Contacts of the helix formed by residues 207 - 222 (chain A) in PDB entry 4C57
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
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Residue Dist Surf HB Arom Phob DC
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205A SER 4.0 2.0 + - - -
206A TRP* 1.3 73.8 - - - +
208A ALA* 1.4 63.7 + - - +
209A GLN* 3.7 20.7 - - - +
210A ARG* 3.1 26.2 + - - +
211A ARG* 3.0 27.1 + - - +
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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
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207A SER* 1.4 72.0 - - - +
209A GLN* 1.4 62.4 + - - +
211A ARG* 3.4 3.6 + - - +
212A ALA* 2.9 36.7 + - - +
235A TYR* 3.9 22.6 + - - +
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Residues in contact with GLN 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* 3.7 15.9 - - - +
208A ALA* 1.4 87.9 + - - +
210A ARG* 1.4 60.3 + - - +
212A ALA* 3.5 4.5 + - - +
213A LEU* 3.0 31.4 + - - +
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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
----------------------------------------------------------
200A HIS* 5.2 5.3 + - - -
205A SER* 5.2 4.0 + - - -
206A TRP* 3.6 63.9 - - + +
207A SER* 3.1 22.5 + - - +
209A GLN* 1.4 77.7 - - - +
211A ARG* 1.4 53.6 + - - +
213A LEU* 3.2 6.3 + - - +
214A VAL* 2.9 42.1 + - + +
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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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202A PRO* 4.6 3.0 - - - +
203A ASP 3.1 24.1 + - - +
204A TYR* 5.4 0.8 - - - +
206A TRP* 2.9 51.6 + - + +
207A SER 3.1 13.7 - - - +
208A ALA* 3.5 8.1 - - - +
210A ARG* 1.4 75.4 - - - +
212A ALA* 1.3 55.9 + - - +
214A VAL* 3.4 2.9 + - - +
215A GLU* 2.8 32.3 + - - +
234A LEU* 2.7 45.0 + - + +
235A TYR* 3.4 48.2 + - + +
237A ASN* 3.6 15.2 + - - -
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Residues in contact with ALA 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 ALA 2.9 21.9 + - - +
209A GLN* 4.0 4.5 - - - +
210A ARG 3.3 0.2 - - - -
211A ARG* 1.3 70.9 - - - +
213A LEU* 1.4 55.4 + - - +
215A GLU* 3.2 9.7 + - - +
216A GLU* 2.7 44.8 + - - +
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Residues in contact with LEU 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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209A GLN 3.0 19.3 + - - +
210A ARG* 3.7 4.9 - - - +
212A ALA* 1.4 74.8 - - - +
214A VAL* 1.4 62.5 + - + +
216A GLU* 3.4 8.3 - - - +
217A GLU* 3.2 23.4 + - - +
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Residues in contact with VAL 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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200A HIS* 4.1 32.5 - - + +
206A TRP* 3.6 28.0 - - + -
210A ARG* 2.9 27.9 + - + +
211A ARG 3.6 4.9 - - - +
213A LEU* 1.4 75.5 - - + +
215A GLU* 1.4 61.5 + - - +
216A GLU 3.3 0.5 + - - -
217A GLU* 3.3 6.6 + - - +
218A ILE* 3.1 46.1 + - + +
234A LEU* 4.3 3.6 - - + -
240A ILE* 4.3 10.1 - - + -
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Residues in contact with GLU 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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211A ARG* 2.8 20.2 + - - +
212A ALA* 3.5 9.8 - - - +
214A VAL* 1.4 72.2 - - - +
216A GLU* 1.4 56.8 + - - +
218A ILE* 3.5 5.3 + - - +
219A THR* 2.9 41.3 + - - +
231A ILE* 3.8 20.7 - - + +
232A ILE* 3.9 14.5 - - - +
234A LEU* 4.0 23.2 - - + +
235A TYR* 5.9 1.9 - - - -
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Residues in contact with GLU 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 ALA* 2.7 29.6 + - - +
213A LEU* 3.4 11.4 - - - +
214A VAL 3.2 0.2 - - - -
215A GLU* 1.4 72.1 - - - +
217A GLU* 1.4 65.6 + - - +
219A THR* 3.6 5.0 + - - -
220A ARG* 3.6 23.7 + - - +
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Residues in contact with GLU 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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172A ARG* 2.9 40.6 + - - -
196A THR* 5.6 0.9 + - - -
200A HIS* 5.6 2.8 + - - -
213A LEU 3.2 11.9 + - - +
214A VAL* 3.3 4.2 + - - +
216A GLU* 1.4 79.4 - - - +
218A ILE* 1.4 64.4 + - - +
220A ARG* 3.7 26.6 + - - +
221A ASN* 2.7 40.9 + - - +
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Residues in contact with ILE 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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172A ARG* 3.9 19.1 - - - +
200A HIS* 4.8 6.7 - - + +
214A VAL* 3.1 41.9 + - + +
215A GLU* 3.5 5.1 + - - +
217A GLU* 1.4 87.0 - - - +
219A THR* 1.4 62.0 + - - +
221A ASN* 3.0 10.6 + - - -
222A THR* 2.9 26.7 + - + +
231A ILE* 3.9 47.1 - - + -
234A LEU* 5.2 0.4 - - + -
240A ILE* 4.0 17.7 - - + -
244A GLN* 4.0 10.8 - - - +
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Residues in contact with THR 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 GLU* 2.9 25.8 + - - +
216A GLU* 4.0 6.1 - - - -
217A GLU 3.5 0.4 - - - -
218A ILE* 1.4 74.7 - - - +
220A ARG* 1.3 59.9 + - - +
221A ASN 3.3 1.0 + - - -
222A THR* 3.3 12.9 + - - +
227A ARG* 2.9 53.3 + - - +
231A ILE* 5.0 3.1 - - - +
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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 GLU* 3.6 10.8 + - - +
217A GLU* 3.7 31.1 + - - +
218A ILE 3.3 0.4 - - - -
219A THR* 1.3 79.0 - - - +
221A ASN* 1.3 79.6 + - - +
222A THR 3.5 0.9 - - - -
1339A EDO 3.7 16.3 + - - -
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Residues in contact with ASN 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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172A ARG* 3.4 32.5 + - - +
173A ASP* 3.8 3.6 - - - +
193A GLY 4.1 5.9 - - - +
194A SER* 2.9 45.0 + - - -
217A GLU* 2.7 41.5 + - - +
218A ILE 3.0 7.8 + - - +
220A ARG* 1.3 98.1 + - - +
222A THR* 1.3 59.8 + - + +
1339A EDO 3.8 5.8 + - - -
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Residues in contact with THR 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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172A ARG* 3.4 23.6 - - + +
173A ASP* 4.1 2.9 - - - -
218A ILE* 2.9 36.0 + - + +
219A THR* 3.3 4.2 + - - +
220A ARG 3.5 0.2 - - - -
221A ASN* 1.3 76.7 - - - +
223A THR* 1.4 60.4 + - - +
224A PRO* 3.8 1.6 - - - +
226A TYR* 5.5 2.2 - - - +
227A ARG* 3.0 57.2 + - + +
231A ILE* 4.0 8.6 - - + +
244A GLN* 5.3 2.5 - - - +
1339A EDO 3.3 15.2 + - - -
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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