Contacts of the helix formed by residues 168 - 180 (chain R) in PDB entry 3SDI
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 GLY 168 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36R THR* 3.5 19.2 + - - +
166R GLY 3.1 1.2 + - - -
167R SER* 1.3 78.8 + - - +
169R SER* 1.3 57.2 + - - +
170R GLU* 3.5 6.5 + - - -
171R GLY* 3.6 2.9 + - - -
172R ALA* 3.0 32.2 + - - +
200R VAL* 3.8 22.2 - - - +
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Residues in contact with SER 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R LYS* 5.3 6.8 - - - +
36R THR* 4.8 0.6 - - - +
164R ALA* 3.4 27.0 - - - +
165R ILE* 3.8 9.4 - - - +
166R GLY 2.6 22.4 + - - -
167R SER 3.4 1.6 - - - -
168R GLY* 1.3 74.0 - - - +
170R GLU* 1.3 61.8 + - - +
172R ALA* 4.3 4.9 - - - -
173R GLN* 2.7 38.4 + - - +
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Residues in contact with GLU 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R SER 3.4 23.3 - - - +
168R GLY* 4.5 2.9 - - - -
169R SER* 1.3 80.7 + - - +
171R GLY* 1.3 69.7 + - - +
173R GLN* 4.0 5.3 - - - +
174R ALA* 3.6 16.6 + - - +
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Residues in contact with GLY 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168R GLY 3.6 2.6 + - - -
169R SER 3.3 0.2 - - - -
170R GLU* 1.3 91.3 - - - +
172R ALA* 1.3 60.8 + - - +
174R ALA* 3.3 10.0 + - - +
175R GLU* 3.2 20.7 + - - +
199R GLN* 6.4 0.2 - - - -
200R VAL* 4.8 7.2 - - - -
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Residues in contact with ALA 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R THR* 5.1 1.1 - - + -
38R ILE* 4.6 4.9 - - + -
164R ALA* 3.6 22.4 - - + -
168R GLY 3.0 20.3 + - - +
171R GLY* 1.3 72.7 - - - +
173R GLN* 1.3 59.8 + - - +
175R GLU* 3.3 3.6 + - - +
176R LEU* 2.9 35.2 + - + +
196R ILE* 3.6 27.9 - - + +
200R VAL* 4.2 8.7 - - + +
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Residues in contact with GLN 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160R TYR* 4.4 0.6 - - - -
162R ALA 3.4 23.4 + - - -
163R LYS* 3.5 13.4 - - - +
164R ALA* 3.0 31.7 + - - +
169R SER 2.7 20.6 + - - +
170R GLU* 4.0 6.1 - - - +
172R ALA* 1.3 72.6 - - - +
174R ALA* 1.3 58.2 + - - +
176R LEU* 3.4 5.5 + - - +
177R LEU* 2.9 37.5 + - + +
56S ASP* 3.4 38.0 + - - +
58S LEU* 4.0 16.2 - - - +
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Residues in contact with ALA 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170R GLU 3.6 9.6 + - - +
171R GLY* 3.3 10.9 + - - +
172R ALA 3.2 0.4 - - - -
173R GLN* 1.3 76.6 - - - +
175R GLU* 1.3 65.4 + - - +
177R LEU* 3.1 19.8 + - - +
178R ASN* 3.2 19.8 + - - +
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Residues in contact with GLU 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R GLY 3.2 10.6 + - - +
172R ALA* 3.3 7.2 + - - +
174R ALA* 1.3 78.6 - - - +
176R LEU* 1.3 56.5 + - - +
178R ASN* 3.4 16.0 + - - +
179R GLU* 3.1 42.6 + - + +
195R LYS* 4.3 11.7 + - - -
196R ILE* 4.0 29.4 - - + -
199R GLN* 3.5 34.8 + - - +
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Residues in contact with LEU 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE* 4.1 9.2 - - + -
40R ILE* 3.9 24.9 - - + -
162R ALA* 3.7 17.5 - - + -
163R LYS* 3.7 35.7 - - - +
164R ALA* 3.8 11.9 - - + +
172R ALA* 2.9 23.0 + - + +
173R GLN* 3.6 9.2 - - - +
175R GLU* 1.3 73.2 - - - +
177R LEU* 1.3 64.2 + - - +
179R GLU* 4.5 2.2 - - - +
180R TRP* 3.1 31.5 + - + +
192R LEU* 5.3 3.1 - - + -
196R ILE* 3.8 20.9 - - + -
58S LEU* 3.8 14.5 - - + +
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Residues in contact with LEU 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173R GLN* 2.9 30.8 + - + +
174R ALA* 3.1 15.4 + - - +
176R LEU* 1.3 77.4 - - - +
178R ASN* 1.3 64.3 + - - +
180R TRP 4.2 7.3 + - - +
56S ASP* 4.9 4.0 - - + +
57S GLU* 4.0 29.2 - - + +
58S LEU* 3.8 35.2 - - + +
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Residues in contact with ASN 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174R ALA* 3.2 15.3 + - - +
175R GLU* 3.6 21.1 + - - +
177R LEU* 1.3 82.7 - - - +
179R GLU* 1.3 69.0 + - + +
180R TRP 3.5 3.3 + - - +
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Residues in contact with GLU 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R GLU* 3.1 30.3 + - + +
176R LEU* 3.5 2.2 + - - +
178R ASN* 1.3 83.7 - - + +
180R TRP* 1.3 71.8 + - - +
184R LEU* 3.9 10.4 - - - +
192R LEU* 3.5 39.6 - - + +
195R LYS* 3.0 30.3 + - + +
196R ILE* 5.3 2.9 - - + -
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Residues in contact with TRP 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ILE* 3.9 16.6 - - + -
41R ALA 3.3 23.0 + - - -
42R THR* 6.1 0.2 - - - -
161R ASN* 3.5 50.2 + - + -
162R ALA* 4.1 12.3 - - + -
176R LEU* 3.1 20.5 + - + +
177R LEU 4.2 5.4 + - - +
178R ASN 3.4 5.7 - - - +
179R GLU* 1.3 76.4 - - - +
180R HIS* 1.3 103.2 + + - +
184R LEU* 3.6 20.6 - - + +
192R LEU* 4.8 2.4 - - + +
58S LEU* 4.7 16.2 - - + +
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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