Contacts of the helix formed by residues 206 - 223 (chain G) in PDB entry 4XLN
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 THR 206 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G THR* 5.9 1.1 - - - -
17G GLY 4.9 2.5 - - - +
18G ASP* 3.3 35.0 - - - +
205G VAL* 1.3 76.4 - - - +
207G PRO* 1.3 70.2 - - - +
208G LEU* 3.5 10.0 + - - +
209G GLU* 3.0 42.2 + - - +
210G ALA* 2.8 25.3 + - - +
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Residues in contact with PRO 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G THR* 5.5 0.4 - - + -
17G GLY 4.5 2.2 - - - +
18G ASP* 3.2 20.0 - - - +
19G HIS 3.3 22.4 - - - +
20G TYR 3.5 18.8 - - - +
21G GLY* 3.6 17.7 - - - +
23G PHE* 3.8 5.2 - - + -
199G ILE* 3.3 36.2 - - + +
201G THR* 3.7 3.1 - - + +
205G VAL 3.8 0.4 - - - -
206G THR* 1.3 86.5 - - - +
208G LEU* 1.3 59.7 + - + +
210G ALA* 3.4 2.9 + - + +
211G LEU* 2.9 24.9 + - - +
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Residues in contact with LEU 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ALA* 4.8 3.1 - - + -
14G THR 5.6 0.2 - - - +
15G THR* 3.4 42.2 - - + +
21G GLY* 5.4 0.7 - - - -
23G PHE* 3.6 30.7 - - + -
206G THR* 3.1 8.9 - - - +
207G PRO* 1.3 82.6 - - + +
209G GLU* 1.3 62.9 + - + +
211G LEU* 3.3 3.6 + - - +
212G ASN* 2.9 39.5 + - - +
228H PRO* 4.7 24.0 - - + -
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Residues in contact with GLU 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ARG* 5.3 8.2 + - - -
204G SER 4.9 0.7 - - - +
205G VAL* 3.6 26.4 - - + +
206G THR* 3.0 37.3 + - - +
208G LEU* 1.3 76.0 - - + +
210G ALA* 1.3 63.7 + - - +
212G ASN* 3.0 12.7 + - - +
213G GLN* 2.9 33.6 + - - +
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Residues in contact with ALA 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 4.1 22.0 - - + -
48G ILE* 3.5 14.4 - - + +
173G PRO* 6.4 0.4 - - + -
174G VAL* 5.5 0.7 - - + +
199G ILE* 4.6 0.9 - - + -
201G THR* 4.5 9.9 - - + -
205G VAL* 3.3 14.0 - - + +
206G THR 2.8 12.7 + - - +
207G PRO* 3.4 13.7 - - + +
209G GLU* 1.3 76.6 - - - +
211G LEU* 1.3 56.0 + - - +
213G GLN* 4.1 5.2 - - - -
214G ALA* 2.9 32.4 + - - +
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Residues in contact with LEU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G PHE* 5.0 0.9 - - + -
23G PHE* 3.5 43.1 - - + -
40G LEU* 3.8 32.5 - - + -
44G LEU* 4.5 7.0 - - + -
197G LEU* 4.3 14.1 - - + -
199G ILE* 3.7 12.0 - - + +
207G PRO 2.9 17.0 + - - +
208G LEU 3.6 5.4 - - - +
210G ALA* 1.3 76.9 - - - +
212G ASN* 1.3 60.9 + - - +
214G ALA* 4.1 2.5 - - - -
215G VAL* 2.9 41.5 + - + +
225H PHE* 3.8 23.6 - - + -
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Residues in contact with ASN 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G LEU* 2.9 29.2 + - - +
209G GLU* 3.0 14.3 + - - +
211G LEU* 1.3 80.0 - - - +
213G GLN* 1.3 62.8 + - - +
215G VAL* 3.1 7.5 + - - +
216G ALA* 2.9 26.8 + - - +
225H PHE* 5.6 9.1 + - - +
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Residues in contact with GLN 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ILE* 3.3 35.0 - - + +
49G PRO* 3.4 19.5 + - + +
205G VAL* 4.3 21.0 - - - +
209G GLU* 2.9 27.5 + - - +
210G ALA 3.6 5.8 - - - +
212G ASN* 1.3 74.2 - - - +
214G ALA* 1.3 58.4 + - - +
216G ALA* 3.4 10.0 - - + +
217G ILE* 2.9 38.5 + - + +
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Residues in contact with ALA 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU* 3.9 14.3 - - + +
43G ILE* 4.0 10.5 - - + +
44G LEU* 4.3 22.0 - - + +
48G ILE* 4.1 13.0 - - + -
210G ALA 2.9 21.3 + - - +
211G LEU* 3.7 8.5 - - - +
213G GLN* 1.3 75.3 - - - +
215G VAL* 1.3 59.6 + - - +
217G ILE* 3.3 3.7 + - - +
218G LEU* 2.9 28.6 + - - +
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Residues in contact with VAL 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU* 3.7 33.0 - - + -
