Contacts of the helix formed by residues 207 - 222 (chain A) in PDB entry 6FQP
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 SER 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER* 3.8 1.3 - - - -
206A LEU* 1.3 75.8 - - - +
208A THR* 1.3 66.0 + - - +
209A LEU* 3.3 8.7 + - - +
210A GLN* 2.8 43.1 + - - +
211A VAL* 2.9 21.8 + - - +
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Residues in contact with THR 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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197A LYS* 5.1 13.9 - - + -
198A ALA* 5.6 3.0 - - - -
201A SER* 3.4 20.7 + - - +
207A SER* 1.3 73.4 - - - +
209A LEU* 1.3 57.9 + - - +
211A VAL* 3.1 3.1 + - - +
212A CYS* 2.8 42.6 + - - -
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Residues in contact with LEU 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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207A SER* 3.2 8.7 + - - +
208A THR* 1.3 78.2 - - - +
210A GLN* 1.3 54.5 + - + +
212A CYS* 3.3 10.0 + - + +
213A ASN* 2.7 59.1 + - - +
6L C 3.7 20.2 - - - +
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Residues in contact with GLN 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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171A LEU* 4.1 15.9 - - + +
205A HIS 5.0 0.3 - - - +
206A LEU* 3.6 25.4 - - + +
207A SER* 2.8 44.6 + - - +
209A LEU* 1.3 77.4 - - + +
211A VAL* 1.3 56.9 + - - +
213A ASN* 3.3 4.7 + - - +
214A TRP* 2.9 30.5 + - - +
5L A 2.9 42.1 + - - +
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Residues in contact with VAL 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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179A LEU* 4.1 10.1 - - + -
197A LYS* 4.4 15.7 - - + +
200A LEU* 4.2 12.6 - - + -
201A SER* 3.5 30.7 - - - +
204A THR* 4.1 4.5 - - - +
206A LEU* 4.0 16.6 - - + -
207A SER 2.9 14.2 + - - +
208A THR* 3.6 6.1 - - - +
210A GLN* 1.3 76.4 - - - +
212A CYS* 1.3 64.8 + - - +
214A TRP* 3.2 6.6 + - - +
215A PHE* 3.1 50.9 + - + -
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Residues in contact with CYS 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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197A LYS* 3.6 38.6 - - - +
208A THR* 2.8 29.0 + - - +
209A LEU* 3.5 14.8 - - + +
211A VAL* 1.3 73.1 - - - +
213A ASN* 1.3 65.5 + - - +
215A PHE* 2.9 17.7 + - - +
216A ILE* 2.9 26.4 + - + +
7M A 6.0 2.0 - - - -
8M G 5.1 0.4 - - - -
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Residues in contact with ASN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 2.7 47.4 + - - +
210A GLN* 3.3 6.7 + - - +
212A CYS* 1.3 73.8 - - - +
214A TRP* 1.3 64.8 + - - +
216A ILE* 3.2 15.8 + - - +
217A ASN* 2.9 36.6 + - - +
4L G 5.6 1.1 - - + -
5L A 4.0 34.9 + - + +
6L C 3.6 29.0 + - - +
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Residues in contact with TRP 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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171A LEU* 4.0 14.6 - - + -
176A VAL* 4.0 19.8 - - + +
179A LEU* 3.6 65.5 - - + -
180A ARG* 3.7 17.5 - - + -
183A LEU* 4.0 13.9 - - + -
210A GLN 2.9 16.9 + - - +
211A VAL 3.6 4.0 - - - +
212A CYS 3.2 0.2 - - - -
213A ASN* 1.3 75.8 - - - +
215A PHE* 1.3 77.7 + + - +
217A ASN* 3.7 9.0 - - + +
218A ALA* 2.8 50.5 + - + +
222A LEU* 4.1 17.9 - - + -
4L G 3.9 20.2 + - - -
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Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 4.0 13.9 - - + -
