Contacts of the helix formed by residues 162 - 174 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.8 24.9 - - - -
158A MET* 5.5 2.7 - - - +
160A LYS 3.5 2.8 + - - -
161A VAL* 1.3 77.8 - - - +
163A VAL* 1.3 63.0 + - - +
164A GLY* 4.0 0.2 - - - -
165A ALA* 3.0 24.6 + - - +
166A THR* 2.9 31.7 + - - -
184A ASN 5.2 0.2 + - - -
186A ALA* 3.9 5.8 - - - +
501A EPZ 2.8 32.2 + - - -
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO* 6.5 0.4 - - + -
95A TRP* 4.8 9.2 - - + -
161A VAL* 5.1 1.3 - - + +
162A SER* 1.3 71.8 - - - +
164A GLY* 1.3 64.7 + - - +
166A THR* 3.6 1.9 + - - -
167A VAL* 3.3 24.6 + - + +
186A ALA* 3.8 9.1 - - + +
188A GLU* 3.5 44.4 - - + +
190A GLU* 6.0 4.9 - - + +
191A ILE* 4.0 14.5 - - + +
501A EPZ 2.8 51.0 + - - +
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TRP* 3.1 24.7 + - - -
125A HIS* 3.1 20.3 - - - -
162A SER* 3.3 2.9 + - - -
163A VAL* 1.3 76.4 - - - +
165A ALA* 1.3 56.5 + - - +
167A VAL 3.3 1.6 + - - -
168A THR 3.0 21.7 + - - -
501A EPZ 3.0 23.9 + - - -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.7 25.6 - - + +
125A HIS* 3.4 16.3 + - + -
158A MET* 3.6 25.1 - - + -
162A SER* 3.0 19.0 + - - +
164A GLY* 1.3 73.0 - - - +
166A THR* 1.3 67.3 + - - +
168A THR* 3.1 1.7 + - - -
169A ILE* 2.9 31.4 + - - +
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MET* 4.3 13.6 - - - -
162A SER 2.9 23.7 + - - -
165A ALA* 1.3 76.0 - - - +
167A VAL* 1.3 56.7 + - - +
170A MET* 3.0 28.5 + - + +
182A ILE* 4.1 7.6 - - + +
185A ALA* 3.8 14.7 - - + -
186A ALA 3.1 15.7 + - - +
191A ILE* 3.7 28.3 - - + -
213A ILE* 3.8 28.3 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO* 4.1 23.1 - - + +
95A TRP* 3.7 30.7 - - + +
163A VAL* 3.3 16.4 + - + +
164A GLY 3.7 7.0 - - - +
165A ALA 3.1 0.4 - - - -
166A THR* 1.3 76.3 - - - +
168A THR* 1.3 65.4 + - - +
170A MET* 4.5 10.1 - - + -
171A CYS* 3.0 39.3 + - - -
190A GLU 5.9 0.4 - - - -
191A ILE* 3.9 26.7 - - + -
194A THR* 4.7 4.9 - - + +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE 5.0 2.5 + - - +
95A TRP* 3.5 14.0 - - - -
97A LEU* 5.9 1.3 - - + -
98A GLY* 4.5 14.1 + - - +
99A PRO* 6.1 1.1 - - - -
125A HIS* 2.7 45.9 + - + +
129A LEU* 4.0 31.0 - - + -
164A GLY 3.0 5.2 + - - -
165A ALA* 3.1 6.5 + - - -
167A VAL* 1.3 78.7 - - - +
169A ILE* 1.3 63.7 + - + +
171A CYS* 4.0 2.7 - - - +
172A ALA* 3.2 22.5 + - - +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU 4.4 3.6 - - - +
128A GLY* 3.6 33.0 - - - -
129A LEU* 5.2 0.4 - - - -
132A LEU* 4.1 11.3 - - + +
156A ILE* 3.9 28.3 - - + -
158A MET* 3.5 38.1 - - + -
165A ALA* 2.9 11.4 + - - +
166A THR* 5.2 0.2 - - - -
168A THR* 1.3 79.8 - - + +
170A MET* 1.3 66.9 + - - +
172A ALA* 3.4 4.8 + - - +
173A ALA* 3.0 22.7 + - - +
180A THR* 4.5 4.9 - - + -
182A ILE* 3.7 23.3 - - + -
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Residues in contact with MET 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A THR* 3.0 21.8 + - + +
167A VAL* 4.0 11.0 - - + +
169A ILE* 1.3 78.2 - - - +
171A CYS* 1.3 60.9 + - - +
173A ALA* 3.5 8.5 + - - +
174A THR* 3.6 13.7 + - - +
182A ILE* 3.8 15.4 - - + +
191A ILE* 3.8 30.7 - - + +
194A THR* 4.2 15.7 - - + -
195A ALA* 3.9 28.7 - - - +
198A LEU* 4.5 4.7 - - + -
205A ILE* 4.2 16.8 - - + -
208A GLN* 5.4 0.4 - - - -
213A ILE* 4.2 24.9 - - - -
215A ILE* 4.2 13.8 - - + +
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Residues in contact with CYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO 5.3 1.1 - - - -
31A ALA* 4.0 21.8 - - - -
34A LEU* 3.5 19.1 - - + +
99A PRO* 4.5 15.7 - - + -
167A VAL* 3.0 35.6 + - - +
168A THR* 4.2 2.9 - - - +
170A MET* 1.3 75.8 - - - +
172A ALA* 1.3 61.5 + - - +
174A THR* 2.8 25.5 + - - -
194A THR* 4.3 6.3 - - - -
198A LEU* 3.9 24.2 - - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY* 4.1 10.1 - - - +
102A ALA* 3.4 26.7 - - + +
129A LEU* 3.8 23.8 - - + -
132A LEU* 3.9 8.5 - - + -
151A LEU* 3.8 20.8 - - + +
168A THR 3.2 18.2 + - - +
171A CYS* 1.3 76.3 - - - +
173A ALA* 1.3 61.8 + - - +
174A THR 3.5 0.5 + - - -
175A LEU 3.5 5.0 + - - -
176A ALA* 3.9 4.5 + - - +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 4.0 5.8 - - + +
169A ILE 3.0 17.8 + - - +
170A MET 3.8 5.6 - - - +
171A CYS 3.2 0.2 - - - -
172A ALA* 1.3 73.3 - - - +
174A THR* 1.3 62.8 + - - +
175A LEU 2.9 7.0 + - - -
176A ALA* 3.0 21.7 + - - +
178A GLY 5.2 0.5 - - - +
180A THR* 3.5 36.6 + - + +
215A ILE* 3.7 18.4 - - + +
217A GLY* 3.8 6.8 + - - -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.5 14.9 - - - +
170A MET 3.6 15.0 - - - +
171A CYS 2.8 18.1 + - - +
173A ALA* 1.3 76.8 - - - +
175A LEU* 1.3 58.4 + - - +
198A LEU* 3.9 18.6 - - + -
203A ALA* 3.8 30.3 - - + -
205A ILE* 4.1 8.3 - - + -
215A ILE* 3.7 11.9 - - + -
216A GLU 5.2 0.7 - - - -
217A GLY* 3.6 2.6 - - - -
218A VAL* 3.1 32.7 + - - +
221A LEU* 3.7 7.4 - - - +
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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