Contacts of the helix formed by residues 208 - 223 (chain A) in PDB entry 4UML
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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60A LYS* 4.0 8.1 - - - -
207A VAL* 1.3 74.0 - - - +
209A ASP* 1.3 64.6 + - - +
210A LEU* 3.4 13.0 + - - +
211A GLU* 2.6 40.6 + - - -
212A GLU* 3.1 13.7 + - - +
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Residues in contact with ASP 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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60A LYS* 3.1 36.3 + - - +
208A SER* 1.3 75.2 - - - +
210A LEU* 1.3 65.2 + - - +
211A GLU 3.3 0.7 + - - -
212A GLU* 3.9 11.5 + - - +
213A GLY 4.8 2.6 + - - -
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Residues in contact with LEU 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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172A ALA* 4.6 21.3 - - + -
178A LEU* 3.9 17.5 - - + +
208A SER* 3.4 12.5 + - - +
209A ASP* 1.3 80.4 - - - +
211A GLU* 1.3 72.8 + - + +
213A GLY 5.2 0.7 + - - -
214A THR* 5.1 1.2 + - - -
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Residues in contact with GLU 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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168A VAL* 3.7 33.3 - - + +
170A ASN 5.4 0.5 - - - +
178A LEU* 3.8 28.9 - - + -
207A VAL* 4.3 2.7 - - + -
208A SER* 2.6 42.9 + - - +
210A LEU* 1.3 92.8 - - + +
212A GLU* 1.3 67.2 + - - +
213A GLY 3.3 2.7 - - - -
214A THR* 3.1 15.1 + - - -
215A TYR* 3.2 29.9 + - + -
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Residues in contact with GLU 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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58A LEU* 4.7 6.6 - - + +
60A LYS* 3.2 44.2 + - + +
207A VAL* 3.8 18.1 - - + +
208A SER 3.1 15.1 + - - +
209A ASP* 3.9 8.3 + - - +
210A LEU 3.8 1.0 - - - -
211A GLU* 1.3 75.2 - - - +
213A GLY* 1.3 57.8 + - - +
215A TYR* 3.1 5.7 + - - +
216A GLN* 2.8 60.3 + - + +
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Residues in contact with GLY 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 ASP 4.8 3.4 + - - -
210A LEU 5.2 0.8 + - - -
211A GLU 3.3 0.8 - - - -
212A GLU* 1.3 78.6 - - - +
214A THR* 1.3 56.7 + - - +
216A GLN* 3.3 15.8 + - - +
217A LYS* 2.8 29.9 + - - +
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Residues in contact with THR 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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178A LEU* 3.8 21.0 - - + +
179A GLU* 4.0 32.1 + - + +
182A THR* 3.6 31.2 - - + +
210A LEU 5.1 1.1 + - - -
211A GLU 3.1 10.2 + - - -
213A GLY* 1.3 74.6 - - - +
215A TYR* 1.3 56.6 + - - +
217A LYS* 3.3 8.1 + - - +
218A LEU* 2.9 35.7 + - + +
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Residues in contact with TYR 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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58A LEU* 3.8 18.8 - - + -
149A TYR* 4.2 7.4 + - - -
167A CYS 5.2 0.5 + - - -
168A VAL* 4.0 21.0 - - + +
170A ASN* 5.1 1.4 + - - -
178A LEU* 5.2 0.4 - - + -
182A THR* 3.7 31.4 + - + -
185A ALA* 4.1 16.6 - - + +
186A LEU* 4.0 23.6 - - + -
205A PHE* 3.8 39.2 - + + -
207A VAL* 3.8 20.4 - - + -
211A GLU* 3.2 25.7 + - + +
212A GLU* 3.1 8.6 + - - +
214A THR* 1.3 80.0 - - - +
216A GLN* 1.3 55.8 + - - +
219A LEU* 2.9 41.9 + - + +
