Contacts of the strand formed by residues 218 - 229 (chain A) in PDB entry 4TZ1
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 GLN 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER* 3.0 31.7 + - - +
199A GLY 2.7 40.6 + - - +
216A GLN* 3.4 4.8 - - - +
217A GLN* 1.3 98.8 - - - +
219A TRP* 1.3 70.1 + - - +
235A ASN* 3.2 24.2 - - + +
236A MET* 3.4 8.0 - - - +
498A PHE* 3.6 19.5 - - + -
500A GLN* 3.7 15.2 - - + +
541A TYR* 2.6 31.6 + - - +
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Residues in contact with TRP 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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170A TRP* 4.5 4.3 - + - -
172A VAL* 3.8 20.0 - - + -
176A ALA 5.8 0.2 - - - -
189A LEU* 3.7 36.1 - - + -
199A GLY* 3.9 1.3 - - - -
200A GLY* 3.5 25.6 - - - +
201A TYR 3.3 17.7 - - - -
202A ILE* 3.5 32.3 - - + +
216A GLN* 3.6 32.5 - - + -
218A GLN* 1.3 83.1 - - - +
220A TYR* 1.3 92.9 + - - +
221A THR* 3.4 11.6 + - - -
229A TRP* 4.0 19.7 - + + -
235A ASN 2.9 8.7 + - - +
236A MET* 3.7 13.5 - - + +
237A THR 2.9 28.1 + - - +
498A PHE* 3.6 9.8 - - - -
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Residues in contact with TYR 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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200A GLY 3.1 12.5 + - - +
201A TYR* 3.4 20.0 - + + -
202A ILE 3.0 22.9 + - - +
219A TRP* 1.3 83.1 + - - +
221A THR* 1.3 74.4 + - - +
222A ARG* 3.3 25.5 - - + +
237A THR* 3.5 11.2 - - + -
239A SER* 2.8 25.6 + - - -
475A THR* 3.3 28.8 - - - +
476A GLY* 3.7 27.4 - - - -
478A PHE* 5.1 0.2 - - + -
497A ILE* 3.7 23.2 - - + +
498A PHE* 3.6 31.1 - - + -
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Residues in contact with THR 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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202A ILE* 3.2 17.2 - - + +
219A TRP* 3.4 20.1 + - - -
220A TYR* 1.3 76.8 - - - +
222A ARG* 1.3 64.0 + - - +
224A SER* 3.9 20.0 - - - +
226A VAL* 5.1 4.5 - - + -
229A TRP* 3.5 20.6 - - + -
237A THR 3.1 6.1 + - - -
238A PHE* 3.3 15.7 - - + -
239A SER 3.1 21.8 + - - -
241A VAL* 3.4 26.6 - - + +
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Residues in contact with ARG 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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179A ARG* 3.7 5.7 - - - +
201A TYR* 3.5 6.7 + - + +
202A ILE 3.0 9.0 + - - +
203A ALA* 3.3 15.3 - - + +
204A ASP 3.2 9.2 + - - +
220A TYR* 3.3 34.1 - - + +
221A THR* 1.3 73.4 - - - +
223A ASP* 1.3 107.1 + - - +
224A SER* 2.8 13.9 + - - -
239A SER* 3.1 12.8 - - - +
241A VAL* 4.1 0.7 - - - -
260A THR* 3.8 12.3 - - - +
263A SER* 3.7 9.7 - - - -
264A ARG 4.2 6.7 + - - -
265A GLU* 2.9 40.2 + - - -
441A ASP* 2.9 42.6 + - - -
475A THR* 4.2 2.4 + - - -
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 2.8 26.3 + - - -
222A ARG* 1.3 97.4 + - - +
224A SER* 1.3 54.7 + - - +
239A SER 2.9 8.4 + - - +
240A GLY* 3.3 8.7 + - - -
260A THR* 2.6 26.5 + - - -
263A SER* 2.7 29.1 + - - -
265A GLU* 4.3 0.2 - - - +
284A ARG* 3.7 7.9 - - - +
287A ALA* 3.3 27.4 - - - +
289A GLY 3.4 22.5 - - - +
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.9 9.8 - - - +
203A ALA 3.6 2.4 - - - -
204A ASP 3.2 2.3 + - - -
205A SER* 3.1 27.0 + - - +
207A ILE* 5.6 0.4 - - - -
221A THR* 3.9 19.7 - - - -
222A ARG 2.8 19.9 + - - -
223A ASP* 1.3 73.8 + - - +
225A SER* 1.3 63.1 + - - +
226A VAL* 5.4 1.8 - - - -
240A GLY 3.3 3.8 + - - -
241A VAL* 3.4 4.8 - - - -
242A GLU 2.9 22.8 + - - -
289A GLY* 3.5 13.6 - - - -
290A THR* 4.1 4.7 - - - -
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Residues in contact with SER 225 (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 SER 2.9 7.9 + - - +
206A LYS* 3.3 26.5 - - - +
207A ILE* 2.7 33.6 + - - +
224A SER* 1.3 75.5 - - - +
226A VAL* 1.3 65.7 + - - +
242A GLU* 3.3 28.9 + - - +
289A GLY* 5.6 0.2 - - - -
290A THR* 4.4 3.5 - - - +
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Residues in contact with VAL 226 (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 ILE* 6.4 0.2 - - + -
207A ILE* 3.3 16.2 - - + -
209A GLY 4.6 0.2 - - - +
211A VAL* 3.6 25.4 - - + -
221A THR* 5.1 5.2 - - + -
224A SER* 5.4 0.2 - - - -
225A SER* 1.3 84.1 + - - +
227A GLY* 1.3 60.9 + - - +
228A GLY 3.4 23.3 - - - +
229A TRP* 4.3 17.0 - - + -
241A VAL* 4.5 11.9 - - + -
242A GLU 2.9 14.3 + - - +
243A GLY* 3.5 32.4 - - - +
244A ALA* 4.2 2.2 - - - +
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Residues in contact with GLY 227 (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 ILE 3.0 13.3 + - - -
208A ASP 3.6 14.1 - - - -
209A GLY* 3.0 11.7 + - - -
226A VAL* 1.3 72.6 - - - +
228A GLY* 1.3 57.3 + - - +
243A GLY* 4.9 3.9 - - - +
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Residues in contact with GLY 228 (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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209A GLY 3.4 4.8 + - - -
210A GLU* 3.9 13.0 - - - +
211A VAL* 2.9 21.0 + - - +
226A VAL* 3.2 17.5 - - - +
227A GLY* 1.3 78.6 - - - +
229A TRP* 1.3 62.8 + - - +
243A GLY 4.4 5.4 - - - -
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Residues in contact with TRP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.7 0.4 - - + -
202A ILE* 5.2 1.3 - - + -
210A GLU* 3.9 3.0 + - - +
211A VAL* 3.5 42.6 - - + -
213A PRO* 3.6 19.0 - - + +
219A TRP* 4.0 19.5 - + + -
221A THR* 3.5 27.4 - - + -
226A VAL* 4.3 16.2 - - + -
228A GLY* 1.3 76.0 - - - -
230A GLY* 1.3 65.7 + - - +
231A ASN 3.3 17.4 + - - -
236A MET* 3.9 14.3 - - + +
238A PHE* 3.5 30.7 - + - -
243A GLY 4.9 1.1 - - - +
245A PRO* 3.9 19.4 - - + +
254A TYR* 3.6 31.2 + + - -
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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