Contacts of the helix formed by residues 184 - 200 (chain A) in PDB entry 4I2D
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 2.7 29.1 + - + +
182A ARG* 3.2 8.9 - - + +
183A GLU* 1.3 72.1 - - - +
185A GLU* 1.3 54.2 + - - +
186A GLY* 3.7 3.8 + - - -
187A SER* 3.2 29.2 + - - -
188A CYS* 3.0 28.1 + - - +
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Residues in contact with GLU 185 (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 GLU* 6.1 1.1 - - - +
183A GLU 3.4 7.9 + - - +
184A ASN* 1.3 72.0 - - - +
186A GLY* 1.3 56.9 + - - +
188A CYS* 3.4 7.8 - - - +
189A LEU* 3.0 41.0 + - + +
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Residues in contact with GLY 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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184A ASN* 3.3 4.6 + - - -
185A GLU* 1.3 75.2 - - - +
187A SER* 1.3 63.1 + - - +
189A LEU* 3.4 12.1 + - - +
190A ALA* 3.1 22.3 + - - +
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 2.8 23.9 + - - -
184A ASN* 3.2 29.7 + - - -
186A GLY* 1.3 70.7 - - - +
188A CYS* 1.4 64.6 + - - +
190A ALA* 3.4 7.0 + - - +
191A PHE* 3.1 38.3 + - - -
220A LYS* 4.7 8.5 - - - +
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Residues in contact with CYS 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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176A ALA* 3.2 24.6 - - - +
179A ASP* 3.5 15.1 + - + -
180A GLU* 4.0 23.1 - - - +
184A ASN 3.0 18.6 + - - +
185A GLU* 3.4 10.1 - - - +
187A SER* 1.4 76.2 - - - +
189A LEU* 1.3 56.5 + - - +
191A PHE* 3.3 4.5 + - - +
192A MET* 2.9 54.0 + - - +
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Residues in contact with LEU 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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185A GLU* 3.0 33.1 + - + +
186A GLY* 3.4 8.7 + - - +
188A CYS* 1.3 74.4 - - + +
190A ALA* 1.4 62.3 + - - +
192A MET* 3.3 24.1 + - + +
193A ARG* 3.0 52.2 + - + +
458A ARG* 5.1 12.3 - - - +
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Residues in contact with ALA 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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186A GLY 3.1 13.6 + - - +
187A SER* 3.7 10.3 - - - +
188A CYS 3.3 0.2 - - - -
189A LEU* 1.4 74.9 - - - +
191A PHE* 1.3 64.3 + - + +
193A ARG* 3.6 6.8 + - - +
194A ALA* 3.2 24.1 + - - +
216A CYS 4.4 2.6 - - - +
221A VAL* 4.4 8.0 - - + +
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Residues in contact with PHE 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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172A LEU* 3.8 16.9 - - + +
175A LEU* 3.8 35.2 - - + -
176A ALA* 3.7 18.4 - - + -
179A ASP* 3.0 30.7 - - - -
187A SER* 3.1 22.9 + - - +
190A ALA* 1.3 76.2 - - + +
192A MET* 1.3 57.4 + - - +
194A ALA* 3.5 3.9 + - - +
195A SER* 3.0 30.7 + - - -
220A LYS* 3.9 24.0 - - + -
221A VAL* 3.9 20.6 - - + -
224A ILE* 3.5 30.3 - - + -
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Residues in contact with MET 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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173A ASP* 5.7 1.6 - - - +
176A ALA* 3.9 15.7 - - + -
188A CYS* 2.9 30.3 + - - +
189A LEU* 3.3 39.7 + - + +
191A PHE* 1.3 76.8 - - - +
193A ARG* 1.3 56.2 + - + +
195A SER* 3.8 5.3 - - - -
196A SER* 3.0 28.8 + - - -
454A ARG* 3.4 29.2 - - - -
455A GLN* 4.0 13.5 - - - +
458A ARG* 3.7 22.0 - - - +
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Residues in contact with ARG 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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152A GLN* 5.7 1.9 - - - +
157A ARG* 4.7 1.8 + - - +
189A LEU* 3.0 41.1 + - + +
190A ALA* 4.1 6.3 - - - +
