Contacts of the strand formed by residues 214 - 224 (chain A) in PDB entry 1AS4
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TYR* 3.5 0.2 - - - -
210A LEU* 2.8 49.8 + - + +
211A SER* 3.0 27.5 + - - +
213A LYS* 1.3 80.2 - - - +
215A TRP* 1.3 69.4 + - - +
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Residues in contact with TRP 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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207A ARG* 3.6 58.1 - - + +
208A PHE 3.2 22.9 - - - +
209A TYR* 3.5 28.0 - + + -
210A LEU* 4.0 4.3 - - - +
212A LYS 5.9 0.2 - - - -
213A LYS* 4.3 15.0 - - + -
214A LYS* 1.3 83.9 - - - +
216A VAL* 1.3 78.4 + - - +
217A MET* 4.3 11.3 - - + +
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Residues in contact with VAL 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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207A ARG* 3.5 3.8 - - - -
208A PHE* 2.9 46.1 + - + +
210A LEU* 3.8 24.9 - - + -
215A TRP* 1.3 83.9 - - - +
217A MET* 1.3 59.8 + - - +
218A VAL* 3.8 19.5 + - + -
390B ASN* 3.9 22.4 - - - +
391B PRO* 4.7 0.2 - - + -
392B LYS* 4.2 14.6 - - + +
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Residues in contact with MET 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 GLN* 3.5 27.9 - - + +
206A SER* 3.4 35.2 - - - +
207A ARG* 4.0 19.3 - - + +
215A TRP* 4.3 11.7 - - + +
216A VAL* 1.3 74.2 - - - +
218A VAL* 1.3 60.5 + - - +
392B LYS* 2.8 29.9 + - - +
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Residues in contact with VAL 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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205A GLN* 3.5 7.1 + - - -
206A SER* 2.9 36.5 + - - +
208A PHE* 3.8 17.5 - - + -
216A VAL* 3.9 15.0 - - + -
217A MET* 1.3 80.6 - - - +
219A PRO* 1.3 73.0 - - + +
220A MET* 3.1 17.4 + - + -
289A PRO* 4.1 14.8 - - + -
290A LYS 5.1 2.0 - - - +
391B PRO* 3.7 24.9 - - + -
392B LYS* 3.9 14.4 - - + +
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Residues in contact with PRO 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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203A THR* 3.8 19.3 - - + -
204A HIS 3.8 5.8 - - - +
205A GLN* 3.3 22.9 - - - +
217A MET 4.9 0.2 - - - +
218A VAL* 1.3 85.6 - - + +
220A MET* 1.3 61.8 + - - +
289A PRO* 3.4 3.6 - - - +
290A LYS* 2.9 52.9 + - + +
392B LYS* 5.0 7.6 - - - -
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Residues in contact with MET 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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202A ASP 3.7 2.4 - - - +
203A THR* 3.3 3.9 - - - +
204A HIS* 2.8 37.7 + - - +
206A SER* 3.8 20.0 - - - +
207A ARG 3.8 22.0 - - - +
208A PHE* 4.9 1.1 - - + -
218A VAL* 3.1 21.0 + - + +
219A PRO* 1.3 71.6 - - - +
221A MET* 1.3 62.0 + - - +
222A SER* 4.9 0.9 - - - -
287A TYR* 3.6 33.2 - - + -
288A LEU 3.7 8.1 - - - -
289A PRO* 3.6 27.4 - - + -
365B ARG* 5.5 2.2 - - + +
366B PHE 4.0 15.0 - - - +
367B ASN* 4.1 9.0 - - + -
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Residues in contact with MET 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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198A PHE* 3.6 36.6 - - + -
203A THR* 3.8 21.3 - - + +
220A MET* 1.3 73.9 - - - +
222A SER* 1.3 60.0 + - - +
287A TYR* 3.2 6.6 - - - +
288A LEU* 2.9 56.0 + - + +
289A PRO 3.9 12.3 - - - +
290A LYS* 3.8 22.4 - - + -
340A VAL* 4.2 7.4 - - + -
341A PHE 3.4 11.0 - - - +
342A GLU* 3.3 37.2 - - - +
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Residues in contact with SER 222 (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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198A PHE* 3.5 17.1 - - - +
199A ASP 4.6 1.0 + - - -
202A ASP* 3.2 37.7 + - - +
203A THR* 5.0 0.2 + - - -
220A MET 4.9 0.4 - - - -
221A MET* 1.3 78.8 - - - +
223A LEU* 1.3 64.3 + - - +
224A HIS* 3.6 21.6 + - - -
286A LEU 3.1 10.8 - - - -
287A TYR* 3.6 26.0 - - - -
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Residues in contact with LEU 223 (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 MET* 3.5 30.3 - - + +
197A PRO 3.5 20.0 - - - +
198A PHE* 3.6 34.8 - - + -
199A ASP 5.4 1.1 - - - +
222A SER* 1.3 74.7 - - - +
224A HIS* 1.3 68.0 + - - +
226A LEU* 3.8 34.5 - - + +
242A LEU* 5.4 5.6 - - + -
285A GLU* 3.4 4.3 - - - +
286A LEU* 2.9 34.0 + - + +
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Residues in contact with HIS 224 (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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202A ASP* 4.8 15.6 + - + -
222A SER* 3.6 27.7 - - - -
223A LEU* 1.3 80.7 - - - +
225A HIS* 1.3 87.3 + + + +
226A LEU* 3.6 3.7 - - - +
284A GLY 3.3 5.2 - - - +
285A GLU* 3.4 38.0 + - + +
287A TYR* 4.4 6.0 + + - -
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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