Contacts of the helix formed by residues 207 - 214 (chain L) in PDB entry 1LWU
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 ASP 207 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239K GLY* 5.2 3.5 - - - -
206L ARG* 1.3 77.4 - - - +
208L TRP* 1.3 58.1 + - - +
209L VAL* 2.8 37.3 + - + +
210L SER* 2.9 24.6 + - - -
211L TYR* 3.0 26.2 + - - -
312L THR* 4.1 1.3 - - - -
313L PRO* 5.8 0.2 - - - -
314L GLU* 3.3 22.4 - - + +
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Residues in contact with TRP 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207L ASP* 1.3 71.7 - - - +
209L VAL* 1.3 67.7 + - + +
210L SER 3.0 1.1 - - - -
211L TYR* 2.7 25.1 + - + +
212L ARG* 2.9 17.6 + - + +
230L ASN* 5.5 0.4 - - - -
268L GLU* 2.5 32.4 + - + -
271L GLU* 4.1 12.8 - - + -
272L TYR* 3.8 42.8 - + - -
310L PHE* 3.2 41.7 - + + -
311L SER* 4.6 0.4 - - - -
312L THR* 3.6 23.3 + - + -
314L GLU* 2.9 22.1 + - - +
315L ARG* 2.9 50.7 - - + +
317L ASN* 4.8 0.7 - - - -
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Residues in contact with VAL 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K ARG 3.7 22.4 - - - +
238K ASN* 4.1 12.1 - - - +
239K GLY* 4.4 2.2 - - - +
207L ASP* 2.8 17.0 - - + +
208L TRP* 1.3 81.2 - - + +
210L SER* 1.3 65.6 + - - +
212L ARG* 3.0 30.1 + - - +
213L GLU* 3.0 30.9 + - + +
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Residues in contact with SER 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238K ASN 4.3 8.5 + - - -
239K GLY* 4.7 9.5 - - - -
206L ARG* 3.3 36.9 + - - +
207L ASP* 2.9 34.3 + - - -
208L TRP 3.0 0.2 - - - -
209L VAL* 1.3 81.8 - - - +
211L TYR* 1.3 56.5 + - - +
214L GLY 2.9 26.0 + - - +
215L PHE* 3.2 15.8 - - - +
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Residues in contact with TYR 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L PHE* 2.7 43.2 + - - +
206L ARG* 3.4 21.5 - - + -
207L ASP 3.0 21.0 + - - +
208L TRP* 2.7 15.2 + - + +
210L SER* 1.3 71.0 - - - +
212L ARG* 1.3 58.3 + - - +
214L GLY 4.1 0.2 - - - -
215L PHE* 3.5 21.5 - + - -
227L TRP* 3.3 36.8 + + - -
229L GLY* 3.5 1.2 - - - -
230L ASN* 2.9 22.3 + - - +
310L PHE* 3.5 25.4 - + + -
312L THR* 4.2 7.9 - - + -
331L GLY 3.5 24.9 + - - -
343L ASN* 3.5 25.4 + - - +
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Residues in contact with ARG 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238K ASN* 5.4 4.4 - - - +
208L TRP* 2.9 15.0 + - + +
209L VAL* 3.0 42.4 + - - +
211L TYR* 1.3 77.6 - - - +
213L GLU* 1.3 85.2 + - - +
229L GLY* 3.8 1.6 - - - -
230L ASN* 3.5 12.1 + - - +
231L GLU* 3.1 30.7 + - + +
232L LYS* 4.5 1.4 + - - +
268L GLU* 3.4 37.3 + - - -
272L TYR* 3.7 25.1 - - + +
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Residues in contact with GLU 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K VAL* 4.4 1.2 - - - +
227K VAL* 4.5 8.2 - - + -
228K SER 5.3 0.7 - - - +
238K ASN* 3.7 55.4 - - + +
209L VAL* 3.0 22.2 + - + +
210L SER 4.2 0.2 - - - +
212L ARG* 1.3 114.9 + - + +
214L GLY* 1.3 61.8 + - - +
228L LEU 3.4 9.9 - - - +
231L GLU* 5.4 3.1 - - - +
232L LYS* 3.5 17.9 + - - -
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Residues in contact with GLY 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K VAL* 3.9 7.0 - - - -
227K VAL* 3.6 17.8 - - - +
238K ASN 4.6 1.7 - - - +
210L SER* 2.9 15.6 + - - +
211L TYR 4.5 0.9 - - - -
212L ARG 3.6 1.4 - - - -
213L GLU* 1.3 83.0 - - - +
215L PHE* 1.3 66.2 + - - +
227L TRP 3.1 16.8 - - - -
228L LEU 3.2 10.1 - - - -
229L GLY* 3.8 2.2 - - - -
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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