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Residues in contact with GLN 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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19A TRP* 4.6 5.8 - - + -
58A LEU* 3.7 20.9 - - + +
212A GLU* 2.8 47.9 + - - +
213A GLY* 3.6 19.1 - - - +
215A TYR* 1.3 71.2 - - - +
217A LYS* 1.3 64.6 + - - +
219A LEU* 4.3 3.5 - - - +
220A PRO* 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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179A GLU* 2.7 35.9 + - - +
213A GLY 2.8 17.9 + - - +
214A THR* 3.3 9.4 - - - +
216A GLN* 1.3 77.8 - - - +
218A LEU* 1.3 70.8 + - + +
220A PRO* 3.5 10.4 - - - +
221A LEU* 5.0 2.1 + - - +
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Residues in contact with LEU 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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179A GLU* 3.8 12.1 - - + +
182A THR* 3.7 22.9 - - + -
183A HIS* 3.7 48.9 - - + +
186A LEU* 3.6 14.8 - - + -
214A THR* 2.9 23.4 + - + +
215A TYR 3.3 0.2 + - - -
217A LYS* 1.3 99.8 - - + +
219A LEU* 1.3 67.2 + - - +
220A PRO* 3.3 3.8 - - - -
221A LEU* 3.0 26.9 + - + +
222A TYR* 3.5 12.6 - - + -
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Residues in contact with LEU 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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19A TRP* 3.6 37.5 - - + -
56A VAL* 4.1 18.8 - - + -
58A LEU* 3.7 35.9 - - + -
186A LEU* 3.8 23.8 - - + +
205A PHE* 4.9 2.0 - - + -
215A TYR* 2.9 29.0 + - + +
216A GLN* 4.3 0.7 - - - +
218A LEU* 1.3 69.2 - - - +
220A PRO* 1.3 60.0 - - + +
221A LEU 3.1 0.5 + - - -
222A TYR 3.2 1.6 + - - -
223A PHE* 2.7 62.0 + - + +
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Residues in contact with PRO 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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19A TRP* 3.7 19.9 - - + -
44A SER* 4.5 2.1 + - - -
216A GLN 3.1 21.1 - - - +
217A LYS 3.5 8.3 - - - +
218A LEU 3.3 4.5 - - - -
219A LEU* 1.3 94.5 - - + +
221A LEU* 1.3 58.8 + - - +
223A PHE 4.1 4.7 - - - +
224A PRO* 3.2 26.2 - - + +
225A ARG* 5.6 5.8 - - - +
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Residues in contact with LEU 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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43A ARG 4.6 5.6 - - - +
44A SER* 3.0 55.0 + - - +
45A PRO* 4.0 9.6 - - + -
46A PHE* 3.6 9.2 - - - +
183A HIS* 3.7 29.2 - - + -
217A LYS 5.0 1.7 + - - +
218A LEU* 3.0 19.5 + - + +
220A PRO* 1.3 78.9 - - - +
222A TYR* 1.3 79.9 + - + +
224A PRO* 4.1 0.2 - - - +
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.5 31.7 - + - +
183A HIS* 2.6 50.1 + + - +
186A LEU* 3.6 28.3 - - + +
187A ARG* 3.6 33.7 + - + +
190A ARG* 3.0 34.4 + - + +
218A LEU* 3.5 16.2 - - + -
219A LEU 3.2 2.1 + - - +
221A LEU* 1.3 93.5 - - + +
223A PHE* 1.3 77.5 + - + +
224A PRO* 3.5 4.4 - - - +
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Residues in contact with PHE 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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19A TRP* 2.8 33.5 + + + +
52A VAL* 3.5 34.1 - - + -
53A ASN* 3.6 17.2 + - - +
56A VAL* 3.5 28.7 - - + -
186A LEU* 3.9 15.7 - - + -
189A VAL* 4.3 7.0 - - + -
190A ARG* 3.6 33.0 - - - +
193A LEU* 4.4 1.6 - - + -
205A PHE* 5.0 1.1 - + - -
219A LEU* 2.7 41.8 + - + +
220A PRO* 3.7 2.1 - - - +
222A TYR* 1.3 93.5 - - + +
224A PRO* 1.4 66.7 - - - +
225A ARG* 3.4 0.7 + - - +
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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