Contacts of the helix formed by residues 200 - 216 (chain A) in PDB entry 1I4A
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ARG* 4.6 1.3 - - - +
160A ASP* 3.0 47.1 + - - +
161A GLU 4.7 0.2 - - - -
162A SER* 3.0 27.5 + - - +
163A ASN* 4.1 0.4 - - - -
164A TYR 2.8 28.6 + - - +
199A ARG* 1.3 76.2 - - - +
201A ARG* 1.3 59.7 + - - +
202A ASN* 3.1 12.5 + - - +
203A HIS* 2.8 32.2 + - - +
204A LEU* 2.8 26.6 + - - +
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Residues in contact with ARG 201 (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 ARG* 5.2 1.2 - - - +
163A ASN* 6.0 1.6 - - - +
199A ARG 3.9 0.4 + - - -
200A ASN* 1.3 73.1 - - - +
202A ASN* 1.3 58.7 + - - +
204A LEU* 3.2 2.0 + - - +
205A LEU* 2.8 61.2 + - + +
241A CYS 5.0 1.8 + - - -
242A MET* 2.9 60.0 + - + +
243A ARG 3.9 12.7 + - - -
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Residues in contact with ASN 202 (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* 3.1 36.9 + - + +
165A LEU* 4.1 18.0 - - - +
200A ASN* 3.1 7.9 + - - +
201A ARG* 1.3 81.0 - - - +
203A HIS* 1.3 62.0 + - - +
205A LEU* 3.5 8.0 + - - +
206A HIS* 2.8 54.8 + - - -
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Residues in contact with HIS 203 (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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164A TYR 4.0 5.8 + - - +
165A LEU* 4.7 4.5 - - - -
166A ASP* 3.7 22.4 + - + +
169A LEU* 3.9 15.7 - - + -
170A MET* 3.4 32.5 - - + +
173A ASP* 2.7 23.7 + - - -
199A ARG* 3.4 27.6 - - + -
200A ASN* 2.8 34.7 + - - +
202A ASN* 1.3 74.0 - - - +
204A LEU* 1.3 57.2 + - - +
206A HIS* 3.1 8.9 + - - +
207A VAL* 2.8 42.5 + - + +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 3.7 25.4 - - - +
195A VAL* 3.4 37.7 - - + +
196A LEU* 3.7 13.9 - - - +
199A ARG* 3.8 15.5 - - + +
200A ASN 2.8 11.8 + - - +
201A ARG* 3.6 5.2 - - - +
203A HIS* 1.3 78.0 - - - +
205A LEU* 1.3 62.2 + - - +
207A VAL* 3.0 7.6 + - + +
208A PHE* 2.9 52.6 + - + -
238A ILE* 4.6 2.0 - - + -
242A MET* 4.1 24.2 - - + -
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Residues in contact with LEU 205 (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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201A ARG* 2.8 66.5 + - + +
202A ASN* 3.9 7.6 - - - +
204A LEU* 1.3 72.2 - - - +
206A HIS* 1.3 65.3 + - + +
208A PHE* 3.3 18.1 + - + +
209A ASP* 3.3 25.8 + - - +
242A MET* 3.9 13.5 - - + +
243A ARG* 3.9 29.2 - - + +
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Residues in contact with HIS 206 (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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165A LEU* 3.5 32.7 - - + +
170A MET* 3.7 27.0 - - + +
202A ASN* 2.8 46.2 + - - +
203A HIS* 3.1 9.2 + - - +
205A LEU* 1.3 75.6 - - + +
207A VAL* 1.3 66.2 + - - +
209A ASP* 3.2 14.7 + - - +
210A GLU 3.0 18.4 + - - -
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Residues in contact with VAL 207 (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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170A MET* 3.4 30.3 - - + +
173A ASP* 3.8 9.6 - - + -
174A ALA* 3.8 24.9 - - - +
177A LEU* 4.2 17.5 - - + -
195A VAL* 4.4 6.1 - - + -
203A HIS* 2.8 40.4 + - + +
204A LEU* 3.0 11.4 + - + +
206A HIS* 1.3 77.2 - - - +
208A PHE* 1.3 61.2 + - + +
210A GLU* 3.2 2.0 + - - +
211A TYR* 2.8 27.4 + - + +
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Residues in contact with PHE 208 (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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177A LEU* 5.3 3.4 - - + -
196A LEU* 4.5 10.8 - - + -
