Contacts of the helix formed by residues 216 - 225 (chain B) in PDB entry 1LFD
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 LYS 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B VAL* 3.5 31.1 - - + +
209B VAL 3.5 28.7 - - - +
210B GLY 2.8 22.7 + - - +
211B ALA 2.8 17.8 + - - -
214B VAL* 3.9 10.5 - - + -
215B GLY* 1.3 76.0 - - - +
217B SER* 1.3 59.0 + - - +
219B LEU* 3.4 6.6 + - - +
220B THR* 3.0 31.7 + - - -
257B ASP* 3.6 11.7 - - - +
258B THR* 3.2 24.7 - - - -
259B ALA 4.2 0.4 - - - -
260B GLY* 3.9 3.1 - - - +
281B VAL* 4.3 2.7 - - + -
1380B GNP 2.9 36.6 + - - +
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LYS* 1.3 72.1 - - - +
218B ALA* 1.3 61.0 + - - +
220B THR* 3.2 1.3 + - - -
221B ILE* 2.8 48.8 + - - +
235B THR* 2.7 22.0 + - - -
238B ASP* 4.9 1.0 + - - -
257B ASP* 2.7 27.9 + - - -
1373B MG 2.9 10.9 - - - -
1380B GNP 2.9 14.7 + - - -
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY 3.8 1.3 - - - +
216B LYS 3.3 0.2 - - - -
217B SER* 1.3 75.1 - - - +
219B LEU* 1.3 57.8 + - - +
221B ILE* 3.8 6.4 - - - +
222B GLN* 2.9 30.7 + - - +
227B HIS 4.8 1.9 - - - +
228B PHE* 4.0 14.3 - - + -
346B ALA* 3.5 21.2 - - + +
1380B GNP 2.9 38.7 + - + +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL* 5.3 0.7 - - + -
215B GLY 3.0 19.1 + - - +
216B LYS* 3.5 5.2 - - - +
218B ALA* 1.3 76.9 - - - +
220B THR* 1.3 62.2 + - - +
222B GLN* 3.3 4.3 + - - +
223B LEU 3.1 17.2 + - - -
279B LEU* 4.6 6.7 - - + -
281B VAL* 4.0 34.3 - - + -
314B VAL* 4.0 6.5 - - + -
316B ASN* 3.3 22.0 - - - +
344B THR* 3.6 20.6 - - + +
346B ALA* 3.6 20.6 - - + +
352B VAL* 3.8 23.2 - - + +
356B PHE* 3.8 18.4 - - + -
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL* 3.5 22.7 - - - +
216B LYS 3.0 18.0 + - - -
217B SER* 3.7 6.5 - - - -
219B LEU* 1.3 77.4 - - - +
221B ILE* 1.3 56.9 + - - +
223B LEU* 3.1 3.2 + - - +
224B ILE* 2.9 37.8 + - + +
240B TYR* 3.5 37.5 - - + -
255B ILE* 3.7 19.6 - - + +
257B ASP* 4.1 7.8 + - + -
356B PHE* 4.0 8.7 - - - -
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 5.1 6.5 - - - +
54A ASN* 6.0 2.7 - - - +
217B SER* 2.8 37.5 + - - +
218B ALA* 4.0 6.5 - - - +
220B THR* 1.3 69.0 - - - +
222B GLN* 1.3 61.1 + - - +
224B ILE* 4.8 2.0 - - - -
225B GLN* 2.8 37.5 + - - +
226B ASN 3.2 4.3 + - - -
227B HIS* 3.5 41.6 + - + +
229B VAL* 6.4 1.1 - - + -
240B TYR* 3.5 30.1 - - + +
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ALA 2.9 19.8 + - - +
219B LEU* 3.5 7.4 - - - +
220B THR 3.2 0.2 - - - -
221B ILE* 1.3 76.1 - - - +
223B LEU* 1.3 54.9 + - - +
226B ASN* 2.9 23.4 + - - +
227B HIS* 3.2 29.7 + - - +
228B PHE* 3.6 16.2 - - - +
346B ALA* 2.6 30.2 + - - +
347B LYS 4.0 5.3 + - - -
349B ARG* 2.7 62.1 + - + +
352B VAL* 4.0 13.7 - - + -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU 3.1 8.1 + - - +
220B THR 3.1 6.8 + - - +
222B GLN* 1.3 81.2 - - - +
224B ILE* 1.3 62.6 + - + +
226B ASN* 3.0 19.4 + - - -
242B LYS* 3.1 12.1 + - + +
253B LEU* 4.5 12.6 - - + -
255B ILE* 3.5 31.0 - - + -
349B ARG* 4.0 6.9 + - - +
352B VAL* 4.0 6.7 - - + +
353B GLU* 4.0 30.3 - - + -
356B PHE* 3.6 37.7 - - + -
357B TYR* 4.3 12.6 - - + +
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN 4.3 0.9 - - - +
28A GLY* 3.8 30.1 - - - +
220B THR* 2.9 30.4 + - + +
221B ILE* 4.5 0.4 - - - +
223B LEU* 1.3 77.3 - - + +
225B GLN* 1.3 64.9 + - + +
226B ASN* 4.0 1.9 - - - +
240B TYR* 3.8 35.0 - - + -
241B ARG 4.6 0.4 - - - -
242B LYS* 3.2 53.2 + - + +
253B LEU* 5.2 1.6 - - + +
255B ILE* 3.6 25.6 - - + -
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Residues in contact with GLN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 3.1 48.8 + - + +
29A ASN* 4.1 3.6 - - - +
32A LYS* 5.5 6.2 + - - +
54A ASN* 5.7 2.3 + - - -
221B ILE* 2.8 20.3 + - - +
224B ILE* 1.3 78.6 - - + +
226B ASN* 1.3 72.6 + - - +
227B HIS* 3.1 37.0 + - + +
240B TYR* 3.8 24.2 - - + -
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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