Contacts of the helix formed by residues 207 - 223 (chain A) in PDB entry 2FY2
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 ARG 3.4 1.6 + - - -
206A LEU* 1.3 76.0 - - - +
208A GLU* 1.3 64.4 + - - +
209A GLY* 3.4 5.6 + - - -
210A ASP* 2.8 49.4 + - - -
211A LEU* 3.0 12.4 + - - +
352A ARG* 3.3 44.0 - - - -
353A SER 4.0 6.2 + - - -
354A PRO* 4.6 1.4 - - - +
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.3 3.3 - - - +
118A ALA* 3.6 20.3 - - + +
119A SER* 3.3 35.5 + - - +
122A SER* 4.0 16.0 + - - +
206A LEU 3.8 1.0 + - - -
207A SER* 1.3 73.0 - - - +
209A GLY* 1.3 59.3 + - - +
211A LEU* 3.5 11.5 + - - +
212A PHE* 3.1 19.8 + - - +
342A HIS* 5.7 1.6 - - - -
349A GLU* 2.5 49.0 + - + +
352A ARG* 4.7 4.2 - - - +
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 2.9 6.5 + - - -
208A GLU* 1.3 79.0 - - - +
210A ASP* 1.3 63.5 + - - +
212A PHE* 3.3 9.4 + - - +
213A THR* 3.1 24.9 + - - -
349A GLU* 4.3 2.4 + - - -
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Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.3 31.3 - - + +
207A SER* 2.8 25.2 + - - +
209A GLY* 1.3 70.2 - - - +
211A LEU* 1.3 60.3 + - - +
213A THR* 3.2 8.5 + - - -
214A GLN* 2.8 35.4 + - - +
353A SER 3.6 4.2 - - - +
354A PRO* 3.5 9.0 - - - +
355A MET* 3.1 33.2 + - - +
359A LEU* 4.2 16.7 - - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 3.5 31.9 - - + +
121A ILE* 4.0 28.0 - - + -
122A SER* 4.3 8.3 - - - +
125A LEU* 5.3 2.7 - - + -
197A LEU* 4.2 11.7 - - + -
199A VAL* 4.1 12.8 - - + -
206A LEU* 3.7 35.9 - - + +
207A SER 3.0 17.6 + - - +
208A GLU* 3.6 13.0 - - - +
210A ASP* 1.3 78.2 - - - +
212A PHE* 1.3 56.3 + - - +
214A GLN* 3.2 5.5 + - - +
215A LEU* 2.8 38.9 + - + +
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Residues in contact with PHE 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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111A ASP* 3.2 52.9 - - + -
114A LEU* 3.9 16.4 - - + -
115A ARG* 3.8 29.4 - - + -
118A ALA* 3.9 8.9 - - + +
208A GLU 3.1 10.8 + - - +
209A GLY* 3.4 12.1 - - - +
210A ASP 3.2 0.2 - - - -
211A LEU* 1.3 80.0 - - - +
213A THR* 1.3 66.2 + - - +
215A LEU* 3.3 6.4 + - - +
216A ARG* 3.1 57.9 + - - +
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Residues in contact with THR 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 GLY 3.1 13.3 + - - -
210A ASP* 3.2 10.5 + - - -
212A PHE* 1.3 85.9 - - - +
214A GLN* 1.3 61.4 + - - +
216A ARG* 3.3 12.7 + - + +
217A LYS* 3.2 32.9 + - + +
359A LEU* 3.9 20.0 - - + -
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Residues in contact with GLN 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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197A LEU* 3.6 31.8 - - + +
198A ASP 5.6 0.6 + - - -
206A LEU* 4.3 10.0 - - + +
210A ASP 2.8 23.0 + - - +
211A LEU* 3.6 4.7 - - - +
213A THR* 1.3 73.0 - - - +
215A LEU* 1.3 66.5 + - - +
217A LYS* 2.9 35.9 + - - +
218A ILE* 3.0 26.7 + - - +
359A LEU* 3.2 21.0 - - + +
360A PRO* 2.4 28.6 + - - +
362A PRO* 3.8 11.1 - - + +
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Residues in contact with LEU 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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114A LEU* 3.4 41.5 - - + +
117A ALA* 3.7 12.8 - - + -
118A ALA* 3.7 20.2 - - + +
121A ILE* 4.6 8.7 - - + -
188A VAL* 4.2 33.2 - - + -
197A LEU* 4.4 11.2 - - + -
211A LEU 2.8 25.4 + - - +
212A PHE* 3.7 5.2 - - - +
214A GLN* 1.3 75.7 - - - +
216A ARG* 1.3 62.6 + - - +
218A ILE* 3.1 7.1 + - + +
219A VAL* 2.9 27.2 + - - +
270A VAL* 5.8 1.1 - - + -
272A LEU* 4.6 9.6 - - + -
