Contacts of the helix formed by residues 162 - 174 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124K LEU* 3.8 17.7 - - - -
158K MET* 5.2 2.2 - - - +
160K LYS 3.2 4.6 + - - -
161K VAL* 1.3 76.6 - - - +
163K VAL* 1.3 61.4 + - - +
165K ALA* 3.1 19.4 + - - +
166K THR* 3.0 32.3 + - - -
184K ASN 5.1 0.4 + - - -
186K ALA* 3.8 6.6 - - - +
501K EPZ 2.7 45.9 + - - -
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Residues in contact with VAL 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K TRP* 4.6 11.7 - - + -
161K VAL* 4.3 1.9 - - + +
162K SER* 1.3 72.2 - - - +
164K GLY* 1.3 66.6 + - - +
166K THR* 3.7 1.9 - - - -
167K VAL* 3.1 29.9 + - + +
186K ALA* 3.7 11.5 - - + +
188K GLU* 3.4 41.5 - - + +
190K GLU* 5.9 5.6 - - + +
191K ILE* 4.2 9.1 - - + +
501K EPZ 3.0 53.2 + - - +
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Residues in contact with GLY 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K TRP* 3.0 31.9 + - - -
125K HIS* 3.2 18.7 - - - -
162K SER* 3.3 2.5 + - - -
163K VAL* 1.3 76.0 - - - +
165K ALA* 1.3 62.3 + - - +
168K THR 3.1 8.7 + - - -
501K EPZ 2.9 25.3 + - - -
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Residues in contact with ALA 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K LEU* 3.6 39.9 - - + +
125K HIS* 3.1 25.8 + - + -
158K MET* 4.3 9.4 - - + -
162K SER* 3.1 15.1 + - - +
164K GLY* 1.3 73.1 - - - +
166K THR* 1.3 63.7 + - - +
168K THR* 3.0 13.0 + - - -
169K ILE* 3.0 19.3 + - - +
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Residues in contact with THR 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K MET* 4.0 15.1 - - - -
162K SER 3.0 24.0 + - - -
163K VAL 3.7 3.6 - - - -
165K ALA* 1.3 75.5 - - - +
167K VAL* 1.3 58.4 + - - +
169K ILE* 4.0 3.0 - - - +
170K MET* 2.8 31.1 + - + +
182K ILE* 4.6 6.5 - - + +
185K ALA* 3.8 8.8 - - + -
186K ALA 3.3 19.3 + - - +
191K ILE* 3.7 26.0 - - + -
213K ILE* 4.0 25.4 - - + -
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Residues in contact with VAL 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K PRO* 4.2 21.8 - - + +
95K TRP* 3.4 43.1 - - + +
163K VAL* 3.1 17.7 + - + +
164K GLY 3.6 0.9 - - - +
166K THR* 1.3 73.2 - - - +
168K THR* 1.3 65.0 + - - +
170K MET* 4.8 7.0 - - - -
171K CYS* 3.1 36.1 + - - +
190K GLU 6.0 0.2 - - - -
191K ILE* 4.0 27.1 - - + -
194K THR* 4.6 5.8 - - + +
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Residues in contact with THR 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K ILE 5.5 1.6 + - - +
95K TRP* 3.6 12.9 - - - -
97K LEU* 6.0 1.3 - - + -
98K GLY* 4.5 13.7 - - - +
99K PRO* 6.5 0.2 - - - -
125K HIS* 2.6 44.3 + - + +
129K LEU* 3.9 33.7 - - + -
164K GLY 3.1 3.9 + - - -
165K ALA* 3.0 9.9 + - - -
167K VAL* 1.3 77.6 - - - +
169K ILE* 1.3 64.1 + - + +
171K CYS* 3.7 2.4 - - - +
172K ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K LEU 4.6 3.6 - - - +
