Contacts of the helix formed by residues 200 - 212 (chain A) in PDB entry 1JQD
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 THR 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.8 6.9 - - - +
173A VAL* 3.4 18.4 - - + -
174A SER 3.8 7.0 - - - -
175A GLY* 3.6 1.8 - - - -
180A ASP* 3.1 37.7 + - + +
183A TRP* 3.9 21.1 - - + -
199A ILE* 1.3 80.8 - - - +
201A SER* 1.3 64.4 + - - +
202A ASP* 3.0 14.6 + - - +
203A ASP* 3.1 23.0 + - - +
204A LEU* 3.1 12.0 + - - +
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Residues in contact with SER 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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172A VAL* 3.5 7.5 - - - +
173A VAL 3.0 7.9 + - - -
174A SER* 3.7 1.2 + - - -
175A GLY* 3.0 17.8 + - - -
200A THR* 1.3 71.8 - - - +
202A ASP* 1.3 56.2 + - - +
204A LEU* 3.7 5.6 - - - -
205A THR* 2.8 35.0 + - - +
217A CYS* 4.3 7.9 - - - -
219A ASP* 4.5 0.9 + - - -
286A SER* 2.8 39.9 + - - -
288A ILE* 4.3 9.6 - - - -
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Residues in contact with ASP 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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175A GLY* 3.4 23.6 - - - +
180A ASP* 4.4 5.0 - - - +
184A LYS* 5.5 6.9 + - - +
200A THR* 3.0 11.0 + - - +
201A SER* 1.3 80.7 + - - +
203A ASP* 1.3 64.6 + - - +
205A THR* 3.2 8.2 + - - -
206A GLN* 3.1 23.8 + - - +
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Residues in contact with ASP 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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180A ASP* 5.4 0.3 - - - +
184A LYS* 6.0 2.2 - - - -
198A TYR 4.3 4.3 - - - +
199A ILE* 3.6 16.7 - - + -
200A THR* 3.1 34.3 + - - +
202A ASP* 1.3 77.7 - - - +
204A LEU* 1.3 58.9 + - - +
206A GLN* 3.3 13.3 + - - +
207A MET* 3.0 43.3 + - + +
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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
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145A LEU* 3.9 19.7 - - + -
151A ILE* 4.4 7.6 - - + -
155A LEU* 3.7 30.1 - - + -
170A ILE* 3.5 28.5 - - + -
172A VAL* 4.0 12.6 - - + -
199A ILE* 5.9 3.6 - - + +
200A THR 3.1 9.8 + - - +
201A SER* 3.6 8.3 - - - +
203A ASP* 1.3 76.8 - - - +
205A THR* 1.3 61.6 + - - +
207A MET* 3.0 7.4 + - + +
208A LEU* 2.8 38.2 + - + +
288A ILE* 3.2 28.5 - - + -
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Residues in contact with THR 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 SER* 2.8 26.2 + - - +
202A ASP* 3.2 11.4 + - - -
204A LEU* 1.3 73.0 - - - +
206A GLN* 1.3 59.2 + - - +
208A LEU* 4.2 4.0 - - - -
209A ASP* 2.8 38.1 + - - +
215A TYR* 3.2 39.0 + - + -
217A CYS* 4.4 13.5 - - + -
288A ILE* 4.3 14.6 - - + -
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Residues in contact with GLN 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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202A ASP 3.1 18.8 + - - +
203A ASP* 3.4 12.0 - - - +
205A THR* 1.3 79.2 + - - +
207A MET* 1.3 58.4 + - + +
209A ASP* 3.3 9.6 + - + +
210A ASN* 3.0 50.6 + - - +
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Residues in contact with MET 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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151A ILE* 3.5 37.2 - - + -
152A PRO* 3.8 29.8 - - + -
155A LEU* 4.3 9.6 - - + -
197A GLN* 6.0 1.6 - - - +
199A ILE* 6.2 1.8 - - + -
203A ASP* 3.0 25.6 + - + +
204A LEU* 3.0 7.6 + - - +
206A GLN* 1.3 77.6 - - + +
208A LEU* 1.3 57.3 + - - +
210A ASN* 3.4 7.9 + - - +
211A LEU* 2.9 35.9 + - + +
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Residues in contact with LEU 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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155A LEU* 3.7 22.9 - - + -
204A LEU* 2.8 31.1 + - + +
205A THR* 3.8 5.8 - - - +
207A MET* 1.3 72.9 - - - +
209A ASP* 1.3 61.1 + - - +
211A LEU* 3.2 4.1 + - + -
212A GLY 2.9 23.0 + - - -
213A LEU* 3.1 35.2 + - + +
215A TYR* 3.8 26.2 - - + -
288A ILE* 3.8 29.2 - - + -
290A ILE* 3.6 26.9 - - + -
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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 THR* 2.8 26.8 + - - +
206A GLN* 3.5 9.0 - - + +
208A LEU* 1.3 76.1 - - - +
210A ASN* 1.3 65.8 + - - +
212A GLY* 3.0 14.8 + - - -
213A LEU 5.2 1.3 - - - -
215A TYR* 2.9 30.6 + - - -
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Residues in contact with ASN 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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206A GLN* 3.0 41.9 + - - +
207A MET* 3.8 5.9 - - - +
209A ASP* 1.3 79.2 - - - +
211A LEU* 1.3 63.1 + - + +
212A GLY* 3.3 0.9 + - - -
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Residues in contact with LEU 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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152A PRO* 3.8 28.5 - - + +
155A LEU* 3.8 37.5 - - + -
156A LYS* 4.3 26.6 + - + +
207A MET 2.9 24.6 + - - +
208A LEU* 3.6 6.3 - - - +
209A ASP 3.2 0.4 - - - -
210A ASN* 1.3 77.1 - - + +
212A GLY* 1.3 61.9 + - - +
213A LEU* 4.1 23.4 - - + +
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Residues in contact with GLY 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 LEU 2.9 4.2 + - - -
209A ASP* 3.0 13.6 + - - -
210A ASN 3.1 1.5 - - - -
211A LEU* 1.3 79.6 - - - +
213A LEU* 1.3 65.1 - - - +
214A LYS 4.1 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