
165X ILE 3.2 0.2 - - - -
166X SER* 1.3 75.2 - - - +
168X SER* 1.3 58.0 + - - +
170X GLY* 3.0 20.3 + - - -
171X ALA 3.5 13.9 - - - +
173X VAL* 3.5 10.1 - - + +
188X ARG 4.0 10.9 + - - -
189X ILE 2.9 29.1 + - - -
190X ALA 4.0 8.0 + - - -
191X ASP* 3.0 46.6 + - - +
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Residues in contact with SER 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X LEU* 3.6 19.4 - - - +
164X LYS 3.0 11.4 + - - -
165X ILE* 2.6 29.7 + - - +
167X ARG* 1.3 76.2 - - - +
169X LEU* 1.3 61.4 + - - +
170X GLY 3.2 1.8 + - - -
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Residues in contact with LEU 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ASN* 3.9 32.8 - - + +
131X ILE* 4.1 16.1 - - + +
132X GLN* 3.7 36.3 - - + +
136X GLY* 3.1 40.1 - - - +
137X LEU* 3.4 9.7 + - + +
139X THR* 4.7 0.7 + - - -
141X SER* 5.8 0.2 - - - -
165X ILE* 3.1 21.5 + - + +
166X SER* 3.0 10.3 + - - +
168X SER* 1.3 80.3 - - - +
170X GLY* 1.3 58.7 + - - +
171X ALA 3.5 1.5 + - - -
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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