Contacts of the helix formed by residues 204 - 219 (chain A) in PDB entry 2JFS
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 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A SER* 3.3 4.2 - - - +
203A PRO* 1.3 78.0 - - - +
205A PRO* 1.4 72.6 - - - +
206A GLN* 2.9 24.4 + - - +
207A VAL* 2.9 39.0 + - + +
208A ALA 2.9 9.7 + - - -
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Residues in contact with PRO 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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6A SER* 3.5 30.3 - - - +
7A ALA 4.4 0.9 - - - -
8A ALA* 3.5 25.4 - - + +
179A ARG* 3.9 6.7 - - - +
203A PRO 3.3 9.4 - - - +
204A ASP* 1.4 89.0 - - - +
206A GLN* 1.3 58.8 + - - +
208A ALA* 3.6 7.2 - - + +
209A VAL* 3.1 21.5 + - - +
229A VAL* 3.8 18.8 - - + +
231A ASP* 3.2 21.8 - - - +
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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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8A ALA* 3.7 17.5 - - + +
9A THR 4.5 7.0 + - - +
10A ALA* 5.7 0.8 - - - +
204A ASP* 2.9 18.4 + - - +
205A PRO* 1.3 79.5 - - - +
207A VAL* 1.3 60.5 + - - +
209A VAL* 3.4 22.0 - - - +
210A ARG* 3.3 51.0 - - - +
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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
----------------------------------------------------------
202A SER* 3.9 10.3 - - - -
204A ASP* 2.9 30.5 + - + +
206A GLN* 1.3 76.3 - - - +
208A ALA* 1.3 65.4 + - - +
210A ARG* 3.1 20.0 + - - +
211A ARG* 2.9 46.7 + - + +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 3.7 24.7 - - - +
199A ALA 3.5 21.5 - - - +
200A ALA* 4.3 4.0 - - - +
202A SER* 3.7 5.6 - - - +
204A ASP 2.9 9.8 + - - +
205A PRO* 3.3 11.0 + - + +
207A VAL* 1.3 75.8 - - - +
209A VAL* 1.3 57.1 + - - +
211A ARG* 3.2 2.6 + - - +
212A LEU* 2.9 34.8 + - - +
229A VAL* 4.3 10.8 - - + -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.6 27.6 - - + +
9A THR* 3.7 16.2 - - - +
10A ALA* 3.7 15.7 - - + -
205A PRO 3.1 16.0 + - - +
206A GLN* 3.4 29.8 - - - +
208A ALA* 1.3 74.5 - - - +
210A ARG* 1.3 64.9 + - - +
212A LEU* 3.4 4.2 + - - +
213A VAL* 3.2 27.4 + - - +
227A VAL* 3.8 17.7 - - + +
229A VAL* 3.6 20.6 - - + -
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Residues in contact with ARG 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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10A ALA* 5.1 4.5 - - + -
206A GLN* 3.3 53.6 + - - +
207A VAL* 3.1 20.8 + - + +
209A VAL* 1.3 79.3 - - + +
211A ARG* 1.3 59.4 + - + +
213A VAL* 3.3 7.2 + - - +
214A GLU* 3.0 39.7 + - - +
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Residues in contact with ARG 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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198A ASP* 2.6 40.1 + - - -
199A ALA* 3.7 19.6 - - + +
202A SER* 2.9 28.0 + - - +
207A VAL* 2.9 32.9 + - + +
208A ALA 3.8 1.6 - - - +
210A ARG* 1.3 79.8 - - + +
212A LEU* 1.3 56.4 + - - +
214A GLU* 3.2 18.2 + - - +
215A VAL* 2.8 34.3 + - + +
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Residues in contact with LEU 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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181A LEU* 3.9 26.7 - - + -
187A LEU* 3.5 29.2 - - + +
196A ILE* 3.6 41.3 - - + +
199A ALA* 3.8 10.1 - - + -
200A ALA* 3.8 15.9 - - + +
208A ALA 2.9 27.8 + - - +
209A VAL* 3.7 4.7 - - - +
210A ARG 3.3 0.2 - - - -
211A ARG* 1.3 76.8 - - - +
213A VAL* 1.3 61.4 + - - +
215A VAL* 3.3 3.6 + - + +
216A ALA* 3.1 18.5 + - - +
225A THR* 5.1 0.7 - - - -
227A VAL* 4.2 15.0 - - + -
229A VAL* 4.2 11.0 - - + -
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Residues in contact with VAL 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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10A ALA* 3.9 21.3 - - + -
11A THR 4.8 0.4 - - - +
12A ASP* 3.4 44.4 - - + +
209A VAL 3.2 11.7 + - - +
210A ARG* 3.7 9.2 - - - +
212A LEU* 1.3 79.3 - - - +
214A GLU* 1.3 60.4 - - + +
216A ALA* 3.3 2.1 + - - +
217A ASN* 2.9 35.7 + - - +
225A THR* 4.2 21.7 - - + +
227A VAL* 4.4 7.9 - - + -
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Residues in contact with GLU 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 ARG* 3.0 26.9 + - + +
211A ARG* 3.2 19.3 + - - +
213A VAL* 1.3 79.6 - - + +
215A VAL* 1.3 58.7 + - + +
217A ASN* 3.3 5.4 + - - +
218A ASP* 2.8 34.3 + - - +
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Residues in contact with VAL 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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187A LEU* 5.3 0.4 - - + -
191A ALA* 3.6 22.0 - - + -
195A LEU* 3.8 38.1 - - + +
196A ILE* 3.9 19.3 - - + +
199A ALA* 4.1 7.9 - - + -
211A ARG* 2.8 22.7 + - + +
212A LEU* 3.7 7.0 - - - +
214A GLU* 1.3 77.4 - - + +
216A ALA* 1.3 63.3 + - - +
218A ASP* 3.9 5.4 - - - +
219A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 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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186A GLY 4.1 11.2 - - - +
187A LEU* 4.1 14.8 - - + +
212A LEU 3.1 16.9 + - - +
213A VAL 3.7 4.0 - - - +
215A VAL* 1.3 79.8 - - - +
217A ASN* 1.3 63.6 + - - +
219A ALA* 3.3 13.8 + - - +
220A GLY 3.5 0.7 + - - -
221A GLY* 3.0 18.3 + - - -
225A THR* 3.5 31.4 - - + +
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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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12A ASP* 2.7 34.1 + - - +
14A GLY* 3.5 18.1 - - - -
15A PRO* 3.7 17.3 - - + +
213A VAL* 2.9 26.1 + - - +
214A GLU* 4.0 5.1 - - - +
216A ALA* 1.3 79.4 - - - +
218A ASP* 1.3 63.2 + - - +
220A GLY* 3.0 14.6 + - - -
221A GLY* 3.4 12.2 + - - +
223A ASP 4.8 2.4 - - - +
225A THR* 5.1 3.5 + - - -
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Residues in contact with ASP 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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195A LEU* 6.0 2.1 - - - +
214A GLU 2.8 19.1 + - - +
215A VAL* 3.9 4.5 - - - +
217A ASN* 1.3 76.9 - - - +
219A ALA* 1.3 59.4 + - - +
220A GLY* 3.1 1.7 + - - -
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Residues in contact with ALA 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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190A ALA* 3.9 20.0 - - + +
191A ALA* 3.6 36.3 - - + +
215A VAL 3.1 17.4 + - - +
216A ALA 3.6 6.1 - - - +
217A ASN 3.1 0.4 - - - -
218A ASP* 1.3 76.2 - - - +
220A GLY* 1.3 54.8 + - - +
221A GLY 3.8 0.9 - - - -
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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