211G LEU* 2.9 27.2 + - + +
212G ASN* 3.6 6.1 - - - +
214G ALA* 1.3 75.8 - - - +
216G ALA* 1.3 57.9 + - - +
218G LEU* 3.4 3.9 - - + +
219G LYS* 2.9 32.8 + - + +
222H LEU* 4.0 31.0 - - + +
223H ASN* 5.9 1.1 - - - +
225H PHE* 4.4 20.0 - - + +
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Residues in contact with ALA 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ASN 2.9 13.4 + - - +
213G GLN* 3.4 15.3 - - + +
214G ALA 3.1 0.2 - - - -
215G VAL* 1.3 74.2 - - - +
217G ILE* 1.3 61.7 + - + +
219G LYS* 3.4 5.3 + - - +
220G GLU* 2.9 32.4 + - - +
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Residues in contact with ILE 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ILE* 3.8 18.8 - - + -
47G SER* 3.7 36.3 - - - +
48G ILE* 5.0 4.0 - - + -
49G PRO* 5.5 2.7 - - + -
213G GLN* 2.9 26.7 + - + +
214G ALA* 3.7 4.9 - - - +
216G ALA* 1.3 74.2 - - + +
218G LEU* 1.3 57.2 + - - +
220G GLU* 3.4 12.5 + - - +
221G HIS* 2.9 51.5 + - + +
32H PHE* 3.9 11.0 - - + -
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Residues in contact with LEU 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G LEU 5.7 0.7 - - - +
39G PRO* 5.2 10.1 - - + -
40G LEU* 3.7 29.4 - - + +
43G ILE* 3.6 25.9 - - + +
214G ALA 2.9 16.9 + - - +
215G VAL* 3.4 5.8 - - - +
217G ILE* 1.3 77.8 - - - +
219G LYS* 1.3 56.4 + - - +
221G HIS* 3.8 4.2 - - + +
222G LEU* 2.9 30.8 + - + +
35H THR* 5.6 3.1 - - + +
36H LEU* 5.9 7.0 - - + -
39H PRO* 6.4 0.9 - - + -
218H LEU* 4.6 11.7 - - + -
222H LEU* 3.6 41.3 - - + -
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Residues in contact with LYS 219 (chain G).
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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215G VAL* 2.9 23.8 + - + +
216G ALA* 3.9 4.9 - - - +
218G LEU* 1.3 70.5 - - - +
220G GLU* 1.3 66.9 - - - +
222G LEU* 3.1 9.4 + - - +
223G ASN* 2.9 33.9 + - - +
219H LYS* 3.4 44.1 - - + +
222H LEU* 4.5 11.0 - - + -
223H ASN* 4.1 23.1 + - - +
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Residues in contact with GLU 220 (chain G).
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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216G ALA 2.9 17.9 + - - +
217G ILE* 3.6 15.0 - - - +
219G LYS* 1.3 76.2 - - - +
221G HIS* 1.3 64.0 + - + +
223G ASN* 2.8 28.8 + - - +
224G TYR* 3.6 31.6 + - + +
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Residues in contact with HIS 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G ILE* 2.9 46.4 + - + +
218G LEU* 4.0 4.3 - - + +
220G GLU* 1.3 78.5 + - - +
222G LEU* 1.3 59.3 + - - +
224G TYR* 3.3 50.9 + + + +
225G PHE* 4.9 1.6 - - - -
7H LYS 6.1 2.5 - - - -
9H PRO* 4.8 3.4 - - + -
25H LEU* 4.8 2.6 - - - +
28H LEU* 3.5 27.9 - - + +
29H GLU* 4.9 5.8 - - + -
32H PHE* 3.7 23.0 - + + -
36H LEU* 4.2 24.6 - - + +
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Residues in contact with LEU 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G LEU* 2.9 20.6 + - + +
219G LYS* 3.2 9.0 - - - +
220G GLU 3.0 0.4 - - - -
221G HIS* 1.3 77.3 - - - +
223G ASN* 1.3 64.0 + - - +
224G TYR 3.2 1.1 - - - -
225G PHE* 3.2 45.6 - - + +
36H LEU* 5.0 6.3 - - + -
40H LEU* 4.8 1.3 - - + -
215H VAL* 3.7 23.6 - - + +
218H LEU* 3.6 28.5 - - + -
219H LYS* 3.5 43.1 - - + +
222H LEU* 4.1 5.4 - - + -
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Residues in contact with ASN 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G LYS* 2.9 32.6 + - - +
220G GLU* 2.8 14.8 + - - +
222G LEU* 1.3 83.0 + - - +
224G TYR* 1.3 57.8 + - + +
225G PHE* 3.0 10.0 + - - -
226G ALA* 3.9 12.1 + - - +
215H VAL* 6.1 1.8 - - - +
219H LYS* 4.0 22.1 + - - +
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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