Contacts of the helix formed by residues 168 - 180 (chain C) 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 ASN 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C GLY 3.4 0.6 + - - -
167C ARG* 1.3 86.6 + - - +
169C SER* 1.3 61.2 + - - +
170C LYS* 3.2 4.7 - - - +
171C THR* 3.4 14.6 + - - +
172C VAL* 3.1 24.6 + - - +
200C VAL* 3.5 31.8 - - + +
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C CYS* 4.7 0.2 - - - -
164C THR* 3.4 4.2 - - - +
165C ILE* 3.7 28.2 - - - -
166C GLY 2.8 24.7 + - - -
167C ARG 3.2 0.8 - - - -
168C ASN* 1.3 74.9 - - - +
170C LYS* 1.3 61.6 + - - +
172C VAL* 3.7 9.4 - - - -
173C ARG* 2.8 54.9 + - - +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LYS* 4.9 12.5 - - - +
168C ASN* 3.2 2.6 - - - +
169C SER* 1.3 84.8 + - - +
171C THR* 1.3 56.9 + - - +
173C ARG* 3.8 23.9 - - - +
174C GLU* 2.9 43.9 + - - +
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Residues in contact with THR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ASN* 3.4 21.1 + - - +
169C SER 3.4 0.4 - - - -
170C LYS* 1.3 77.5 - - - +
172C VAL* 1.3 58.0 + - - +
174C GLU* 3.1 11.3 - - + +
175C PHE* 3.0 24.3 + - - +
199C GLU* 4.2 23.1 - - + +
200C VAL* 3.9 17.0 - - + -
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C CYS* 3.8 13.5 - - - -
38C VAL* 4.2 7.6 - - + -
164C THR* 3.6 31.9 - - + +
168C ASN 3.1 18.2 - - - +
169C SER* 3.7 6.5 - - - -
171C THR* 1.3 73.0 - - - +
173C ARG* 1.3 64.9 + - - +
175C PHE* 3.3 8.5 + - - +
176C LEU* 3.0 28.1 + - + +
196C SER* 3.6 38.1 - - - +
197C LEU* 5.7 1.1 - - + -
199C GLU* 5.3 0.2 - - - -
200C VAL* 4.0 7.9 - - + -
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Residues in contact with ARG 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C TRP* 5.0 2.2 - - - -
163C GLN* 3.1 26.8 + - - +
164C THR* 3.2 29.3 + - + +
165C ILE* 4.9 2.2 - - - +
169C SER* 2.8 42.1 + - - +
170C LYS* 3.8 28.7 - - - +
172C VAL* 1.3 71.8 - - - +
174C GLU* 1.3 54.6 + - - +
176C LEU* 3.2 6.5 + - - +
177C GLU* 2.8 55.8 + - - +
56D SER* 4.4 15.9 - - - -
58D LEU* 4.2 13.0 - - + -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LYS* 2.9 36.6 + - - +
171C THR* 3.1 13.0 - - - +
173C ARG* 1.3 76.2 - - - +
175C PHE* 1.3 65.5 + - - +
177C GLU* 3.2 27.4 + - - +
178C LYS* 3.4 28.7 + - - +
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Residues in contact with PHE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C THR 3.0 12.2 + - - +
172C VAL* 3.4 12.8 - - - +
173C ARG 3.3 0.2 - - - -
174C GLU* 1.3 76.3 - - - +
176C LEU* 1.3 62.8 + - + +
178C LYS* 3.2 7.5 + - + +
179C ASN* 3.0 49.8 + - + +
192C LEU* 4.1 17.3 - - + -
195C ARG* 3.6 47.8 - - + -
196C SER* 3.4 34.5 - - - -
199C GLU* 3.6 38.6 - - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.9 24.0 - - + -
40C VAL* 3.8 20.0 - - + -
162C ALA* 4.3 17.5 - - + -
163C GLN* 4.5 5.4 - - - +
164C THR* 4.4 8.3 - - + -
172C VAL* 3.0 26.0 + - + +
173C ARG* 3.7 4.5 - - + +
175C PHE* 1.3 80.7 - - + +
177C GLU* 1.3 58.0 + - - +
179C ASN* 4.3 2.0 - - - +
180C TYR* 2.8 40.1 + - + +
192C LEU* 4.7 15.0 - - + -
196C SER* 3.7 26.0 - - - +
58D LEU* 4.3 12.0 - - + +
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Residues in contact with GLU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 2.8 40.7 + - - +
174C GLU* 3.2 21.2 + - - +
176C LEU* 1.3 74.3 - - - +
178C LYS* 1.3 58.1 + - - +
180C TYR 4.4 6.4 - - - +
56D SER* 3.9 8.0 + - - -
57D PRO* 3.7 30.5 - - + +
58D LEU* 3.7 25.8 - - + +
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Residues in contact with LYS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLU* 3.4 34.3 + - - +
175C PHE* 3.2 6.4 + - + +
176C LEU 3.2 0.2 - - - -
177C GLU* 1.3 77.4 - - - +
179C ASN* 1.3 80.9 + - - +
180C TYR 3.4 4.5 + - - +
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Residues in contact with ASN 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 3.0 46.8 + - + +
176C LEU* 4.6 0.9 - - - +
178C LYS* 1.3 93.8 - - - +
180C TYR* 1.3 61.4 + - - +
192C LEU* 4.0 28.5 - - + +
195C ARG* 2.9 32.8 + - - +
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Residues in contact with TYR 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 4.6 2.9 - - + -
41C LYS* 2.9 34.7 + - - +
161C SER* 3.5 41.5 + - - -
162C ALA* 4.2 11.4 - - + -
176C LEU* 2.8 29.1 + - + +
177C GLU 4.4 7.6 - - - +
178C LYS 4.5 3.1 - - - +
179C ASN* 1.3 72.9 - - - +
180C ASP* 1.3 91.4 + - - +
182C PRO* 3.8 12.3 - - + +
183C PRO* 3.9 19.5 - - + -
192C LEU* 4.2 19.1 - - + -
58D LEU* 4.2 16.1 - - + +
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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