Contacts of the helix formed by residues 208 - 221 (chain A) in PDB entry 4YC3
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LEU* 3.9 12.8 - - - +
206A GLY 3.4 1.7 - - - -
207A ASP* 1.3 95.3 + - - +
209A GLU* 1.3 60.8 + - - +
210A ILE* 3.9 2.1 - - - +
211A ASP* 3.2 12.7 + - - +
212A GLN* 2.9 29.1 + - - +
21C HIS* 4.1 2.8 - - - -
23C MET* 4.7 4.2 - - - -
63C GLU* 3.8 5.4 - - - -
65C HIS* 5.8 0.2 - - - -
66C ILE* 3.3 32.9 - - - +
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Residues in contact with GLU 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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161A THR 5.7 1.4 - - - +
167A LEU* 3.4 25.1 - - + +
170A ARG* 5.9 0.9 - - - -
175A LEU* 3.8 28.7 - - + +
208A SER* 1.3 71.7 - - - +
210A ILE* 1.3 62.4 + - - +
212A GLN* 3.3 5.1 + - - +
213A LEU* 3.2 25.9 + - - +
60C HIS* 3.3 23.2 + - - +
62C PRO* 3.9 16.7 - - - +
63C GLU* 2.8 31.5 + - - +
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Residues in contact with ILE 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 SER* 3.9 5.2 - - - +
209A GLU* 1.3 79.3 - - - +
211A ASP* 1.3 66.4 + - - +
213A LEU* 3.3 16.9 + - + +
214A PHE* 3.1 59.4 + - + -
241A PHE* 4.3 4.9 - - + -
21C HIS* 4.7 4.0 - - + +
58C MET* 4.2 11.7 - - + -
60C HIS* 4.1 26.9 - - + +
63C GLU* 3.1 14.6 + - - +
66C ILE* 3.8 30.1 - - + -
68C LEU* 3.9 21.5 - - + -
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Residues in contact with ASP 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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206A GLY* 3.4 0.7 - - - -
207A ASP* 2.9 47.5 + - - +
208A SER* 3.2 10.2 + - - +
209A GLU 3.3 0.2 - - - -
210A ILE* 1.3 82.2 - - - +
212A GLN* 1.3 62.1 + - - +
214A PHE* 3.5 10.4 + - - +
215A ARG* 2.9 56.1 + - - +
12C TYR* 5.5 2.1 - - - -
21C HIS* 3.3 21.3 + - + -
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Residues in contact with GLN 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.4 25.3 + - + +
168A TRP* 3.4 22.4 + - - +
170A ARG 5.0 1.6 + - - +
175A LEU* 3.9 18.2 - - + -
188A TRP* 6.1 0.2 - - - +
204A PHE* 3.0 38.6 + - - +
206A GLY* 2.9 30.2 + - - -
208A SER 2.9 17.0 + - - +
209A GLU* 3.5 9.4 - - - +
211A ASP* 1.3 73.6 - - - +
213A LEU* 1.3 65.9 + - - +
215A ARG* 3.3 4.5 + - - +
216A ILE* 3.1 33.9 + - + +
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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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172A PRO* 4.4 11.2 - - + -
175A LEU* 3.6 40.6 - - + +
176A LEU* 3.9 30.3 - - + -
209A GLU 3.2 13.0 + - - +
210A ILE* 3.5 22.9 - - + +
212A GLN* 1.3 78.0 - - - +
214A PHE* 1.3 54.8 + - + +
216A ILE* 3.1 7.9 + - + +
217A PHE* 2.7 67.6 + - + -
241A PHE* 4.8 2.5 - - + -
60C HIS* 4.7 6.5 - - + -
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Residues in contact with PHE 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 ILE* 3.1 47.9 + - + +
211A ASP* 3.8 10.5 - - - +
212A GLN 3.3 0.2 - - - -
213A LEU* 1.3 78.2 - - + +
215A ARG* 1.3 53.5 + - + +
217A PHE* 3.2 12.1 + + - -
218A ARG* 2.7 36.6 + - - +
241A PHE* 3.8 22.7 - + - -
242A PRO* 3.7 21.3 - - + -
244A TRP* 3.4 18.3 - + + -
12C TYR* 3.6 39.3 - + + -
21C HIS* 5.5 1.8 - + - -
57C TYR* 3.8 17.0 - - - -
58C MET* 4.4 3.1 - - - -
