Contacts of the helix formed by residues 162 - 174 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.7 25.6 - - - -
158H MET* 5.5 2.2 - - - +
160H LYS 3.4 2.8 + - - -
161H VAL* 1.3 78.2 - - - +
163H VAL* 1.3 63.5 + - - +
165H ALA* 3.0 24.5 + - - +
166H THR* 3.0 31.8 + - - -
184H ASN 5.2 0.6 + - - -
186H ALA* 4.0 4.9 - - - +
501H EPZ 2.8 32.5 + - - -
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Residues in contact with VAL 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TRP* 4.8 7.2 - - + -
161H VAL* 5.1 1.3 - - + +
162H SER* 1.3 71.1 - - - +
164H GLY* 1.3 62.9 + - - +
166H THR* 3.5 1.7 + - - -
167H VAL* 3.2 25.4 + - + +
186H ALA* 3.9 10.2 - - + +
188H GLU* 3.4 44.4 - - + +
190H GLU* 6.0 4.7 - - + +
191H ILE* 4.1 13.8 - - + +
501H EPZ 2.7 55.4 + - - +
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Residues in contact with GLY 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TRP* 3.1 21.0 + - - -
125H HIS* 3.0 25.1 - - - -
162H SER* 3.3 1.5 - - - -
163H VAL* 1.3 76.2 - - - +
165H ALA* 1.3 56.1 + - - +
167H VAL 3.3 1.0 + - - -
168H THR 3.0 21.1 + - - -
501H EPZ 2.9 25.2 + - - -
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Residues in contact with ALA 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.6 26.2 - - + +
125H HIS* 3.3 16.3 + - + +
158H MET* 3.6 24.0 - - + -
162H SER* 3.0 19.0 + - - +
164H GLY* 1.3 73.0 - - - +
166H THR* 1.3 65.7 + - - +
168H THR* 3.1 2.1 + - - -
169H ILE* 3.0 31.0 + - + +
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Residues in contact with THR 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H MET* 4.2 13.8 - - - -
162H SER 3.0 24.6 + - - -
163H VAL 3.9 0.2 - - - -
165H ALA* 1.3 76.6 - - - +
167H VAL* 1.3 57.9 + - - +
170H MET* 3.0 28.7 + - + +
182H ILE* 4.1 7.3 - - + +
185H ALA* 3.7 15.0 - - + +
186H ALA 3.1 16.8 + - - -
191H ILE* 3.7 28.7 - - + -
213H ILE* 3.8 27.6 - - + -
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Residues in contact with VAL 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PRO* 4.1 23.3 - - + +
95H TRP* 3.6 33.4 - - + +
163H VAL* 3.2 18.0 + - + +
164H GLY 3.7 4.0 - - - +
165H ALA 3.1 0.6 - - - -
166H THR* 1.3 76.9 - - - +
168H THR* 1.3 65.3 + - - +
170H MET* 4.6 10.8 - - + -
171H CYS* 3.0 39.3 + - - -
190H GLU 5.6 0.2 - - - +
191H ILE* 3.9 26.9 - - + -
194H THR* 4.7 4.0 - - + +
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Residues in contact with THR 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H ILE 5.0 3.6 + - - -
95H TRP* 3.5 13.1 - - - -
97H LEU* 6.0 1.6 - - + -
98H GLY* 4.5 14.4 + - - +
99H PRO* 6.2 0.9 - - - -
125H HIS* 2.7 46.1 + - + +
129H LEU* 4.0 31.4 - - + -
164H GLY 3.0 6.5 + - - -
165H ALA* 3.1 6.2 + - - +
167H VAL* 1.3 78.5 - - - +
169H ILE* 1.3 63.9 + - + +
171H CYS* 4.0 3.3 - - - +
172H ALA* 3.2 22.3 + - - +
