Contacts of the strand formed by residues 213 - 225 (chain A) in PDB entry 4Z4H
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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46A GLU* 3.6 3.8 - - - -
47A MET* 2.8 49.3 + - + +
49A ILE* 4.0 22.7 - - + -
143A LEU* 4.0 11.7 - - + -
147A LEU* 3.6 22.8 - - + +
159A ILE* 3.6 27.6 - - + -
162A LEU* 4.0 7.0 - - + -
206A VAL* 3.2 35.4 - - + -
207A ARG 3.5 12.8 - - - +
208A PRO* 3.6 17.9 - - - -
212A LYS* 1.3 76.8 - - - +
214A MET* 1.3 55.7 + - - +
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Residues in contact with MET 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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44A PHE* 3.8 38.8 - - + -
45A PHE 3.6 1.1 - - - -
46A GLU* 4.0 15.9 - - + -
47A MET* 4.0 5.4 - - - +
205A SER 3.7 0.3 - - - +
206A VAL* 3.5 5.0 - - - -
207A ARG* 2.8 41.0 + - + +
209A SER* 3.5 29.6 - - - +
211A TRP* 3.9 28.0 - - + -
212A LYS 4.2 2.9 - - - +
213A MET* 1.3 76.1 - - - +
215A LEU* 1.3 60.2 + - - +
216A ASN 3.7 0.6 + - - +
406A THR* 3.5 33.2 - - + +
739A LYS 4.0 11.0 - - - +
740A ILE* 4.8 3.4 - - + -
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Residues in contact with LEU 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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44A PHE* 4.4 0.9 - - - -
45A PHE* 2.8 52.4 + - + +
47A MET* 3.9 12.6 - - + +
166A MET* 4.1 17.3 - - + -
204A GLN* 3.9 20.9 - - + -
205A SER 3.6 11.9 - - - +
206A VAL* 4.0 17.0 - - + -
214A MET* 1.3 71.0 - - - +
216A ASN* 1.3 58.6 + - - +
217A ILE* 3.7 26.9 - - + -
383A MET* 4.8 0.9 - - + -
388A PHE* 3.8 26.5 - - + -
401A VAL* 4.0 17.0 - - + -
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Residues in contact with ASN 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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43A ASN* 3.4 11.5 + - - +
44A PHE* 3.1 35.1 - - + -
203A HIS* 3.5 3.0 + - - +
204A GLN* 3.4 7.6 - - - -
205A SER* 2.8 47.7 + - - +
207A ARG* 3.8 18.0 - - + +
214A MET 3.7 1.6 + - - -
215A LEU* 1.3 70.3 - - - +
217A ILE* 1.3 65.9 + - - +
712A HIS* 3.1 40.6 + - - +
713A THR* 3.7 3.2 + - - -
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Residues in contact with ILE 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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43A ASN* 3.0 32.2 + - - +
45A PHE* 4.0 11.2 - - + -
202A PHE* 4.5 6.3 - - + -
203A HIS 3.4 11.9 - - - +
204A GLN* 4.0 12.8 - - + +
215A LEU* 3.7 33.9 - - + +
216A ASN* 1.3 83.5 + - - +
218A ASP* 1.3 65.2 + - - +
379A ILE* 3.9 8.2 - - + +
382A LEU* 3.8 29.2 - - + -
383A MET* 3.7 26.7 - - + -
388A PHE* 4.1 11.4 - - + -
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Residues in contact with ASP 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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43A ASN* 3.6 14.4 - - - +
202A PHE* 3.1 4.8 - - - -
203A HIS* 2.6 42.3 + - + +
217A ILE* 1.3 79.0 - - - +
219A VAL* 1.3 76.7 + - - +
