Contacts of the helix formed by residues 168 - 182 (chain C) in PDB entry 3F22
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 PRO 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C SER* 4.1 1.1 - - - +
166C GLY 4.5 1.8 - - - +
167C THR* 1.3 94.9 - - + +
169C LYS* 1.3 67.2 - - - +
170C LYS* 4.5 7.9 - - + +
171C GLU* 3.0 27.5 + - + +
172C ILE* 3.1 9.2 + - - +
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Residues in contact with LYS 169 (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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158C ALA* 4.1 15.7 - - + -
159C HIS* 3.8 39.3 - - + +
162C SER* 3.3 18.8 + - - +
168C PRO* 1.3 71.1 - - - +
170C LYS* 1.3 58.3 + - - +
172C ILE* 3.1 2.5 + - - +
173C ASN* 2.7 41.4 + - - +
2F G 5.7 5.0 + - - +
3F T 4.3 11.9 + - - +
4F A 3.2 20.3 + - - -
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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
----------------------------------------------------------
168C PRO* 3.1 7.0 + - + +
169C LYS* 1.3 76.9 - - - +
171C GLU* 1.3 59.8 + - - +
173C ASN* 3.3 2.8 + - - +
174C ARG* 2.9 27.3 + - + +
4F A 3.5 33.9 + - - +
5F C 3.1 33.6 + - - +
6F G 3.2 24.6 + - - -
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Residues in contact with GLU 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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135C ILE* 4.9 5.2 - - - +
136C TYR* 4.7 14.5 - - + -
139C GLN* 3.1 33.3 - - + +
167C THR* 3.7 18.9 - - + +
168C PRO* 3.0 21.2 + - + +
170C LYS* 1.3 78.2 - - - +
172C ILE* 1.3 68.0 + - - +
174C ARG* 3.1 8.8 + - + +
175C VAL* 3.1 30.6 + - + +
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Residues in contact with ILE 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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139C GLN* 5.1 1.6 - - + +
143C ILE* 3.9 22.6 - - + +
158C ALA* 3.8 21.3 - - + +
161C LEU* 3.8 7.4 - - + -
162C SER* 3.6 24.9 - - - +
165C LEU* 4.0 19.7 - - + -
167C THR* 3.8 22.9 - - + +
168C PRO 3.1 11.8 + - - +
169C LYS* 3.1 10.5 + - - +
171C GLU* 1.3 77.4 - - - +
173C ASN* 1.3 57.8 + - - +
175C VAL* 3.3 3.3 + - - +
176C LEU* 2.9 54.4 + - + +
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Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ALA* 3.3 20.2 - - - +
169C LYS* 2.7 31.8 + - - +
170C LYS 3.6 0.4 - - - +
172C ILE* 1.3 71.1 - - - +
174C ARG* 1.3 66.3 + - - +
176C LEU* 4.1 6.9 - - - +
177C TYR* 3.0 49.4 + - + +
195C TRP* 4.5 2.4 + - - -
3F T 3.9 15.2 + - - -
4F A 2.6 49.7 + - - +
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Residues in contact with ARG 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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181B LYS* 6.2 0.7 - - - +
136C TYR* 4.1 26.8 + - + +
170C LYS* 2.9 13.2 + - + +
171C GLU* 3.1 13.4 + - + +
173C ASN* 1.3 75.8 - - - +
175C VAL* 1.3 63.8 + - - +
177C TYR* 4.2 1.2 - - - +
178C SER* 3.1 27.7 + - - -
4F A 3.6 15.5 + - - +
5F C 2.4 39.9 + - - +
6F G 3.8 32.9 + - - -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C TYR* 3.6 36.3 - - + +
139C GLN* 5.2 5.2 - - + -
140C GLU* 3.8 25.8 - - + -
143C ILE* 3.4 26.2 - - + -
171C GLU* 3.1 21.2 + - + +
172C ILE 3.6 6.1 - - - +
174C ARG* 1.3 75.9 - - + +
176C LEU* 1.3 60.2 + - - +
178C SER* 3.2 1.8 + - - -
179C LEU* 2.9 43.3 + - + +
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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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143C ILE* 4.0 13.5 - - + -
147C LEU* 4.8 0.4 - - + -
158C ALA* 3.8 11.0 - - + -
161C LEU* 3.8 20.9 - - + -
172C ILE* 2.9 43.7 + - + +
173C ASN* 3.4 6.2 + - - +
175C VAL* 1.3 73.7 - - - +
177C TYR* 1.3 58.3 + - - +
179C LEU* 3.3 1.7 + - - +
180C ALA* 2.9 29.6 + - - +
185C LEU* 3.5 27.5 - - + +
195C TRP* 3.7 52.3 - - + +
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Residues in contact with TYR 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 ASN* 3.0 41.5 + - - +
174C ARG 4.2 1.8 - - - +
176C LEU* 1.3 76.6 - - - +
178C SER* 1.3 57.0 + - - +
180C ALA* 3.4 8.5 + - + +
181C LYS* 3.0 28.5 + - - +
187C LYS* 3.9 21.8 + - + +
193C PRO* 3.9 11.6 - - - +
195C TRP* 3.7 21.8 - + - -
2F G 4.0 1.0 + - - -
3F T 2.4 36.7 + - - -
4F A 3.5 44.0 + + + +
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Residues in contact with SER 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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181B LYS* 2.9 33.7 + - - +
136C TYR* 4.4 11.2 + - - -
140C GLU* 5.4 1.0 + - - -
174C ARG* 3.1 24.2 + - - -
175C VAL* 3.5 7.9 - - - -
177C TYR* 1.3 74.7 - - - +
179C LEU* 1.3 62.4 + - - +
181C LYS* 3.1 6.2 + - - +
182C LYS* 2.9 38.7 + - - +
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Residues in contact with LEU 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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140C GLU* 3.6 29.4 - - + +
143C ILE* 4.8 3.8 - - + -
144C LEU* 4.2 29.4 - - + -
175C VAL* 2.9 39.6 + - + +
178C SER* 1.3 72.7 - - - +
180C ALA* 1.3 61.3 + - - +
182C LYS* 3.1 20.2 + - + -
183C GLY 2.9 7.6 + - - -
184C LYS* 2.8 41.3 + - + -
185C LEU* 4.0 29.4 - - + -
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Residues in contact with ALA 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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176C LEU 2.9 18.6 + - - +
177C TYR* 3.5 8.3 - - + +
178C SER 3.1 0.2 - - - -
179C LEU* 1.3 78.3 - - - +
181C LYS* 1.3 57.4 + - - +
183C GLY* 3.0 17.2 + - - -
185C LEU* 3.6 20.8 - - + +
187C LYS* 4.9 9.4 - - + +
195C TRP* 3.9 19.5 - - + -
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Residues in contact with LYS 181 (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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178B SER* 3.5 39.3 + - - +
181B LYS* 3.9 27.5 - - + +
182B LYS* 3.2 45.5 - - + +
177C TYR 3.0 14.3 + - - +
178C SER* 3.1 10.7 + - - +
180C ALA* 1.3 73.7 - - - +
182C LYS* 1.3 56.3 + - - +
183C GLY* 3.0 8.4 + - - -
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Residues in contact with LYS 182 (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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181B LYS* 3.2 40.3 + - + +
182B LYS 5.0 5.8 - - - +
140C GLU* 5.4 4.0 - - - +
178C SER* 2.9 29.3 + - - +
179C LEU* 3.1 23.3 + - + +
181C LYS* 1.3 76.7 - - - +
183C GLY* 1.3 62.0 + - - +
184C LYS* 3.2 16.7 + - + +
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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