Contacts of the helix formed by residues 185 - 195 (chain C) in PDB entry 3IFS
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 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C SER* 3.4 16.4 - - - -
184C ARG* 1.3 78.4 - - - +
186C ALA* 1.3 64.5 + - - -
187C LEU 3.3 2.5 - - - -
188C LYS 3.7 0.2 + - - -
189C THR* 2.9 28.4 + - - -
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Residues in contact with ALA 186 (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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146C SER 2.8 11.0 + - - +
147C GLY 4.2 5.2 - - - +
148C THR* 4.2 10.8 - - + +
185C GLY* 1.3 71.6 - - - -
187C LEU* 1.3 57.9 + - - +
189C THR* 3.5 6.3 + - - -
190C LEU* 2.9 28.8 + - - +
348D LEU* 3.1 40.8 - - + +
349D ASP* 3.9 9.9 - - + -
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Residues in contact with LEU 187 (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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142C VAL* 3.9 48.9 - - + +
144C SER* 3.6 31.6 - - - +
146C SER 3.5 3.4 + - - -
147C GLY* 3.7 17.8 - - - +
156C PHE* 4.7 5.8 - - + -
178C ALA* 4.3 8.3 - - + -
180C THR* 3.7 20.9 - - + +
185C GLY 3.3 0.8 - - - -
186C ALA* 1.3 75.3 - - - +
188C LYS* 1.3 56.2 + - - +
190C LEU* 3.1 20.2 + - + +
191C ALA* 2.7 37.8 + - + +
196C TYR* 5.7 1.8 - - + -
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Residues in contact with LYS 188 (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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180C THR* 3.8 11.0 + - + +
181C ASP 3.7 20.2 - - - +
182C LYS* 3.4 20.4 + - - +
183C ALA* 3.9 18.6 - - - +
184C ARG 3.6 20.4 - - - +
185C GLY 3.7 2.1 + - - +
186C ALA 3.5 0.2 - - - -
187C LEU* 1.3 77.7 - - - +
189C THR* 1.3 58.7 + - - +
191C ALA* 3.7 1.7 - - + -
192C ASP* 2.8 66.1 + - - +
198C THR* 4.4 25.2 - - + +
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Residues in contact with THR 189 (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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183C ALA 5.5 2.6 + - - -
185C GLY 2.9 17.5 + - - -
186C ALA* 3.7 6.5 - - - -
187C LEU 3.2 0.4 - - - -
188C LYS* 1.3 80.0 - - - +
190C LEU* 1.3 56.6 + - - +
192C ASP* 3.6 7.0 - - - +
193C ASN* 2.9 52.3 + - - +
348D LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 190 (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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156C PHE* 3.7 32.1 - - + -
160C ARG* 4.4 20.9 - - - +
186C ALA 2.9 18.6 + - - +
187C LEU* 3.6 12.1 - - + +
189C THR* 1.3 72.5 - - - +
191C ALA* 1.3 60.1 + - - +
193C ASN* 3.1 4.4 + - + +
194C GLU* 2.9 52.4 + - + +
196C TYR* 4.2 11.2 - - + -
346D ASN* 6.2 2.7 - - + +
348D LEU* 3.7 24.0 - - + +
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Residues in contact with ALA 191 (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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178C ALA* 3.8 21.5 - - + -
187C LEU* 2.7 22.5 + - + +
188C LYS* 3.8 5.8 - - - +
190C LEU* 1.3 74.0 - - - +
192C ASP* 1.3 58.2 + - - +
195C GLY* 2.9 27.0 + - - -
196C TYR* 3.2 24.2 + - + +
198C THR* 3.5 25.6 - - + +
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Residues in contact with ASP 192 (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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188C LYS* 2.8 60.3 + - - +
189C THR* 3.6 7.3 - - - +
191C ALA* 1.3 78.3 - - - +
193C ASN* 1.3 66.7 + - - +
195C GLY* 3.6 7.2 + - - -
198C THR* 5.2 1.6 + - - -
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Residues in contact with ASN 193 (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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189C THR* 2.9 37.0 + - - +
190C LEU* 3.1 6.7 + - + +
192C ASP* 1.3 81.5 - - - +
194C GLU* 1.3 71.9 + - - +
195C GLY 3.7 0.2 + - - -
346D ASN* 5.5 6.0 - - - +
348D LEU* 4.2 14.1 - - - +
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Residues in contact with GLU 194 (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 ARG* 4.9 8.3 + - - +
164C GLU* 5.6 0.9 - - - +
169C LYS* 6.0 2.3 - - - +
173C ARG* 3.0 26.4 - - + +
190C LEU* 2.9 40.4 + - + +
193C ASN* 1.3 85.1 - - - +
195C GLY* 1.3 58.1 + - - +
196C TYR* 3.6 33.6 + - + +
346D ASN* 5.2 7.6 + - - -
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Residues in contact with GLY 195 (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* 3.1 27.2 + - - -
191C ALA 2.9 8.8 + - - -
192C ASP 3.6 5.6 + - - -
193C ASN 3.4 3.2 + - - -
194C GLU* 1.3 79.4 - - - +
196C TYR* 1.3 65.6 + - - +
197C GLU 3.7 0.5 + - - -
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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