68C LEU* 3.8 11.7 - - + -
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Residues in contact with ARG 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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204A PHE* 3.9 18.5 - - + -
205A HIS* 3.3 59.8 + - - +
206A GLY 3.6 4.5 - - - +
207A ASP* 5.3 4.0 + - - +
211A ASP* 2.9 47.7 + - - +
212A GLN* 3.6 4.5 - - - +
214A PHE* 1.3 71.5 - - + +
216A ILE* 1.3 66.0 + - - +
218A ARG* 3.5 7.1 + - - +
219A ALA* 3.3 22.7 + - - +
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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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170A ARG 4.4 6.1 - - - +
172A PRO* 5.0 5.8 - - + -
175A LEU* 4.3 13.7 - - + -
188A TRP* 3.9 26.7 - - + -
204A PHE* 3.6 30.7 - - + -
212A GLN* 3.1 36.0 + - + +
213A LEU* 3.4 10.8 - - + +
215A ARG* 1.3 76.6 - - - +
217A PHE* 1.3 59.4 + - + +
219A ALA* 3.3 1.7 + - - -
220A LEU* 3.0 32.4 + - + +
270A TYR* 3.4 29.9 + - + +
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Residues in contact with PHE 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 PRO* 5.5 1.3 - - + -
176A LEU* 4.7 6.5 - - + -
213A LEU* 2.7 53.4 + - + -
214A PHE* 3.6 18.2 - + - +
216A ILE* 1.3 73.8 - - + +
218A ARG* 1.3 61.6 + - - +
221A GLY* 2.7 30.5 + - - -
222A THR* 3.8 17.9 - - + +
223A PRO* 3.4 28.7 - - + -
241A PHE* 3.5 45.5 - + + -
242A PRO* 4.8 0.4 - - + -
244A TRP* 3.6 20.0 - + + +
270A TYR* 3.5 22.0 - + - -
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Residues in contact with ARG 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 PHE 2.7 21.2 + - - +
215A ARG* 3.9 7.4 - - - +
216A ILE 3.3 0.2 - - - -
217A PHE* 1.3 74.4 - - - +
219A ALA* 1.3 60.2 + - - +
244A TRP* 3.7 42.6 - - + +
245A LYS 4.5 3.8 - - - +
247A GLY 4.2 6.1 - - - +
252A HIS* 4.8 3.9 + - - +
12C TYR* 3.3 35.1 - - - +
13C PHE* 3.7 37.4 + - - +
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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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204A PHE* 3.7 24.2 - - + -
215A ARG 3.3 15.7 + - - +
216A ILE 3.8 0.4 - - - +
217A PHE 3.1 0.6 - - - -
218A ARG* 1.3 78.8 - - - +
220A LEU* 1.3 63.5 + - + +
221A GLY 3.5 0.6 + - - -
246A PRO* 4.2 0.3 - - - +
247A GLY 2.9 22.7 - - - +
248A SER* 3.0 13.5 + - - -
249A LEU* 5.6 1.8 - - + -
252A HIS* 3.7 30.7 - - + +
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Residues in contact with LEU 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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188A TRP* 3.8 22.9 - - + -
204A PHE* 4.3 13.0 - - + -
216A ILE* 3.0 21.2 + - + +
219A ALA* 1.3 81.6 - - + +
221A GLY* 1.3 59.4 + - - +
246A PRO* 3.3 24.4 - - - +
248A SER* 4.3 6.3 - - - +
249A LEU* 3.9 28.9 - - + -
268A LEU* 3.7 33.2 - - + +
270A TYR* 3.6 21.2 - - + +
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Residues in contact with GLY 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 PHE* 2.7 22.4 + - - +
219A ALA 3.5 1.6 + - - -
220A LEU* 1.3 71.5 - - - +
222A THR* 1.3 65.1 + - - -
244A TRP 3.2 13.0 - - - -
245A LYS 3.7 1.9 - - - -
246A PRO* 3.6 16.9 - - - -
270A TYR* 2.7 28.7 + - - -
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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