182A TRP* 3.7 37.0 - + - -
183A LEU* 4.4 14.8 - - + -
190A ALA 4.2 3.8 - - - -
192A PRO* 4.0 16.2 - - + -
197A LYS* 5.8 0.9 - - + -
200A LEU* 3.8 18.4 - - + -
211A VAL* 3.1 42.4 + - + -
212A CYS* 2.9 10.3 + - - +
214A TRP* 1.3 98.2 - + - +
216A ILE* 1.3 62.3 + - - +
218A ALA* 4.3 1.1 - - + +
219A ARG* 2.9 61.9 + - + +
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Residues in contact with ILE 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 CYS* 2.9 20.4 + - + +
213A ASN* 3.8 20.0 - - - +
215A PHE* 1.3 78.2 - - - +
217A ASN* 1.3 60.1 + - - +
219A ARG* 3.8 21.4 - - - +
220A ARG* 3.4 25.6 + - - +
6L C 5.2 5.4 - - - +
8M G 4.4 11.9 - - + +
9M C 3.8 38.6 + - + +
10M T 3.6 32.3 - - + +
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Residues in contact with ASN 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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213A ASN* 2.9 27.0 + - - +
214A TRP* 3.8 7.9 - - + +
216A ILE* 1.3 76.4 - - - +
218A ALA* 1.3 59.8 + - - +
220A ARG* 3.0 19.2 + - - +
221A ARG* 2.8 57.3 + - - +
4L G 3.7 14.5 - - - +
5L A 3.1 46.7 + - - -
6L C 4.5 2.4 + - - +
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Residues in contact with ALA 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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183A LEU* 3.8 14.0 - - + +
214A TRP* 2.8 55.8 + - + +
215A PHE* 4.2 1.8 - - - +
217A ASN* 1.3 69.6 - - - +
219A ARG* 1.3 63.0 + - - +
220A ARG 3.1 1.6 - - - -
221A ARG* 4.1 3.8 - - - +
222A LEU* 2.9 34.3 + - + +
223A LEU* 3.0 9.5 + - - +
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Residues in contact with ARG 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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183A LEU* 5.0 4.5 - - + +
190A ALA* 3.1 29.3 + - + +
191A TYR* 3.3 42.1 - - - +
192A PRO* 4.4 2.6 - - - +
215A PHE* 2.9 43.0 + - + +
216A ILE* 3.8 20.4 - - - +
218A ALA* 1.3 75.6 - - - +
220A ARG* 1.3 62.3 + - + +
223A LEU* 3.5 35.3 - - + +
224A PRO* 3.6 8.1 - - - +
8M G 3.5 21.4 + - - +
9M C 2.7 37.3 + - - +
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Residues in contact with ARG 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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216A ILE* 3.4 17.9 + - - +
217A ASN* 3.0 32.5 + - - +
219A ARG* 1.3 81.0 - - + +
221A ARG* 1.3 71.8 + - + +
224A PRO* 3.9 15.2 - - - +
5L A 3.2 5.1 - - - +
6L C 4.3 1.8 - - - +
9M C 5.9 0.7 - - + -
10M T 3.5 42.4 - - + +
11M G 2.7 51.7 + - - -
12M T 3.5 9.5 + - - +
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Residues in contact with ARG 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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217A ASN* 2.8 41.7 + - - +
218A ALA* 4.7 0.2 - - - -
220A ARG* 1.3 85.7 - - + +
222A LEU* 1.3 76.1 + - + +
224A PRO* 4.7 1.8 - - - -
225A ASP* 5.0 8.8 - - - -
3L T 3.6 38.3 + - - +
4L G 3.0 46.5 + - - -
5L A 3.5 5.9 - - - +
12M T 3.3 19.8 + - - +
13M C 4.6 0.2 - - - +
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Residues in contact with LEU 222 (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 ARG* 3.8 37.0 - - + +
183A LEU* 4.3 9.6 - - + -
214A TRP* 4.1 18.8 - - + -
218A ALA* 2.9 16.7 + - + +
221A ARG* 1.3 94.2 - - + +
223A LEU* 1.3 69.2 + - - +
224A PRO* 3.4 1.7 - - - -
225A ASP* 3.5 9.3 + - - +
226A MET* 3.3 28.5 + - + +
3L T 4.7 13.9 - - - +
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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