Contacts of the helix formed by residues 200 - 216 (chain A) in PDB entry 4N78
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 ASP 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ALA* 1.3 75.6 - - - +
201A PRO* 1.3 69.4 - - + +
202A GLN* 3.1 21.8 - - - +
203A SER* 2.8 41.1 + - - -
204A ILE* 2.9 12.1 + - - +
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Residues in contact with PRO 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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199A ALA 4.6 0.4 - - - +
200A ASP* 1.3 89.1 - - + +
202A GLN* 1.3 56.3 + - - +
204A ILE* 3.3 12.0 + - + +
205A GLN* 2.9 30.3 + - - +
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Residues in contact with GLN 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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200A ASP* 3.1 16.3 + - - +
201A PRO* 1.3 76.7 - - - +
203A SER* 1.3 61.4 + - - +
205A GLN* 3.4 5.8 + - - +
206A GLU* 2.8 41.1 + - + +
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Residues in contact with SER 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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123A MET* 5.5 0.3 - - - +
199A ALA* 3.8 14.5 - - - +
200A ASP* 2.8 36.9 + - - -
202A GLN* 1.3 76.7 - - - +
204A ILE* 1.3 58.5 + - - +
206A GLU* 3.5 14.9 + - - +
207A SER* 3.1 25.8 + - - -
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Residues in contact with ILE 204 (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 LYS* 5.1 0.9 + - - +
199A ALA* 3.8 28.0 - - + +
200A ASP 2.9 16.4 + - - +
201A PRO* 3.7 10.1 - - + +
202A GLN 3.1 0.2 - - - -
203A SER* 1.3 74.1 - - - +
205A GLN* 1.3 62.3 + - - +
206A GLU 3.1 1.3 - - - -
207A SER* 3.3 7.5 + - - -
208A GLN* 2.9 28.6 + - + +
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Residues in contact with GLN 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 PRO 2.9 17.0 + - - +
202A GLN* 3.9 5.2 - - - +
204A ILE* 1.3 76.9 - - - +
206A GLU* 1.3 57.6 + - - +
208A GLN* 3.4 15.4 + - - +
209A ASN* 2.9 60.6 + - - +
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Residues in contact with GLU 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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123A MET* 3.4 33.2 - - + +
126A MET* 4.3 1.8 - - + +
127A TYR* 2.6 37.3 + - + +
202A GLN* 2.8 27.2 + - + +
203A SER* 3.5 15.5 + - - +
205A GLN* 1.3 77.8 - - - +
207A SER* 1.3 62.0 + - - +
209A ASN* 3.3 10.1 + - - +
210A LEU* 3.2 17.2 + - - +
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Residues in contact with SER 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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123A MET* 3.8 13.4 - - - +
185A HIS* 4.0 7.1 + - - -
189A LYS* 2.4 37.8 + - - +
203A SER 3.1 14.0 + - - -
204A ILE* 3.3 7.4 + - - -
206A GLU* 1.3 78.2 - - - +
208A GLN* 1.3 63.1 + - - +
210A LEU* 3.3 3.5 + - - +
211A SER* 3.1 24.3 + - - -
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Residues in contact with GLN 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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189A LYS* 4.0 13.6 + - - +
204A ILE* 2.9 19.1 + - + +
205A GLN* 3.6 20.6 - - - +
206A GLU 3.3 0.2 - - - -
207A SER* 1.3 76.7 - - - +
209A ASN* 1.3 63.4 + - - +
211A SER* 3.4 5.4 + - - -
212A MET* 3.2 56.3 + - + +
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Residues in contact with ASN 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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126A MET* 3.6 16.6 - - + +
130A ARG* 5.0 13.5 - - - +
205A GLN* 2.9 51.1 + - - +
206A GLU* 3.7 8.1 - - - +
207A SER 3.3 0.2 - - - -
208A GLN* 1.3 76.7 - - - +
210A LEU* 1.3 61.4 + - - +
212A MET* 3.5 7.6 + - - +
213A PHE* 3.0 28.2 + - - +
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Residues in contact with LEU 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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119A VAL* 4.0 10.5 - - + -
122A LEU* 4.0 34.1 - - + +
123A MET* 3.6 25.4 - - + +
126A MET* 3.6 19.9 - - + -
185A HIS* 3.3 33.7 - - + +
206A GLU 3.2 12.8 + - - +
207A SER 3.3 8.5 + - - +
209A ASN* 1.3 75.2 - - - +
211A SER* 1.3 60.1 + - - +
213A PHE* 3.2 5.2 + - + +
214A LEU* 2.9 52.3 + - + +
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Residues in contact with SER 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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185A HIS* 3.2 25.1 + - - -
189A LYS* 3.3 26.2 - - - +
207A SER 3.1 5.8 + - - -
208A GLN* 3.7 11.9 - - - -
209A ASN 3.3 0.2 - - - -
210A LEU* 1.3 76.3 - - - +
212A MET* 1.3 65.3 + - - +
214A LEU* 3.2 4.8 + - - +
215A ALA* 2.9 31.4 + - - +
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Residues in contact with MET 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 GLN* 3.2 39.5 + - + +
209A ASN* 3.9 7.6 - - - +
211A SER* 1.3 86.0 - - - +
213A PHE* 1.3 60.7 + - - +
215A ALA* 3.4 10.0 + - + -
216A ASN* 2.1 43.2 + - - +
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Residues in contact with PHE 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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125A PHE* 3.7 26.5 - + - -
126A MET* 3.9 26.7 - - + -
129A GLN* 3.4 43.3 - - + -
175A LYS* 2.8 51.8 + - + -
209A ASN 3.0 18.4 + - - +
210A LEU* 3.4 7.2 - - + +
212A MET* 1.3 77.6 - - - +
214A LEU* 1.3 72.3 + - + +
215A ALA 3.2 1.0 + - - -
216A ASN* 3.3 9.7 + - - +
219A LYS* 3.7 27.7 - - + +
220A ILE* 4.2 6.3 - - + -
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Residues in contact with LEU 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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122A LEU* 4.3 12.3 - - + -
125A PHE* 5.7 3.6 - - + -
175A LYS* 4.1 18.9 + - + +
181A VAL* 3.9 20.0 - - + -
182A LYS* 3.6 39.4 - - + +
185A HIS* 3.7 41.3 - - + +
210A LEU* 2.9 31.5 + - + +
211A SER* 3.9 3.8 - - - +
213A PHE* 1.3 92.2 - - + +
215A ALA* 1.3 58.2 + - - +
216A ASN 3.4 0.4 - - - -
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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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182A LYS* 4.0 21.6 - - - +
211A SER 2.9 17.9 + - - +
212A MET* 4.0 15.0 - - + +
213A PHE 3.1 0.4 - - - -
214A LEU* 1.3 77.8 - - - +
216A ASN* 1.3 63.1 + - - +
217A HIS* 3.7 2.9 + - - +
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Residues in contact with ASN 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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175A LYS* 2.9 25.1 + - - -
212A MET* 2.1 50.2 + - - +
213A PHE 3.3 1.0 + - - +
214A LEU 3.4 0.4 - - - -
215A ALA* 1.3 80.3 - - - +
217A HIS* 1.3 65.9 + - - +
219A LYS* 3.4 41.4 + - + +
222A GLN* 5.6 0.4 - - - +
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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