Contacts of the helix formed by residues 185 - 195 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A SER* 3.3 16.8 - - - -
184A ARG* 1.3 82.4 - - - +
186A ALA* 1.3 64.6 + - - -
187A LEU 3.3 3.3 + - - -
188A LYS 3.4 0.8 + - - -
189A THR* 3.1 26.0 + - - -
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER 2.9 5.9 + - - -
147A GLY 3.7 20.0 - - - +
148A THR* 4.1 7.9 - - + +
185A GLY* 1.3 72.1 - - - -
187A LEU* 1.3 57.7 + - - +
189A THR* 3.5 7.0 + - - -
190A LEU* 3.0 27.9 + - - +
348B LEU* 3.3 40.9 - - + +
349B ASP* 3.8 5.8 - - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 3.7 54.3 - - + +
144A SER* 3.7 24.5 - - - +
147A GLY* 3.8 16.9 - - - -
156A PHE* 4.1 19.3 - - + -
178A ALA* 4.0 12.6 - - + -
179A THR 4.0 1.1 - - - +
180A THR* 3.7 20.6 - - - +
185A GLY 3.3 0.8 - - - -
186A ALA* 1.3 75.8 - - - +
188A LYS* 1.3 61.2 + - - +
190A LEU* 3.8 7.4 - - + +
191A ALA* 2.8 31.6 + - - +
196A TYR* 5.3 1.6 - - + -
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A THR* 3.9 13.5 + - + +
181A ASP 3.7 21.3 - - - +
182A LYS* 3.5 21.8 + - - +
183A ALA* 4.1 18.2 - - - +
184A ARG* 3.6 20.2 - - - +
185A GLY 3.4 3.8 + - - +
187A LEU* 1.3 76.3 - - - +
189A THR* 1.3 61.9 - - - +
191A ALA* 3.3 2.8 + - - +
192A ASP* 2.9 59.7 + - - +
198A THR* 4.6 17.6 - - + +
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG* 5.9 0.5 - - - -
185A GLY 3.1 14.9 + - - -
186A ALA* 3.6 8.7 - - - -
188A LYS* 1.3 78.8 - - - +
190A LEU* 1.3 64.1 + - - +
192A ASP* 3.2 7.9 + - - +
193A ASN* 2.9 40.7 + - - +
348B LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 3.3 34.5 - - + -
160A ARG* 3.9 23.6 - - - +
186A ALA 3.0 17.7 + - - +
187A LEU* 3.8 7.6 - - + +
189A THR* 1.3 75.3 - - - +
191A ALA* 1.3 58.2 + - - +
193A ASN* 3.1 5.1 + - + +
194A GLU* 2.8 60.9 + - + +
196A TYR* 3.6 22.9 - - + +
346B ASN* 6.1 0.7 - - - +
348B LEU* 3.7 21.7 - - + +
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ALA* 4.1 11.0 - - + -
187A LEU 2.8 21.8 + - - +
188A LYS* 3.6 7.0 - - - +
190A LEU* 1.3 72.2 - - - +
192A ASP* 1.3 60.7 + - - +
195A GLY* 2.8 26.3 + - - -
196A TYR* 3.1 32.1 + - + +
198A THR* 3.4 26.7 - - + +
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LYS* 2.9 57.3 + - - +
189A THR* 3.7 6.1 - - - +
191A ALA* 1.3 80.2 - - - +
193A ASN* 1.3 68.0 + - - +
194A GLU 3.5 0.2 + - - -
195A GLY* 3.7 6.5 + - - -
198A THR* 5.0 2.4 + - - -
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Residues in contact with ASN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 2.9 36.5 + - - +
190A LEU* 3.5 8.8 - - + +
192A ASP* 1.3 81.9 - - - +
194A GLU* 1.3 68.7 + - + +
346B ASN* 4.0 21.0 - - - +
348B LEU* 4.0 7.1 - - - +
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 5.0 5.7 + - - -
164A GLU* 5.0 4.9 - - - +
169A LYS* 5.3 14.8 - - - +
173A ARG* 2.9 35.3 - - + +
190A LEU* 2.8 37.5 + - + +
193A ASN* 1.3 81.3 - - + +
195A GLY* 1.3 58.5 + - - +
196A TYR* 3.4 40.6 + - + +
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 4.1 13.4 + - - +
191A ALA 2.8 16.6 + - - -
192A ASP 3.7 5.6 + - - -
193A ASN 3.5 2.4 - - - -
194A GLU* 1.3 76.7 - - - +
196A TYR* 1.3 64.3 + - - +
197A GLU 3.7 0.9 + - - -
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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