Contacts of the strand formed by residues 211 - 219 (chain A) in PDB entry 4LEY
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 GLU 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A TYR* 3.8 18.9 + - - +
205A LYS* 3.6 27.7 - - + +
209A PRO* 3.7 1.7 - - - +
210A ASN* 1.3 88.7 + - - +
212A PHE* 1.3 66.1 + - - +
213A ASP* 4.2 9.9 + - - +
305A SER* 3.4 15.6 + - - +
307A ASP* 5.5 4.3 - - - +
406A GLU* 5.2 5.2 - - - +
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Residues in contact with PHE 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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164A ILE 5.4 0.4 - - - -
167A ALA* 4.0 15.0 - - + -
168A ALA* 4.5 7.6 - - + -
171A VAL* 3.6 31.4 - - + -
200A TYR* 3.4 49.6 - + - -
201A TYR* 3.5 24.2 - + + +
209A PRO* 3.4 29.8 - - + -
211A GLU* 1.3 74.8 - - - +
213A ASP* 1.3 64.5 + - - +
214A VAL* 4.8 2.2 - - + -
304A ILE* 3.5 26.5 - - + -
305A SER 2.9 11.4 + - - +
306A VAL* 3.4 10.1 - - + +
307A ASP 2.9 26.9 + - - -
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Residues in contact with ASP 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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196A ASN* 3.8 0.3 - - - -
197A THR* 2.9 54.7 + - - +
198A GLY* 4.1 12.6 - - - -
199A SER 5.4 1.1 - - - -
200A TYR* 5.9 0.2 - - - +
201A TYR* 3.8 7.0 - - - -
211A GLU* 4.7 10.0 - - - +
212A PHE* 1.3 79.0 + - - +
214A VAL* 1.3 63.3 + - - +
307A ASP* 3.8 22.1 - - - +
309A ILE* 4.3 12.0 - - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 5.4 0.9 - - + -
175A VAL* 4.0 23.3 - - + -
194A GLN* 3.7 22.7 - - + +
195A LEU 4.0 2.2 - - - -
196A ASN* 3.6 21.3 - - - +
197A THR* 4.8 0.2 - - - -
201A TYR* 4.8 5.4 - - - +
212A PHE* 4.4 7.9 - - + +
213A ASP* 1.3 79.0 - - - +
215A MET* 1.3 64.2 + - - +
216A PHE* 3.7 18.7 + - + -
306A VAL* 4.3 13.2 - - + -
307A ASP 2.9 9.3 + - - +
308A ILE* 3.5 8.4 - - + +
309A ILE* 2.9 27.8 + - - +
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Residues in contact with MET 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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193A GLU 3.1 5.2 - - - +
194A GLN* 3.3 3.8 - - - -
195A LEU* 2.9 58.5 + - + +
197A THR* 4.3 18.4 - - - +
214A VAL* 1.3 73.4 - - - +
216A PHE* 1.3 65.9 + - - +
217A LYS* 4.8 2.9 - - + +
309A ILE* 3.5 25.1 - - + +
311A ALA* 4.5 15.5 - - + -
346A TYR* 4.7 18.6 - - + -
348A VAL* 4.8 6.1 - - + -
366A SER* 3.3 33.0 - - - +
368A SER* 3.6 20.4 - - - +
369A HIS 5.6 1.8 - - - -
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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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175A VAL* 4.1 15.7 - - + -
178A LEU* 4.2 15.5 - - + -
179A LEU* 3.9 48.7 - - + -
182A MET* 4.3 8.5 - - + -
192A VAL* 3.4 25.8 - - + +
193A GLU 3.4 3.4 - - - -
194A GLN* 4.5 3.1 - - + -
214A VAL* 3.7 23.7 + - + -
215A MET* 1.3 80.3 - - - +
217A LYS* 1.3 59.2 + - - +
266A PHE* 3.8 32.5 - + + -
308A ILE* 3.9 20.6 - - + -
309A ILE 2.9 10.4 + - - +
310A LEU* 3.8 4.5 - - - +
311A ALA* 2.9 25.4 + - - +
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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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191A GLY 4.4 1.0 - - - +
192A VAL* 3.3 2.8 - - - +
193A GLU* 2.5 82.9 + - - +
194A GLN 4.9 1.6 - - - -
195A LEU* 3.7 26.9 - - + -
215A MET* 5.1 4.5 - - + -
216A PHE* 1.3 73.6 - - - +
218A LEU* 1.3 60.8 + - - +
219A GLU* 4.4 1.0 + - - +
311A ALA* 3.4 10.5 - - + -
313A GLU* 2.7 28.7 + - + +
346A TYR* 3.4 42.0 - - + +
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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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188A GLU 4.1 18.6 - - - +
189A PHE* 4.4 12.8 - - + -
190A LYS 3.8 23.3 - - - +
191A GLY 4.2 4.0 - - - +
192A VAL* 4.0 22.4 - - + +
216A PHE 5.2 0.2 - - - +
217A LYS* 1.3 73.4 - - - +
219A GLU* 1.3 73.1 + - - +
220A VAL* 3.5 4.6 + - + +
248A LEU* 4.3 12.3 - - + -
262A MET* 4.2 23.6 - - + -
310A LEU* 5.7 1.8 - - + -
311A ALA 2.9 14.0 + - - +
312A LEU* 3.3 9.8 - - + -
313A GLU* 2.9 18.7 + - - +
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Residues in contact with GLU 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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191A GLY 5.7 1.0 + - - -
193A GLU* 6.1 0.7 - - - +
217A LYS* 4.3 1.2 - - - +
218A LEU* 1.3 80.0 - - - +
220A VAL* 1.3 63.9 + - - +
221A PRO* 3.3 29.7 - - + +
313A GLU* 3.3 30.5 - - - +
314A SER* 5.5 0.2 - - - -
315A LYS* 3.5 46.3 + - + +
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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