Contacts of the helix formed by residues 162 - 174 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124J LEU* 3.5 29.2 - - - -
158J MET* 5.6 2.8 - - - +
160J LYS 3.3 3.6 + - - -
161J VAL* 1.3 74.0 - - - +
163J VAL* 1.3 56.5 + - - +
165J ALA* 2.8 27.0 + - - +
166J THR* 2.7 30.7 + - - -
184J ASN 5.4 0.2 + - - -
186J ALA* 3.6 5.8 - - - +
501J EPZ 2.8 31.8 + - - -
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Residues in contact with VAL 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J TRP* 5.1 2.2 - - + -
161J VAL* 5.7 1.1 - - + +
162J SER* 1.3 73.9 - - - +
164J GLY* 1.3 59.5 + - - +
166J THR 4.2 0.2 - - - -
167J VAL* 2.9 35.8 + - + +
186J ALA* 4.1 6.1 - - + -
188J GLU* 3.4 41.1 - - + +
190J GLU* 6.2 3.4 - - + -
191J ILE* 4.1 15.8 - - + +
501J EPZ 2.7 57.8 + - - +
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Residues in contact with GLY 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J TRP* 3.3 19.5 + - - -
125J HIS* 2.7 27.7 + - - -
162J SER* 3.1 3.7 + - - -
163J VAL* 1.3 79.3 - - - +
165J ALA* 1.3 58.2 + - - +
166J THR 3.4 0.2 - - - -
168J THR* 2.9 17.0 + - - -
501J EPZ 3.0 21.2 + - - -
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Residues in contact with ALA 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J LEU* 3.4 33.4 - - + +
125J HIS* 3.3 19.0 - - - +
158J MET* 4.2 11.0 - - + -
162J SER* 2.8 23.3 + - - +
164J GLY* 1.3 71.9 - - - +
166J THR* 1.3 61.4 + - - +
168J THR* 3.3 1.2 + - - -
169J ILE* 2.9 37.2 + - + +
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Residues in contact with THR 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J MET* 4.6 11.9 - - - -
162J SER 2.7 24.4 + - - -
163J VAL 4.3 0.2 - - - -
164J GLY 3.4 0.4 - - - -
165J ALA* 1.3 78.3 - - - +
167J VAL* 1.3 54.4 + - - +
169J ILE* 3.1 4.6 + - - +
170J MET* 2.6 38.8 + - + +
182J ILE* 4.4 9.5 - - + +
185J ALA* 4.1 26.0 - - + -
186J ALA 3.4 13.2 + - - -
191J ILE* 4.1 24.9 - - + -
213J ILE* 4.3 13.2 - - + -
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Residues in contact with VAL 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PRO* 3.9 24.0 - - + +
95J TRP* 3.5 36.6 - - + +
163J VAL* 2.9 22.2 + - + +
164J GLY 4.1 0.2 - - - +
165J ALA 3.3 0.2 - - - -
166J THR* 1.3 77.3 - - - +
168J THR* 1.3 62.3 + - - +
170J MET* 4.4 8.1 - - - -
171J CYS* 3.2 36.5 + - - -
191J ILE* 4.0 22.2 - - + -
194J THR* 4.3 8.7 - - + +
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Residues in contact with THR 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J ILE 5.3 1.5 + - - +
95J TRP* 3.3 18.9 - - - +
97J LEU* 5.7 2.5 - - + -
98J GLY* 4.7 13.9 - - - +
99J PRO* 5.8 2.0 - - - +
125J HIS* 3.1 28.8 - - + +
129J LEU* 4.1 30.7 - - + -
164J GLY 2.9 18.4 + - - -
165J ALA* 3.3 5.1 + - - -
166J THR 3.1 0.8 - - - -
167J VAL* 1.3 78.8 - - - +
169J ILE* 1.3 65.4 + - + +
171J CYS* 4.0 1.8 - - - +
172J ALA* 3.1 22.5 + - - +
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Residues in contact with ILE 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J LEU 4.6 3.6 - - - +