204A LEU* 2.9 50.3 + - + -
205A LEU* 3.5 30.3 - - + +
206A HIS 3.2 0.2 - - - -
207A VAL* 1.3 81.5 - - + +
209A ASP* 1.3 64.6 + - - +
211A TYR* 3.2 7.2 + - - +
212A LYS* 3.0 22.9 + - - +
218A ASP* 5.7 0.2 - - - +
219A ILE* 3.7 33.4 + - + +
239A VAL* 3.8 36.1 - - + -
242A MET* 4.5 5.8 - - + -
243A ARG* 3.9 30.4 + - + +
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Residues in contact with ASP 209 (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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205A LEU 3.3 13.2 + - - +
206A HIS* 3.2 16.7 + - - +
208A PHE* 1.3 77.7 - - - +
210A GLU* 1.3 64.3 + - - +
212A LYS* 3.1 11.1 + - - +
213A ARG* 3.0 20.1 + - - +
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Residues in contact with GLU 210 (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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170A MET* 3.6 31.2 - - + +
171A ARG* 3.9 34.6 + - - +
174A ALA* 3.3 19.1 - - + -
206A HIS 3.0 5.5 + - - -
207A VAL 3.6 4.7 - - - +
209A ASP* 1.3 75.3 - - - +
211A TYR* 1.3 62.7 + - - +
213A ARG* 2.7 47.7 + - - +
214A ILE* 3.1 28.6 + - + +
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Residues in contact with TYR 211 (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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174A ALA* 3.7 22.6 - - + +
177A LEU* 3.8 17.3 + - + -
178A TYR* 3.5 34.5 + - + -
192A PHE* 5.5 1.0 - + - -
207A VAL* 2.8 16.2 + - + +
208A PHE* 3.4 12.3 - - + +
210A GLU* 1.3 77.9 - - - +
212A LYS* 1.3 53.6 + - - +
214A ILE* 3.3 5.2 - - - +
215A ALA* 2.8 54.7 + - + +
217A LYS 3.4 21.3 - - - -
219A ILE* 3.8 33.9 - - + -
222A SER* 2.6 35.1 + - - -
226A GLU* 4.0 6.6 + - - -
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Residues in contact with LYS 212 (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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208A PHE 3.0 12.7 + - - +
209A ASP* 3.1 13.2 + - - +
211A TYR* 1.3 75.3 - - - +
213A ARG* 1.3 57.7 + - - +
216A GLN* 2.8 34.6 + - - -
217A LYS* 3.4 18.6 - - - +
218A ASP* 3.2 50.6 + - - +
221A GLN* 4.8 0.9 - - - -
243A ARG* 5.4 0.2 - - - +
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Residues in contact with ARG 213 (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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171A ARG* 5.5 3.0 - - - +
209A ASP 3.0 11.7 + - - +
210A GLU* 2.7 45.4 + - - +
212A LYS* 1.3 81.2 - - - +
214A ILE* 1.3 75.9 + - - +
216A GLN* 4.0 11.8 + - - +
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Residues in contact with ILE 214 (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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174A ALA* 3.5 41.1 - - + +
175A GLN* 3.8 24.9 - - + +
178A TYR* 3.8 31.3 + - + -
210A GLU* 3.1 15.2 + - - +
211A TYR* 3.3 11.0 - - - +
213A ARG* 1.3 105.3 - - - +
215A ALA* 1.3 62.0 + - - +
216A GLN* 4.8 3.0 - - - +
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Residues in contact with ALA 215 (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 TYR* 3.7 29.3 - - + -
211A TYR* 2.8 45.0 + - + +
214A ILE* 1.3 75.4 - - + +
216A GLN* 1.3 72.4 + - - +
217A LYS* 3.2 17.1 + - + +
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Residues in contact with GLN 216 (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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212A LYS* 2.8 26.3 + - - -
213A ARG 4.1 12.1 + - - +
214A ILE 4.8 2.5 - - - +
215A ALA* 1.3 75.7 - - - +
217A LYS* 1.3 65.1 + - - +
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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