Contacts of the helix formed by residues 208 - 220 (chain A) in PDB entry 4P9U
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 LEU 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.5 31.2 - - + +
83A LEU* 3.7 25.8 - - + -
101A LEU* 4.0 17.2 - - + +
104A ALA* 5.7 1.3 - - + -
204A ILE* 3.1 34.2 + - + +
205A PHE* 3.2 7.8 + - + +
207A GLY* 1.3 75.6 - - - +
209A LYS* 1.3 57.5 + - - +
210A LYS 3.4 2.5 - - - -
211A LEU* 3.3 14.0 + - + +
212A TYR* 2.8 31.2 + - + +
200B ILE* 3.9 28.0 - - + -
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Residues in contact with LYS 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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155A GLU* 5.4 12.5 - - - +
183A PHE* 6.2 1.4 - - - -
186A TYR* 3.5 39.2 - - + +
205A PHE 3.1 10.1 + - - +
206A ASN* 3.5 15.7 - - - +
207A GLY 3.2 3.8 + - - -
208A LEU* 1.3 78.1 - - - +
210A LYS* 1.3 60.2 + - + +
212A TYR* 3.4 6.7 - - - +
213A ASP* 2.4 65.8 + - - +
76B GLU 5.4 7.6 - - - +
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Residues in contact with LYS 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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81A HIS* 5.9 4.3 - - + +
84A ASP* 3.3 35.7 - - + +
207A GLY 4.9 4.6 + - - +
208A LEU 3.4 0.6 - - - -
209A LYS* 1.3 78.1 - - + +
211A LEU* 1.3 59.1 + - - +
213A ASP* 3.9 5.4 - - - +
214A ARG* 2.9 27.0 + - - +
277A ASP* 5.9 3.1 - - - -
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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
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83A LEU* 3.9 25.6 - - + +
84A ASP* 3.3 19.2 + - + +
87A MET* 3.7 34.1 - - + -
97A ILE* 3.9 22.0 - - + -
98A VAL* 5.3 0.7 - - + -
101A LEU* 3.6 32.8 - - + -
208A LEU* 3.3 14.4 + - + +
210A LYS* 1.3 74.9 - - - +
212A TYR* 1.3 59.7 + - - +
214A ARG* 3.8 3.7 - - + +
215A VAL* 2.9 47.3 + - + +
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Residues in contact with TYR 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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101A LEU* 4.1 28.5 - - + -
105A ARG* 2.9 29.0 + - - -
182A ASN* 3.2 13.1 - - - +
185A ASP* 2.8 29.0 + - - -
186A TYR* 3.5 43.1 - + + -
189A PHE* 3.1 18.2 - - - -
205A PHE* 3.8 25.6 - + - -
208A LEU* 2.8 17.8 + - + +
209A LYS* 3.2 11.2 + - - +
211A LEU* 1.3 78.7 - - - +
213A ASP* 1.3 55.8 + - - +
215A VAL* 3.9 1.4 - - - +
216A GLY* 2.9 23.9 + - - -
220A PHE* 6.1 0.2 - + - -
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Residues in contact with ASP 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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182A ASN* 2.9 26.2 + - - +
183A PHE* 5.3 1.0 - - - -
186A TYR* 4.3 14.0 - - - +
209A LYS* 2.4 52.2 + - - +
210A LYS* 3.9 5.2 - - - +
212A TYR* 1.3 75.9 - - - +
214A ARG* 1.3 58.8 + - - +
217A SER* 2.7 39.9 + - - +
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Residues in contact with ARG 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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84A ASP* 3.0 35.7 + - - +
87A MET* 3.4 42.5 - - + +
88A THR* 4.2 7.3 - - - +
210A LYS 2.9 17.3 + - - +
211A LEU* 3.8 5.4 - - - +
213A ASP* 1.3 77.4 - - - +
215A VAL* 1.3 64.9 + - + +