192A MET* 1.3 72.0 - - + +
194A ALA* 1.3 59.1 + - - +
196A SER* 3.5 7.2 + - - -
197A VAL* 3.0 30.0 + - - +
216A CYS* 4.0 26.2 - - + +
455A GLN* 3.7 21.0 - - - +
459A ASP* 4.7 1.4 + - - +
462A ARG* 3.5 53.6 - - - +
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Residues in contact with ALA 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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172A LEU* 4.1 6.7 - - + -
190A ALA 3.2 16.8 + - - +
191A PHE* 3.7 4.3 - - - +
193A ARG* 1.3 72.6 - - - +
195A SER* 1.3 64.7 + - - +
197A VAL* 3.2 9.7 - - - +
198A LEU* 3.2 26.0 + - - +
216A CYS 3.4 23.2 + - - +
217A LEU* 3.9 1.8 - - + -
221A VAL* 3.7 31.0 - - + -
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Residues in contact with SER 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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169A THR* 3.4 21.9 + - - +
172A LEU* 3.8 21.7 - - - +
173A ASP* 2.6 29.8 + - - -
191A PHE 3.0 18.6 + - - -
192A MET* 3.8 6.1 - - - -
194A ALA* 1.3 74.3 - - - +
196A SER* 1.4 56.6 + - - +
198A LEU 3.3 2.1 + - - -
199A LYS* 3.0 36.4 + - - +
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Residues in contact with SER 196 (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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157A ARG* 3.0 21.3 + - - -
159A THR* 4.5 3.6 + - - +
192A MET 3.0 19.5 + - - -
193A ARG* 3.5 7.4 - - - -
194A ALA 3.3 0.2 - - - -
195A SER* 1.4 74.8 - - - +
197A VAL* 1.4 62.1 + - - +
199A LYS* 3.2 26.1 + - - +
200A SER* 3.4 6.4 + - - -
455A GLN* 3.4 25.8 - - - +
510A ALA* 3.5 17.6 - - - +
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Residues in contact with VAL 197 (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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150A ILE* 3.7 26.9 - - + -
157A ARG* 3.6 23.7 - - - +
193A ARG 3.0 16.8 + - - +
194A ALA* 3.2 19.7 - - - +
196A SER* 1.4 75.0 - - - +
198A LEU* 1.3 62.5 + - + +
200A SER* 2.7 23.6 + - - +
201A LEU* 3.7 5.6 + - + +
214A ILE* 3.7 25.4 - - + -
215A PRO* 3.4 26.0 - - + +
216A CYS* 4.3 2.0 - - + -
217A LEU* 4.0 5.4 - - + -
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Residues in contact with LEU 198 (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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163A ASN* 4.3 0.7 - - - +
165A ASN* 3.5 16.8 + - + +
168A PHE* 3.8 24.7 - - + -
169A THR* 3.7 15.3 - - + -
172A LEU* 3.8 27.4 - - + -
194A ALA 3.2 11.8 + - - +
195A SER 3.3 0.6 + - - +
197A VAL* 1.3 77.7 - - + +
199A LYS* 1.4 62.6 + - - +
201A LEU* 3.1 39.5 + - + +
205A ILE* 4.5 10.3 - - + -
214A ILE* 4.6 4.0 - - + -
217A LEU* 4.1 27.1 - - + -
225A ILE* 4.1 15.7 - - + -
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Residues in contact with LYS 199 (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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159A THR* 3.5 21.9 - - + +
160A THR 4.4 7.7 + - - +
162A ASN 4.9 1.7 - - - +
163A ASN* 3.8 30.3 - - + +
169A THR* 3.9 16.4 - - + +
173A ASP* 3.1 31.6 + - - -
195A SER* 3.0 31.7 + - - +
196A SER* 3.2 9.3 + - - +
198A LEU* 1.4 76.1 - - - +
200A SER* 1.4 58.9 + - - +
201A LEU 3.6 4.3 + - - +
509A ASN 4.2 13.2 - - - +
510A ALA 4.4 13.8 + - - -
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Residues in contact with SER 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 4.5 4.9 - - - +
157A ARG* 3.6 31.1 - - - -
158A ARG 3.8 17.4 - - - +
159A THR* 3.7 22.6 - - - +
196A SER 3.4 2.7 + - - -
197A VAL* 2.7 22.1 + - - +
199A LYS* 1.4 77.1 - - - +
201A LEU* 1.3 66.1 + - - +
202A PRO* 3.6 4.9 - - - +
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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