125J HIS* 5.1 1.1 - - - +
128J GLY* 3.2 35.0 - - - +
129J LEU* 4.9 1.6 - - - +
132J LEU* 4.0 12.1 - - + -
156J ILE* 4.0 25.6 - - + -
158J MET* 3.6 31.2 - - + -
165J ALA* 2.9 18.6 + - - +
166J THR* 3.8 2.0 - - - +
168J THR* 1.3 79.9 - - + +
170J MET* 1.3 64.7 + - - +
171J CYS 3.2 0.2 + - - -
172J ALA* 3.8 3.7 - - - +
173J ALA* 3.0 22.9 + - - +
180J THR* 4.7 7.4 - - + -
182J ILE* 4.2 20.6 - - + -
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Residues in contact with MET 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J THR* 2.6 22.2 + - + +
167J VAL* 3.9 8.3 - - - +
168J THR 3.3 0.2 - - - -
169J ILE* 1.3 76.4 - - - +
171J CYS* 1.3 61.8 + - - +
173J ALA* 3.5 3.3 + - - +
174J THR* 3.2 22.7 + - - +
182J ILE* 4.1 14.9 - - + +
191J ILE* 3.5 44.6 - - + +
194J THR* 4.2 14.6 - - + -
195J ALA* 3.9 24.7 - - + +
198J LEU* 4.6 2.5 - - + -
205J ILE* 4.0 26.5 - - + -
208J GLN* 5.4 0.2 - - - -
213J ILE* 4.6 16.2 - - - -
215J ILE* 4.1 8.8 - - + +
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Residues in contact with CYS 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PRO 5.2 1.1 - - - -
31J ALA* 4.2 17.5 - - + -
34J LEU* 3.9 18.6 - - + +
98J GLY 5.7 0.2 - - - -
99J PRO* 5.0 13.2 - - + -
167J VAL* 3.2 32.5 + - - +
168J THR* 4.2 1.8 - - - +
170J MET* 1.3 74.6 - - - +
172J ALA* 1.3 65.0 + - - +
174J THR* 2.6 24.8 + - - -
175J LEU 4.2 0.3 + - - -
194J THR* 4.2 8.7 - - - -
198J LEU* 3.6 26.2 - - + -
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Residues in contact with ALA 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J GLY* 4.3 15.7 - - - +
102J ALA* 3.5 24.7 - - - +
129J LEU* 3.5 29.6 - - + -
132J LEU* 4.1 8.3 - - + -
151J LEU* 4.2 12.1 - - + +
168J THR 3.1 19.0 + - - +
169J ILE 3.8 2.9 - - - +
171J CYS* 1.3 76.4 - - - +
173J ALA* 1.3 61.4 + - - +
175J LEU 3.6 4.2 + - - -
176J ALA* 3.9 3.8 + - - +
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Residues in contact with ALA 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J LEU* 4.0 8.7 - - + +
169J ILE 3.0 17.5 + - - +
170J MET 3.9 4.3 - - - +
171J CYS 3.2 0.2 - - - -
172J ALA* 1.3 73.8 - - - +
174J THR* 1.3 52.5 + - - +
175J LEU 2.7 7.1 + - - -
176J ALA* 2.4 40.1 + - + +
178J GLY 5.4 0.3 - - - +
180J THR* 3.5 37.9 + - + +
215J ILE* 3.9 12.7 - - + +
217J GLY* 4.5 2.9 + - - -
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Residues in contact with THR 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J LEU* 3.8 14.4 - - - +
170J MET 3.2 18.2 - - - +
171J CYS 2.6 16.7 + - - +
173J ALA* 1.3 76.4 - - - +
175J LEU* 1.3 60.2 + - - +
176J ALA 3.4 0.4 - - - -
198J LEU* 3.6 23.5 - - + +
203J ALA* 4.5 13.2 - - + -
204J LYS 5.8 0.4 - - - +
205J ILE* 3.9 12.3 - - + -
215J ILE* 3.6 18.6 - - + +
216J GLU 4.1 3.7 - - - +
218J VAL* 3.2 34.5 + - - +
221J LEU* 4.6 7.0 - - - +
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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