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Residues in contact with ARG 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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111A ASP* 2.9 37.7 + - - +
114A LEU* 3.8 19.5 - - + -
115A ARG* 5.2 1.8 - - - +
212A PHE* 3.1 41.9 + - + +
213A THR* 3.4 14.8 - - + +
214A GLN 3.2 0.2 - - - -
215A LEU* 1.3 77.4 - - - +
217A LYS* 1.3 62.6 + - + +
219A VAL* 3.4 5.2 + - - +
220A LYS* 3.1 22.2 + - - +
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Residues in contact with LYS 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 THR* 3.2 23.7 + - + +
214A GLN* 2.9 34.3 + - - +
216A ARG* 1.3 76.4 - - + +
218A ILE* 1.3 64.8 + - - +
220A LYS* 3.1 9.2 + - - +
221A MET* 3.0 31.7 + - + +
359A LEU* 3.5 33.5 + - - +
360A PRO 4.0 4.6 + - - -
361A ALA* 4.2 8.9 - - + +
362A PRO* 3.8 17.7 - - + -
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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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188A VAL* 3.6 45.3 - - + -
190A CYS* 4.1 11.9 - - + -
195A PHE* 3.8 31.7 - - + -
197A LEU* 4.7 6.5 - - + -
214A GLN 3.0 13.0 + - - +
215A LEU* 3.4 16.6 - - + +
217A LYS* 1.3 75.8 - - - +
219A VAL* 1.3 58.8 + - - +
220A LYS 3.1 0.3 + - - -
221A MET* 3.1 8.1 + - - +
222A ALA* 2.8 31.7 + - - +
272A LEU* 4.7 2.2 - - + -
362A PRO* 3.2 34.8 - - + -
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Residues in contact with VAL 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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110A THR* 4.6 16.2 - - + -
113A GLN* 5.7 0.9 - - - +
114A LEU* 3.9 28.9 - - + -
190A CYS* 4.3 15.4 - - - -
215A LEU 2.9 18.5 + - - +
216A ARG* 3.7 8.7 - - - +
217A LYS 3.4 0.2 - - - -
218A ILE* 1.3 74.7 - - - +
220A LYS* 1.3 55.7 + - - +
222A ALA* 3.6 2.6 + - - +
223A SER* 2.7 36.4 + - - +
272A LEU* 4.0 13.9 - - + -
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Residues in contact with LYS 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 ARG 3.1 12.2 + - - +
217A LYS* 3.1 11.6 + - - +
218A ILE 3.1 0.8 - - - -
219A VAL* 1.3 75.8 - - - +
221A MET* 1.3 66.2 + - + +
223A SER* 3.1 19.4 + - - -
224A ASN* 3.7 4.9 + - - +
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Residues in contact with MET 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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195A PHE* 3.8 18.8 - - + -
217A LYS* 3.0 24.5 + - + +
218A ILE 3.8 2.7 - - - +
220A LYS* 1.3 75.7 - - + +
222A ALA* 1.3 52.8 + - - +
223A SER 3.0 0.2 - - - -
224A ASN* 2.8 28.2 + - - +
361A ALA* 4.9 6.7 - - + -
362A PRO* 3.4 50.7 - - + +
364A ARG* 2.8 35.8 + - - +
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Residues in contact with ALA 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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190A CYS* 3.7 45.1 - - + +
191A CYS* 4.0 18.3 - - - +
193A GLN* 4.4 9.1 - - - +
195A PHE* 3.9 14.2 - - + -
218A ILE 2.8 16.7 + - - +
219A VAL 3.8 3.1 - - - +
221A MET* 1.3 76.5 - - - +
223A SER* 1.3 58.1 + - - +
224A ASN 3.2 4.4 + - - +
228A ARG* 4.5 7.1 + - - +
364A ARG* 4.4 3.0 + - - +
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Residues in contact with SER 223 (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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191A CYS* 5.2 6.1 - - - -
219A VAL* 2.7 23.3 + - - +
220A LYS* 3.1 13.6 + - - -
221A MET 2.9 1.4 + - - -
222A ALA* 1.3 77.4 - - - +
224A ASN* 1.3 59.1 + - - +
225A ALA* 3.4 3.6 + - - +
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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
------------------------------------------------------------
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