Contacts of the helix formed by residues 213 - 221 (chain A) in PDB entry 1LAP
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 MET 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TRP* 4.0 16.6 - - + -
208A ILE* 3.5 27.9 + - + +
209A GLU 4.7 0.2 + - - -
211A GLN* 3.2 22.2 - - + +
212A GLU* 1.3 72.6 - - - +
214A GLY* 1.3 58.5 + - - +
216A PHE* 4.3 6.1 - - + -
217A LEU* 2.9 36.1 + - - +
229A PHE* 4.0 29.2 - - + -
321A ARG* 4.2 7.9 - - - +
341A ASP* 3.2 33.7 - - + +
345A TYR* 3.8 35.4 - - + -
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Residues in contact with GLY 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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212A GLU 2.9 11.7 + - - -
213A MET* 1.3 73.0 - - - +
215A SER* 1.3 56.7 + - - +
217A LEU* 3.5 7.8 + - - +
218A SER* 3.0 28.2 + - - -
318A VAL* 4.4 4.5 - - - +
319A ARG* 3.2 17.5 + - - -
341A ASP* 3.5 0.8 + - - -
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Residues in contact with SER 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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214A GLY* 1.3 68.9 - - - +
216A PHE* 1.3 65.1 + - - +
218A SER* 3.0 19.5 + - - -
219A VAL* 3.5 12.8 + - - +
318A VAL* 4.0 12.6 - - - -
319A ARG 3.4 4.0 + - - -
320A ALA* 3.4 15.6 - - - +
326A ILE* 3.6 18.6 - - - +
337A LEU* 3.4 24.5 + - - +
340A ALA* 4.1 0.9 - - - +
341A ASP* 2.9 24.8 + - - -
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Residues in contact with PHE 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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208A ILE* 3.4 47.8 - - + -
213A MET* 3.8 12.8 - - + +
215A SER* 1.3 76.2 - - - +
217A LEU* 1.3 62.7 + - + +
219A VAL* 3.1 13.7 + - - +
220A ALA* 3.1 10.0 + - + +
227A PRO* 4.0 6.5 - - + -
228A VAL 3.7 20.2 - - - -
229A PHE* 4.2 8.3 - + - -
301A PRO* 4.0 24.2 - - + -
302A LEU 4.0 7.0 - - - -
303A CYS* 3.9 25.1 - - + -
337A LEU 4.0 0.8 + - - -
338A ILE* 3.4 37.2 - - + +
341A ASP* 2.9 17.0 + - + +
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Residues in contact with LEU 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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205A LYS* 4.7 25.4 - - + +
208A ILE* 3.6 30.7 - - + +
209A GLU* 3.8 35.2 - - + +
212A GLU* 6.1 0.2 - - - -
213A MET 2.9 24.8 + - - +
214A GLY* 3.7 7.6 - - - +
216A PHE* 1.3 78.9 - - + +
218A SER* 1.3 58.3 + - - +
220A ALA* 3.4 4.4 + - + +
221A LYS* 3.2 25.3 + - - +
227A PRO* 4.9 9.2 - - + -
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Residues in contact with SER 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 GLY 3.0 11.2 + - - -
215A SER* 3.0 14.7 + - - -
216A PHE 3.1 0.2 + - - -
217A LEU* 1.3 73.9 - - - +
219A VAL* 1.3 66.3 + - - +
221A LYS* 3.3 29.7 - - - +
222A GLY 4.7 0.2 + - - -
312A ASN* 3.2 33.2 + - - +
318A VAL* 3.3 29.8 - - - +
337A LEU* 5.0 2.1 - - - +
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Residues in contact with VAL 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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215A SER 3.7 10.8 - - - +
216A PHE 3.1 2.3 + - - +
218A SER* 1.3 79.3 + - - +
220A ALA* 1.3 64.0 + - - +
221A LYS 3.3 0.5 + - - -
222A GLY* 3.6 8.5 + - - -
223A SER 5.1 0.2 + - - -
252A ILE* 4.2 0.4 - - + -
303A CYS* 3.6 9.4 - - - -
304A GLU 4.1 5.5 - - - +
305A ASN* 4.1 23.2 + - + +
306A MET 5.3 0.7 + - - -
311A ALA* 6.0 0.2 - - - -
312A ASN* 4.0 5.4 + - - +
334A GLU* 3.7 36.1 - - + +
337A LEU* 3.8 19.1 - - + -
338A ILE* 3.5 34.8 - - + -
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Residues in contact with ALA 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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216A PHE* 3.1 11.5 + - + +
217A LEU* 3.8 11.7 - - + +
218A SER 3.3 0.2 - - - -
219A VAL* 1.3 80.0 - - - +
221A LYS* 1.3 63.5 + - - +
222A GLY 3.0 2.3 + - - -
223A SER* 3.2 21.1 + - - +
225A GLU 5.0 4.0 - - - +
227A PRO* 3.9 36.5 - - + +
303A CYS* 3.9 17.5 - - + -
304A GLU 4.4 2.4 + - - +
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Residues in contact with LYS 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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205A LYS* 6.5 1.8 - - - +
217A LEU 3.2 9.8 + - - +
218A SER* 3.3 30.9 - - - +
220A ALA* 1.3 75.5 - - - +
222A GLY* 1.3 61.1 + - - +
223A SER 3.2 6.7 + - - +
310A LYS* 3.2 52.1 + - + +
311A ALA 4.6 1.2 + - - -
312A ASN* 3.5 26.0 - - - +
313A LYS* 5.8 1.8 - - - +
316A ASP* 5.2 3.6 + - - -
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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