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Residues in contact with ILE 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU 4.3 4.5 - - - +
128H GLY* 3.6 31.4 - - - -
129H LEU* 5.2 0.9 - - + -
132H LEU* 4.1 10.1 - - + +
156H ILE* 3.8 29.2 - - + -
158H MET* 3.4 38.4 - - + -
165H ALA* 3.0 11.2 + - - +
168H THR* 1.3 79.1 - - + +
170H MET* 1.3 65.7 + - - +
172H ALA* 3.4 4.5 + - - +
173H ALA* 3.0 23.4 + - - +
180H THR* 4.6 5.4 - - + -
182H ILE* 3.7 23.6 - - + -
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Residues in contact with MET 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H THR* 3.0 21.0 + - + +
167H VAL* 4.1 9.9 - - + +
168H THR 3.4 0.2 - - - -
169H ILE* 1.3 80.4 - - - +
171H CYS* 1.3 62.8 + - - +
173H ALA* 3.6 6.4 + - - +
174H THR* 3.5 15.1 + - - +
182H ILE* 3.8 13.7 - - + +
191H ILE* 3.7 29.8 - - + +
194H THR* 4.2 15.7 - - + -
195H ALA* 3.9 29.6 - - - +
198H LEU* 4.5 4.7 - - + -
205H ILE* 4.2 14.6 - - + -
208H GLN* 5.3 0.2 - - - -
213H ILE* 4.2 26.5 - - - -
215H ILE* 4.2 13.3 - - + +
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Residues in contact with CYS 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PRO 5.2 1.3 - - - -
31H ALA* 4.0 20.4 - - - -
34H LEU* 3.5 19.4 - - + +
99H PRO* 4.6 16.2 - - + -
167H VAL* 3.0 36.0 + - - +
168H THR* 4.1 2.5 - - - +
170H MET* 1.3 76.5 - - - +
172H ALA* 1.3 62.4 + - - +
174H THR* 2.8 26.0 + - - -
194H THR* 4.2 6.5 - - - -
198H LEU* 3.8 23.3 - - - -
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Residues in contact with ALA 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLY* 4.2 10.4 - - - +
102H ALA* 3.4 28.0 - - + +
129H LEU* 3.8 24.9 - - + -
132H LEU* 3.9 8.5 - - + -
151H LEU* 3.8 20.5 - - + +
168H THR 3.2 17.9 + - - +
169H ILE 3.9 0.2 - - - +
171H CYS* 1.3 75.7 - - - +
173H ALA* 1.3 61.8 + - - +
174H THR 3.4 0.5 + - - -
175H LEU 3.4 5.4 + - - -
176H ALA* 3.9 4.0 + - - +
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Residues in contact with ALA 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H LEU* 4.1 5.4 - - + +
169H ILE 3.0 16.9 + - - +
170H MET 3.8 3.8 - - - +
171H CYS 3.1 0.6 - - - -
172H ALA* 1.3 74.8 - - - +
174H THR* 1.3 61.4 + - - +
175H LEU 2.9 7.6 + - - -
176H ALA* 3.0 22.0 + - - +
178H GLY 5.2 0.7 - - - +
180H THR* 3.6 33.1 + - + +
215H ILE* 3.7 24.5 - - + +
217H GLY* 3.8 6.4 + - - -
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Residues in contact with THR 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 3.5 15.8 - - - +
170H MET 3.5 15.5 - - - +
171H CYS 2.8 16.8 + - - +
173H ALA* 1.3 75.9 - - - +
175H LEU* 1.3 59.9 + - - +
176H ALA 3.6 0.4 - - - -
198H LEU* 4.0 17.7 - - + -
203H ALA* 3.7 29.8 - - + -
205H ILE* 4.0 8.3 - - + -
215H ILE* 3.8 11.2 - - + -
216H GLU 5.2 0.9 - - - -
217H GLY* 3.6 1.9 - - - -
218H VAL* 3.1 32.2 + - - +
221H LEU* 3.7 8.2 - - - +
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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