Contacts of the helix formed by residues 162 - 174 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C LEU* 3.8 24.9 - - - -
158C MET* 5.4 3.1 - - - +
160C LYS 3.5 2.4 + - - -
161C VAL* 1.3 77.8 - - - +
163C VAL* 1.3 62.0 + - - +
165C ALA* 3.0 23.6 + - - +
166C THR* 2.9 33.0 + - - -
184C ASN 5.2 0.8 + - - -
186C ALA* 3.9 6.0 - - - +
501C EPZ 2.8 33.8 + - - -
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 6.5 0.2 - - + -
95C TRP* 4.8 10.3 - - + -
161C VAL* 5.2 1.1 - - + +
162C SER* 1.3 71.3 - - - +
164C GLY* 1.3 62.8 + - - +
166C THR* 3.9 1.6 - - - -
167C VAL* 3.2 25.0 + - + +
186C ALA* 3.9 9.8 - - + +
188C GLU* 3.5 43.3 - - + +
190C GLU* 5.9 4.7 - - + -
191C ILE* 4.1 14.8 - - + +
501C EPZ 2.8 51.2 + - - +
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Residues in contact with GLY 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TRP* 3.1 24.6 + - - -
125C HIS* 3.1 21.5 - - - -
162C SER* 3.3 1.1 - - - -
163C VAL* 1.3 76.8 - - - +
165C ALA* 1.3 56.3 + - - +
167C VAL 3.4 0.5 + - - -
168C THR 3.0 22.2 + - - -
501C EPZ 2.9 25.2 + - - -
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 3.7 26.0 - - + +
125C HIS* 3.4 17.1 - - + +
158C MET* 3.6 24.2 - - + -
162C SER* 3.0 19.3 + - - +
164C GLY* 1.3 74.0 - - - +
166C THR* 1.3 65.5 + - - +
168C THR* 3.2 1.4 + - - -
169C ILE* 3.0 30.7 + - - +
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Residues in contact with THR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C MET* 4.3 12.7 - - - -
162C SER 2.9 23.0 + - - -
163C VAL 3.9 0.2 - - - -
165C ALA* 1.3 76.8 - - - +
167C VAL* 1.3 56.6 + - - +
170C MET* 2.9 32.9 + - + +
182C ILE* 4.1 7.7 - - + +
185C ALA* 3.8 15.5 - - + -
186C ALA 3.1 15.6 + - - +
191C ILE* 3.8 27.6 - - + -
213C ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 4.1 23.1 - - + +
95C TRP* 3.7 31.0 - - + +
163C VAL* 3.2 18.7 + - + +
164C GLY 3.7 3.6 - - - +
165C ALA 3.1 0.4 - - - -
166C THR* 1.3 76.1 - - - +
168C THR* 1.3 64.9 - - - +
170C MET* 4.5 10.8 - - + -
171C CYS* 3.0 39.5 + - - -
190C GLU 5.9 0.2 - - - -
191C ILE* 3.9 27.8 - - + -
194C THR* 4.7 3.8 - - + +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE 5.0 3.3 + - - -
95C TRP* 3.5 13.8 - - - -
97C LEU* 6.0 1.3 - - + -
98C GLY* 4.5 14.2 + - - +
99C PRO* 6.2 1.3 - - - -
125C HIS* 2.7 43.8 + - + +
129C LEU* 4.1 31.2 - - + -
164C GLY 3.0 9.2 + - - -
165C ALA* 3.2 7.4 + - - +
167C VAL* 1.3 78.5 - - - +
169C ILE* 1.3 64.2 + - + +
171C CYS* 4.1 3.0 - - - +
172C ALA* 3.2 22.3 + - - +
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Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU 4.4 3.4 - - - +
125C HIS* 5.1 0.4 - - - +
128C GLY* 3.6 31.6 - - - -
129C LEU* 5.3 0.9 - - + -
132C LEU* 4.1 10.4 - - + +
156C ILE* 3.9 28.7 - - + -
158C MET* 3.5 37.5 - - + -
165C ALA 3.0 11.9 + - - +
166C THR* 5.2 0.2 - - - -
168C THR* 1.3 79.1 - - + +
170C MET* 1.3 66.9 + - - +
172C ALA* 3.3 4.4 + - - +
173C ALA* 3.0 23.0 + - - +
180C THR* 4.5 5.4 - - + -
182C ILE* 3.7 24.0 - - + -
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Residues in contact with MET 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C THR* 2.9 21.0 + - + +
167C VAL* 4.1 10.8 - - + +
169C ILE* 1.3 78.9 - - - +
171C CYS* 1.3 61.4 + - - +
173C ALA* 3.5 6.8 + - - +
174C THR* 3.5 16.1 + - - +
182C ILE* 3.7 14.8 - - + +
191C ILE* 3.8 31.0 - - + +
194C THR* 4.2 15.5 - - + -
195C ALA* 3.9 29.2 - - - +
198C LEU* 4.5 4.7 - - + -
205C ILE* 4.3 14.6 - - + -
208C GLN* 5.4 0.7 - - - -
213C ILE* 4.2 26.0 - - - -
215C ILE* 4.2 13.7 - - + +
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Residues in contact with CYS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO 5.2 0.9 - - - -
31C ALA* 4.1 19.3 - - - -
34C LEU* 3.5 19.7 - - + +
99C PRO* 4.6 15.7 - - + -
167C VAL* 3.0 36.4 + - - +
168C THR* 4.2 2.9 - - - +
170C MET* 1.3 74.6 - - - +
172C ALA* 1.3 62.7 + - - +
174C THR* 2.8 26.5 + - - -
175C LEU 4.5 0.2 + - - -
194C THR* 4.2 7.0 - - - -
198C LEU* 3.9 24.5 - - - -
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLY* 4.3 9.9 - - - +
102C ALA* 3.4 23.7 - - + +
129C LEU* 3.8 24.9 - - + -
132C LEU* 3.9 13.0 - - + -
151C LEU* 3.9 15.1 - - + +
168C THR 3.2 19.0 + - - +
169C ILE 3.9 0.2 - - - +
171C CYS* 1.3 76.2 - - - +
173C ALA* 1.3 62.9 + - - +
174C THR 3.4 0.3 + - - -
175C LEU 3.4 9.0 + - - -
176C ALA* 3.9 4.9 + - - +
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 4.1 5.4 - - + +
169C ILE 3.0 17.4 + - - +
170C MET 3.8 3.6 - - - +
171C CYS 3.2 0.2 - - - -
172C ALA* 1.3 74.1 - - - +
174C THR* 1.3 58.0 + - - +
175C LEU 2.9 11.9 + - - -
176C ALA* 3.0 22.0 + - - +
178C GLY 5.2 0.5 - - - +
180C THR* 3.6 34.1 + - + +
215C ILE* 3.7 22.1 - - + +
217C GLY* 3.8 6.8 + - - -
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Residues in contact with THR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.5 14.7 - - - +
170C MET 3.5 15.5 - - - +
171C CYS 2.8 17.0 + - - +
173C ALA* 1.3 75.3 - - - +
175C LEU* 1.3 59.0 + - - +
198C LEU* 4.0 18.4 - - + -
203C ALA* 3.8 28.9 - - + +
204C LYS 6.0 0.2 - - - +
205C ILE* 4.0 8.7 - - + -
215C ILE* 3.8 12.8 - - + -
216C GLU 5.1 0.9 - - - -
217C GLY* 3.6 2.6 - - - -
218C VAL* 3.1 32.2 + - - +
221C 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
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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