Contacts of the helix formed by residues 209 - 221 (chain A) in PDB entry 1RQG
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 LYS 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A PRO 4.1 0.2 + - - -
208A TRP* 1.3 72.8 - - - +
210A PRO* 1.3 62.8 - - + +
211A ASN* 4.2 15.9 - - + +
212A VAL* 2.7 50.5 + - + +
213A LYS 2.9 10.4 + - - -
334A ALA 5.6 4.2 + - - -
377A GLU 6.3 0.8 - - - -
378A THR* 5.9 7.5 - - - +
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Residues in contact with PRO 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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208A TRP 3.5 6.5 - - - +
209A LYS* 1.3 79.3 - - + +
211A ASN* 1.3 59.6 + - - +
212A VAL 2.5 17.2 + - - -
213A LYS* 4.0 9.9 - - + -
214A ASN* 2.8 47.3 + - - +
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Residues in contact with ASN 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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209A LYS* 3.1 19.3 + - + +
210A PRO* 1.3 78.7 - - - +
212A VAL* 1.3 56.8 + - + +
215A MET* 2.7 31.9 - - - +
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Residues in contact with VAL 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 TRP* 4.7 9.0 - - + -
209A LYS* 2.7 30.8 + - + +
210A PRO 2.5 5.6 + - - -
211A ASN* 1.3 80.0 - - + +
213A LYS* 1.3 68.8 + - - +
214A ASN 2.9 1.8 + - - -
215A MET* 3.0 3.9 + - - -
216A VAL* 2.7 33.8 + - + +
300A ILE* 3.5 45.8 - - + -
332A ILE* 4.7 10.5 - - + -
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Residues in contact with LYS 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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203A ILE* 3.3 22.6 - - + +
204A GLU* 2.8 47.4 + - - +
206A GLN 3.7 17.5 - - - +
208A TRP* 4.0 21.7 - - + +
209A LYS 2.9 12.6 + - - +
210A PRO* 4.0 8.7 - - + -
212A VAL* 1.3 79.7 - - - +
214A ASN* 1.3 62.6 + - - +
216A VAL* 3.3 7.3 - - - +
217A LEU* 2.9 38.8 + - + +
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Residues in contact with ASN 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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210A PRO* 2.8 39.6 + - - +
213A LYS* 1.3 76.5 + - - +
215A MET* 1.3 63.0 + - + +
216A VAL 2.9 1.3 - - - -
217A LEU* 2.7 39.4 + - - +
218A SER* 2.9 11.9 + - - -
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Residues in contact with MET 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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210A PRO 5.2 0.4 - - - +
211A ASN* 2.7 35.9 - - - +
212A VAL* 3.0 6.0 + - - +
214A ASN* 1.3 75.2 - - + +
216A VAL* 1.3 61.0 + - + +
218A SER* 3.5 11.5 - - - -
219A TRP* 3.1 35.1 + - + -
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Residues in contact with VAL 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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203A ILE* 3.4 31.4 - - + -
208A TRP* 5.4 1.8 - - + -
212A VAL* 2.7 41.1 + - + +
213A LYS* 3.3 10.1 - - - +
215A MET* 1.3 75.8 - - + +
217A LEU* 1.3 66.0 + - - +
219A TRP* 3.1 10.7 + - - +
220A ILE* 3.0 30.5 + - + +
300A ILE* 4.4 7.0 - - + +
301A PRO* 5.8 2.2 - - + -
304A ALA* 4.3 17.0 - - + -
305A ILE* 3.9 17.7 - - + -
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Residues in contact with LEU 217 (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 LYS* 3.5 40.4 - - + +
203A ILE* 3.5 28.5 - - + -
204A GLU* 4.0 14.8 - - - +
213A LYS* 2.9 32.8 - - + +
214A ASN* 2.7 28.5 + - - +
216A VAL* 1.3 72.0 - - - +
218A SER* 1.3 50.9 + - - +
220A ILE* 3.0 7.8 + - - +
221A GLU* 2.8 44.5 + - - +
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Residues in contact with SER 218 (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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214A ASN 2.9 10.7 + - - -
215A MET* 3.5 20.2 + - - +
217A LEU* 1.3 74.5 - - - +
219A TRP* 1.3 55.7 + - - +
221A GLU* 2.6 25.2 + - - +
222A GLU* 2.5 29.4 + - - +
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Residues in contact with TRP 219 (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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215A MET* 3.1 23.5 + - + +
216A VAL* 3.1 13.9 + - - +
218A SER* 1.3 83.6 + - - +
220A ILE* 1.3 57.5 + - - +
222A GLU* 2.3 27.0 - - - +
223A GLY 4.3 6.6 - - - +
224A LEU* 4.6 3.0 - - - +
301A PRO* 4.2 35.4 - - + -
305A ILE* 4.3 15.7 - - + -
306A PHE* 5.1 14.1 - + - -
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Residues in contact with ILE 220 (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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196A ALA* 4.0 31.4 - - + +
199A LEU* 4.7 6.3 - - + -
200A LYS* 4.6 17.3 - - + +
203A ILE* 3.6 30.5 - - + -
216A VAL* 3.1 20.0 - - + +
217A LEU* 3.0 10.3 + - - +
218A SER 2.9 0.6 - - - -
219A TRP* 1.3 72.6 - - - +
221A GLU* 1.3 57.2 + - - +
222A GLU 2.7 18.1 + - - -
223A GLY* 3.5 12.2 + - - +
224A LEU* 4.1 21.0 - - + +
305A ILE* 3.8 21.3 - - + -
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Residues in contact with GLU 221 (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 LYS* 3.4 32.5 + - - +
217A LEU* 2.8 27.7 + - - +
218A SER* 2.6 24.3 + - - +
220A ILE* 1.3 69.8 - - - +
222A GLU* 1.3 59.5 + - - +
223A GLY 3.9 0.8 + - - -
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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