Contacts of the helix formed by residues 162 - 174 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G LEU* 3.8 17.9 - - - -
158G MET* 5.5 2.0 - - - +
160G LYS 3.4 3.0 + - - -
161G VAL* 1.3 78.4 - - - +
163G VAL* 1.3 63.0 + - - +
165G ALA* 3.0 23.8 + - - +
166G THR* 3.0 28.0 + - - -
184G ASN 5.2 0.4 + - - -
186G ALA* 3.9 5.6 - - - +
501G EPZ 2.9 40.3 + - - -
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Residues in contact with VAL 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TRP* 4.8 7.0 - - + -
161G VAL* 5.1 1.5 - - + +
162G SER* 1.3 71.6 - - - +
164G GLY* 1.3 63.5 + - - +
166G THR* 3.9 1.2 - - - -
167G VAL* 3.2 25.7 + - + +
186G ALA* 3.8 10.9 - - + +
188G GLU* 3.5 42.6 - - + +
190G GLU* 6.0 4.3 - - + -
191G ILE* 4.1 15.0 - - + +
501G EPZ 2.8 54.2 + - - +
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Residues in contact with GLY 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TRP* 3.1 24.9 + - - -
125G HIS* 3.1 20.0 - - - -
162G SER* 3.3 2.6 + - - -
163G VAL* 1.3 75.9 - - - +
165G ALA* 1.3 57.4 + - - +
167G VAL 3.3 1.9 + - - -
168G THR 3.0 21.1 + - - -
501G EPZ 2.8 22.8 + - - -
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Residues in contact with ALA 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 3.7 26.7 - - + +
125G HIS* 3.4 16.7 + - + -
158G MET* 3.6 24.0 - - + -
162G SER* 3.0 18.2 + - - +
164G GLY* 1.3 70.9 - - - +
166G THR* 1.3 67.1 + - - +
168G THR* 4.3 0.9 - - - -
169G ILE* 3.0 31.4 + - - +
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Residues in contact with THR 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G MET* 4.3 12.8 - - - -
162G SER 3.0 20.9 + - - -
165G ALA* 1.3 75.1 - - - +
167G VAL* 1.3 58.4 + - - +
169G ILE* 5.0 0.2 - - - -
170G MET* 3.0 29.0 + - + +
182G ILE* 4.1 8.7 - - + +
185G ALA* 3.7 14.7 - - + -
186G ALA 3.1 16.2 + - - +
191G ILE* 3.7 27.4 - - + -
213G ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO* 4.1 23.8 - - + +
95G TRP* 3.6 30.7 - - + +
163G VAL* 3.2 16.1 + - + +
164G GLY 3.6 7.2 - - - +
165G ALA 3.1 0.4 - - - -
166G THR* 1.3 75.7 - - - +
168G THR* 1.3 65.4 + - - +
170G MET* 4.0 10.7 - - + +
171G CYS* 3.0 39.7 + - - -
190G GLU 5.9 0.4 - - - -
191G ILE* 3.8 27.4 - - + -
194G THR* 4.7 5.6 - - + +
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Residues in contact with THR 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G ILE 5.0 1.7 + - - -
95G TRP* 3.5 15.4 - - - -
97G LEU* 6.0 1.3 - - + -
98G GLY* 4.5 14.1 + - - +
99G PRO* 6.2 1.3 - - - -
125G HIS* 2.7 44.2 + - + +
129G LEU* 4.1 31.9 - - + -
164G GLY 3.0 7.2 + - - -
165G ALA* 3.2 6.3 + - - +
167G VAL* 1.3 79.1 - - - +
169G ILE* 1.3 65.1 + - + +
171G CYS* 4.0 3.1 - - - +
172G ALA* 3.2 22.5 + - - +
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Residues in contact with ILE 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU 4.3 3.4 - - - +
125G HIS 5.1 0.7 - - - +
128G GLY* 3.6 31.2 - - - -
129G LEU* 5.2 0.7 - - - -
132G LEU* 4.1 10.6 - - + +
156G ILE* 3.9 28.7 - - + -
158G MET* 3.5 37.7 - - + -
165G ALA 3.0 12.3 + - - +
168G THR* 1.3 77.1 - - + +
170G MET* 1.3 67.7 + - - +
172G ALA* 3.4 4.9 + - - +
173G ALA* 3.0 22.5 + - - +
180G THR* 4.6 5.2 - - + -
182G ILE* 3.7 22.7 - - + -
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Residues in contact with MET 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G THR* 3.0 21.0 + - + +
167G VAL* 4.0 9.9 - - + +
169G ILE* 1.3 78.3 - - - +
171G CYS* 1.3 61.9 + - - +
173G ALA* 3.5 8.5 + - - +
174G THR* 3.5 13.9 + - - +
182G ILE* 3.8 14.7 - - + +
191G ILE* 3.7 30.5 - - + +
194G THR* 4.2 15.5 - - + -
195G ALA* 3.9 29.8 - - - +
198G LEU* 4.5 4.7 - - + -
205G ILE* 4.2 14.6 - - + -
213G ILE* 4.1 28.3 - - - -
215G ILE* 4.2 12.8 - - + +
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Residues in contact with CYS 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G PRO 5.3 0.7 - - - -
31G ALA* 4.1 19.3 - - + -
34G LEU* 3.6 19.5 - - + +
99G PRO* 4.6 15.7 - - + -
167G VAL* 3.0 35.9 + - - +
168G THR* 4.1 2.9 - - - +
170G MET* 1.3 75.1 - - - +
172G ALA* 1.3 63.7 + - - +
173G ALA 3.2 0.2 + - - -
174G THR* 2.8 25.1 + - - -
194G THR* 4.2 7.6 - - - -
198G LEU* 3.8 25.1 - - - -
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Residues in contact with ALA 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLY* 4.2 10.9 - - - +
102G ALA* 3.4 26.1 - - + +
129G LEU* 3.8 25.1 - - + -
132G LEU* 3.9 8.5 - - + -
151G LEU* 3.8 21.1 - - + +
168G THR 3.2 17.8 + - - +
171G CYS* 1.3 76.5 - - - +
173G ALA* 1.3 62.1 + - - +
174G THR 3.4 0.3 + - - -
175G LEU 3.4 5.7 + - - -
176G ALA* 3.9 4.3 + - - +
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Residues in contact with ALA 173 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU* 4.0 5.6 - - + +
169G ILE 3.0 18.0 + - - +
170G MET 3.8 5.4 - - - +
171G CYS 3.2 0.4 - - - -
172G ALA* 1.3 73.8 - - - +
174G THR* 1.3 62.4 + - - +
175G LEU 2.9 6.9 + - - -
176G ALA* 3.0 21.4 + - - +
178G GLY 5.2 0.5 - - - +
180G THR* 3.5 36.4 + - + +
215G ILE* 3.7 18.7 - - + +
217G GLY* 3.8 7.1 + - - -
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Residues in contact with THR 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 3.5 15.6 - - - +
170G MET 3.5 15.9 - - - +
171G CYS 2.8 16.2 + - - +
173G ALA* 1.3 75.1 - - - +
175G LEU* 1.3 61.6 + - - +
198G LEU* 3.9 18.2 - - + -
203G ALA* 3.8 28.9 - - + -
205G ILE* 4.0 8.5 - - + -
215G ILE* 3.8 12.1 - - + -
216G GLU 5.1 0.7 - - - -
217G GLY* 4.1 2.5 - - - -
218G VAL* 3.1 31.7 + - - +
221G 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