220A SER* 5.5 0.2 - - - -
375A ARG* 2.6 32.6 + - - -
379A ILE* 3.7 14.6 - - - +
712A HIS* 4.0 21.9 - - + +
714A ARG* 3.9 24.2 + - - +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE* 6.5 0.4 - - + -
201A GLY 3.4 9.6 - - - +
202A PHE* 4.1 0.2 - - - +
218A ASP* 1.3 93.8 + - - +
220A SER* 1.3 64.1 + - - +
370A ARG* 5.7 5.8 - - - -
375A ARG* 3.5 23.2 + - + +
378A GLU* 3.9 34.8 - - + +
379A ILE* 4.3 11.6 - - + +
382A LEU* 3.7 26.7 - - + -
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Residues in contact with SER 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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180A SER* 4.2 9.2 + - - -
182A PHE* 3.3 23.6 - - - -
200A PHE* 3.6 6.8 - - - -
201A GLY 2.8 37.2 + - - +
202A PHE* 4.1 2.8 + - - -
203A HIS* 5.3 2.2 - - - -
218A ASP 5.0 1.3 - - - -
219A VAL* 1.3 77.3 - - - +
221A ALA* 1.3 62.7 + - - +
8B U 4.9 12.6 - - - -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A PHE* 3.8 4.9 - - - -
198A VAL* 3.8 6.3 - - + -
199A TRP 3.3 13.0 - - - +
200A PHE* 3.8 13.9 - - + -
220A SER* 1.3 79.6 + - - +
222A THR* 1.3 62.9 + - - +
364A MET* 4.9 4.6 - - - +
368A THR* 3.5 33.2 - - + -
7B U 5.4 1.2 + - - -
8B U 4.7 15.2 + - - +
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A PHE* 3.5 27.8 - - + -
198A VAL* 3.6 2.4 - - - -
199A TRP* 2.9 29.0 + - - +
221A ALA* 1.3 75.1 - - - +
223A ALA* 1.3 68.3 + - - +
224A PHE* 3.3 30.4 + - + -
351A ARG* 3.7 25.9 + - - +
352A CYS 5.2 1.2 + - - -
364A MET* 4.1 10.8 - - - -
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.7 23.1 - - + -
196A ARG* 5.1 1.6 - - + -
197A GLU 3.6 5.4 - - - -
222A THR* 1.3 78.5 + - - +
224A PHE* 1.3 63.1 + - - +
351A ARG* 3.5 11.3 - - - +
352A CYS* 2.8 34.1 + - + +
356A LEU* 3.8 21.5 - - + -
364A MET* 3.8 10.7 - - + +
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Residues in contact with PHE 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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175A THR* 4.1 12.6 - - + -
177A VAL* 4.3 7.6 - - + -
182A PHE* 3.7 15.5 - - + -
196A ARG* 3.3 5.2 - - - -
197A GLU* 2.8 33.3 + - - +
199A TRP* 3.4 65.3 - + + +
222A THR* 3.3 26.2 - - + -
223A ALA* 1.3 78.3 - - - +
225A TYR* 1.3 65.1 + - - +
349A GLY* 3.8 14.4 - - - -
350A GLN 3.3 26.5 - - - -
351A ARG* 3.5 23.8 - - + -
352A CYS* 4.2 2.0 - - - +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLY 3.5 3.1 - - - +
196A ARG* 3.6 40.8 + - + +
197A GLU* 4.7 2.8 - - - +
199A TRP* 5.3 2.9 - - - -
224A PHE* 1.3 77.2 - - - +
226A LYS* 1.3 65.6 + - - +
227A ALA* 3.4 3.3 + - - +
233A PHE* 4.0 25.8 - + + -
261A GLU* 4.3 2.4 + - - -
265A LEU* 3.4 38.1 - - + -
346A ILE* 4.2 19.8 - - + +
347A VAL 5.1 1.4 - - - +
348A ALA* 5.2 0.2 - - - -
349A GLY 5.0 8.3 + - - -
350A GLN* 3.1 27.8 + - + +
351A ARG 3.8 4.9 - - - -
352A CYS* 3.7 28.1 - - - -
353A ILE 4.9 1.4 + - - -
354A LYS* 3.4 26.2 + - - +
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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