Contacts of the helix formed by residues 162 - 174 (chain B) in PDB entry 3SWD
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 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.7 16.2 - - - -
158B MET* 5.4 2.2 - - - +
160B LYS 3.5 3.0 + - - -
161B VAL* 1.3 77.8 - - - +
163B VAL* 1.3 63.5 + - - +
165B ALA* 3.0 20.7 + - - +
166B THR* 2.9 33.0 + - - -
184B ASN 5.2 0.4 + - - -
186B ALA* 3.9 4.5 - - - +
501B EPZ 2.8 44.6 + - - -
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 4.8 10.8 - - + -
161B VAL* 5.1 1.7 - - + +
162B SER* 1.3 71.5 - - - +
164B GLY* 1.3 64.0 + - - +
166B THR* 3.9 1.4 - - - -
167B VAL* 3.2 24.8 + - + +
186B ALA* 3.8 9.1 - - + +
188B GLU* 3.5 44.0 - - + +
190B GLU* 6.0 4.5 - - + -
191B ILE* 4.1 14.1 - - + +
501B EPZ 2.6 50.6 + - - +
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 3.1 23.2 + - - -
125B HIS* 3.1 20.2 - - - -
163B VAL* 1.3 78.3 - - - +
165B ALA* 1.3 56.9 + - - +
168B THR 3.1 21.1 + - - -
501B EPZ 3.1 27.7 + - - -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.6 26.2 - - + +
125B HIS* 3.3 16.7 - - + +
158B MET* 3.6 24.5 - - + -
162B SER* 3.0 19.7 + - - +
164B GLY* 1.3 71.6 - - - +
166B THR* 1.3 65.8 + - - +
168B THR* 3.2 1.6 + - - -
169B ILE* 3.0 31.0 + - + +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B MET* 4.3 12.6 - - - -
162B SER 2.9 22.6 + - - -
163B VAL 3.9 0.2 - - - -
165B ALA* 1.3 76.8 - - - +
167B VAL* 1.3 56.1 + - - +
169B ILE* 5.1 0.2 - - - -
170B MET* 3.0 28.5 + - + +
182B ILE* 4.1 8.5 - - + +
185B ALA* 3.8 16.1 - - + +
186B ALA 3.1 15.6 + - - +
191B ILE* 3.7 28.9 - - + -
213B ILE* 3.8 27.6 - - + -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PRO* 4.0 24.0 - - + +
95B TRP* 3.6 31.2 - - + +
163B VAL* 3.2 14.6 + - + +
164B GLY 3.7 7.0 - - - +
165B ALA 3.1 0.6 - - - -
166B THR* 1.3 76.1 - - - +
168B THR* 1.3 64.5 + - - +
170B MET* 4.0 10.5 - - + +
171B CYS* 3.0 39.6 + - - -
190B GLU 5.9 0.2 - - - -
191B ILE* 3.9 27.1 - - + -
194B THR* 4.7 5.4 - - + +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE 5.1 2.3 + - - +
95B TRP* 3.5 15.1 - - - -
97B LEU* 6.0 0.9 - - + -
98B GLY* 4.4 14.4 + - - +
99B PRO* 6.1 1.1 - - - -
125B HIS* 2.7 44.3 + - + +
129B LEU* 4.1 31.0 - - + -
164B GLY 3.1 5.3 + - - -
165B ALA* 3.2 6.3 + - - -
167B VAL* 1.3 78.6 - - - +
169B ILE* 1.3 64.2 + - + +
171B CYS* 4.1 2.9 - - - +
172B ALA* 3.2 23.0 + - - +
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 4.4 3.8 - - - +
125B HIS* 5.0 0.4 - - - +
128B GLY* 3.6 33.4 - - - -
129B LEU* 4.7 2.0 - - + +
132B LEU* 4.1 12.9 - - + +
156B ILE* 3.9 28.9 - - + -
158B MET* 3.5 37.7 - - + -
165B ALA* 3.0 11.3 + - - +
166B THR* 5.2 0.2 - - - -
168B THR* 1.3 78.7 - - + +
170B MET* 1.3 67.7 + - - +
172B ALA* 3.4 2.2 + - - +
173B ALA* 3.0 22.9 + - - +
180B THR* 4.5 5.4 - - + -
182B ILE* 3.7 23.3 - - + -
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 3.0 22.0 + - + +
167B VAL* 4.0 10.1 - - + +
169B ILE* 1.3 78.9 - - - +
171B CYS* 1.3 60.7 + - - +
173B ALA* 3.5 8.5 + - - +
174B THR* 3.5 14.7 + - - +
182B ILE* 3.8 14.5 - - + +
191B ILE* 3.8 30.7 - - + +
194B THR* 4.2 15.5 - - + -
195B ALA* 3.9 28.9 - - - +
198B LEU* 4.4 4.7 - - + -
205B ILE* 4.2 15.5 - - + -
213B ILE* 4.1 27.4 - - - -
215B ILE* 4.2 12.6 - - + +
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Residues in contact with CYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PRO 5.2 1.1 - - - -
31B ALA* 4.0 21.1 - - - -
34B LEU* 3.5 19.2 - - + +
99B PRO* 4.6 15.7 - - + -
167B VAL* 3.0 36.0 + - - +
168B THR* 4.2 3.6 - - - +
170B MET* 1.3 75.6 - - - +
172B ALA* 1.3 61.1 + - - +
174B THR* 2.8 25.5 + - - -
175B LEU 4.5 0.2 + - - -
194B THR* 4.2 6.5 - - - -
198B LEU* 3.9 24.2 - - - -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 4.2 10.7 - - - +
102B ALA* 3.4 27.0 - - + +
129B LEU* 3.8 23.8 - - + -
132B LEU* 3.9 8.5 - - + -
151B LEU* 3.8 21.3 - - + +
168B THR 3.2 18.8 + - - +
169B ILE 3.4 0.4 + - - +
171B CYS* 1.3 75.3 - - - +
173B ALA* 1.3 62.0 + - - +
175B LEU 3.5 5.7 + - - -
176B ALA* 3.9 4.9 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.1 5.8 - - + +
169B ILE 3.0 17.4 + - - +
170B MET 3.7 5.8 - - - +
171B CYS 3.2 0.6 - - - -
172B ALA* 1.3 73.9 - - - +
174B THR* 1.3 61.5 + - - +
175B LEU 2.9 7.7 + - - -
176B ALA* 3.0 21.6 + - - +
178B GLY 5.2 0.7 - - - +
180B THR* 3.5 36.5 + - + +
215B ILE* 3.6 18.5 - - + +
217B GLY* 3.8 6.4 + - - -
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.5 14.6 - - - +
170B MET 3.5 15.3 - - - +
171B CYS 2.8 17.8 + - - +
173B ALA* 1.3 76.5 - - - +
175B LEU* 1.3 58.7 + - - +
176B ALA 3.6 0.2 - - - -
198B LEU* 4.0 18.2 - - + -
203B ALA* 3.7 30.1 - - + -
205B ILE* 4.1 4.5 - - + -
215B ILE* 3.6 16.1 - - + +
216B GLU 5.1 0.9 - - - -
217B GLY* 3.6 2.4 - - - -
218B VAL* 3.1 32.6 + - - +
221B LEU* 3.6 8.9 - - - +
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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
------------------------------------------------------------
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