217A SER* 3.7 9.2 + - - -
218A TYR* 3.9 5.4 + - - +
274A PHE* 3.1 43.9 + - + +
275A THR* 4.3 0.4 - - - +
276A GLU 2.7 34.1 + - - +
277A ASP* 4.7 4.4 + - - +
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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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87A MET* 5.4 0.9 - - + -
98A VAL* 3.8 43.5 - - + -
101A LEU* 3.9 17.7 - - + -
102A LEU* 5.0 9.4 - - + -
211A LEU* 2.9 29.6 + - + +
212A TYR 3.9 2.9 - - - +
214A ARG* 1.3 78.4 - - + +
216A GLY* 1.3 60.2 + - - +
218A TYR* 3.3 5.9 + - - +
219A TYR* 2.9 30.1 + - + +
263A TRP* 4.7 11.4 - - + -
274A PHE* 4.5 10.8 - - + -
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Residues in contact with GLY 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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182A ASN* 3.2 24.6 - - - +
212A TYR* 2.9 12.3 + - - -
213A ASP 3.4 0.2 + - - -
215A VAL* 1.3 74.7 - - - +
217A SER* 1.3 55.2 + - - +
218A TYR 3.0 5.6 - - - -
219A TYR* 4.3 5.2 - - - -
220A PHE* 2.9 46.1 + - - +
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Residues in contact with SER 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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175A ILE* 4.9 7.4 - - - +
178A ALA* 3.1 30.7 - - - +
179A LYS* 3.8 28.7 - - - +
182A ASN* 4.0 9.2 + - - +
213A ASP* 2.7 26.6 + - - +
214A ARG* 4.1 6.5 - - - -
215A VAL 3.3 0.4 - - - -
216A GLY* 1.3 74.6 - - - +
218A TYR* 1.3 57.8 + - - +
221A SER* 4.4 2.1 - - - -
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Residues in contact with TYR 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 ARG 3.9 2.5 + - - +
215A VAL 3.3 4.8 + - - +
216A GLY 3.0 0.2 - - - -
217A SER* 1.3 79.9 - - - +
219A TYR* 1.3 65.4 + - - +
220A PHE 3.1 1.6 - - - -
221A SER* 2.5 34.3 + - - -
263A TRP* 3.9 16.6 - + - -
266A MET* 2.7 53.8 + - + +
269A THR* 2.7 29.7 + - - -
270A LEU* 3.8 11.4 - - + -
271A PRO* 3.5 30.1 - - + -
274A PHE* 4.1 24.9 - + + -
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Residues in contact with TYR 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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102A LEU* 6.5 0.4 - - + -
105A ARG* 6.3 0.7 - - - -
215A VAL* 2.9 28.0 + - + +
216A GLY* 4.2 3.1 - - - +
218A TYR* 1.3 79.6 - - - +
220A PHE* 1.3 92.7 + + - +
221A SER 3.2 2.6 + - - -
222A ASN 3.7 5.0 + - - -
225A ALA* 3.4 32.9 + - + +
228A LEU* 5.6 0.5 - - - +
255A TYR* 4.4 9.9 + - - -
259A SER* 3.1 41.7 - - - -
262A ILE* 3.6 26.8 - - + +
263A TRP* 4.3 21.1 - + + -
266A MET* 3.7 20.0 - - - +
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Residues in contact with PHE 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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105A ARG* 6.1 0.4 - - - -
178A ALA* 3.2 24.1 - - - +
181A PHE* 3.5 35.0 - + + -
182A ASN* 3.5 21.5 - - + -
185A ASP* 3.6 42.0 - - + -
216A GLY* 2.9 29.4 + - - +
219A TYR* 1.3 105.6 - + - +
221A SER* 1.3 50.0 + - - +
222A ASN 3.1 5.8 - - - +
225A ALA 4.4 1.6 - - - -
226A ARG* 2.7 41.7 + - + -
229A ALA* 3.9 11.7 - - + -
255A TYR* 4.8 2.7 - - - -
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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