125K HIS 5.3 0.2 - - - +
128K GLY* 3.3 36.3 - - - +
129K LEU* 4.7 1.6 - - + +
132K LEU* 3.8 21.8 - - + -
156K ILE* 4.0 22.9 - - + -
158K MET* 3.7 30.3 - - + -
165K ALA 3.0 12.4 + - - +
166K THR 4.1 1.3 - - - +
168K THR* 1.3 77.8 - - + +
170K MET* 1.3 70.1 + - - +
171K CYS 2.9 0.5 + - - -
172K ALA* 3.0 1.6 + - - +
173K ALA* 2.9 22.5 + - - +
180K THR* 4.4 5.8 - - + -
182K ILE* 3.9 20.9 - - + -
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Residues in contact with MET 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K THR* 2.8 23.6 + - + +
167K VAL* 4.8 8.3 - - - -
169K ILE* 1.3 75.4 - - - +
171K CYS* 1.3 60.9 + - - +
173K ALA* 3.5 3.1 + - - +
174K THR* 3.2 23.2 + - - +
182K ILE* 3.9 15.8 - - + +
191K ILE* 4.0 23.6 - - + +
194K THR* 3.8 29.2 - - + -
195K ALA* 3.6 32.8 - - + +
198K LEU* 4.5 5.6 - - + -
205K ILE* 3.8 22.2 - - + -
213K ILE* 4.2 10.1 - - + -
215K ILE* 4.0 15.0 - - + +
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Residues in contact with CYS 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K PRO 5.1 1.3 - - - -
31K ALA* 4.2 17.9 - - - -
34K LEU* 3.9 16.2 - - + +
98K GLY 5.7 0.2 - - - -
99K PRO* 4.9 13.9 - - + -
167K VAL* 3.1 30.9 + - - +
168K THR* 3.8 3.1 - - - +
169K ILE 2.9 1.2 + - - -
170K MET* 1.3 75.4 - - - +
172K ALA* 1.3 63.3 + - - +
174K THR* 2.6 26.2 + - - -
194K THR* 4.2 19.7 - - - -
198K LEU* 4.0 22.0 - - + -
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Residues in contact with ALA 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K GLY 4.1 14.0 + - - +
102K ALA* 3.8 14.6 - - - +
129K LEU* 3.9 20.6 - - + -
132K LEU* 4.0 4.7 - - + -
151K LEU* 3.6 33.2 - - + +
168K THR 3.0 19.1 + - - +
169K ILE 4.0 2.0 - - - +
171K CYS* 1.3 73.1 - - - +
173K ALA* 1.3 63.4 + - - +
174K THR 3.2 0.9 + - - -
175K LEU 3.4 8.8 + - - -
176K ALA 3.8 3.6 + - - -
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Residues in contact with ALA 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132K LEU* 4.1 7.5 - - + +
169K ILE 2.9 16.5 + - - +
170K MET 3.6 5.8 - - - +
172K ALA* 1.3 79.5 - - - +
174K THR* 1.3 58.4 + - - +
175K LEU 2.9 6.9 + - - -
176K ALA* 3.0 22.2 + - - +
178K GLY 5.4 0.2 - - - +
180K THR* 3.7 35.3 + - + +
215K ILE* 3.8 16.3 - - + +
217K GLY* 3.9 8.8 + - - -
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Residues in contact with THR 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K LEU* 3.6 16.6 - - - +
170K MET 3.2 17.9 - - - +
171K CYS 2.6 16.9 + - - +
173K ALA* 1.3 75.6 - - - +
175K LEU* 1.3 58.2 + - - +
176K ALA 3.7 0.2 - - - -
198K LEU* 3.4 26.2 - - + -
203K ALA* 4.2 17.3 - - + +
205K ILE* 4.0 6.3 - - + -
215K ILE* 3.7 18.2 - - + -
216K GLU 4.3 2.0 - - - +
217K GLY* 3.7 2.7 - - - -
218K VAL* 3.3 29.5 + - - +
221K LEU* 4.0 6.8 - - - +
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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