Contacts of the strand formed by residues 220 - 229 (chain A) in PDB entry 2ZA5
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 THR 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A THR* 3.9 19.3 - - + +
215A CYS 3.5 0.3 - - - +
216A LYS* 3.5 1.3 - - - -
217A VAL* 2.7 40.6 + - - +
218A ASN 3.2 5.1 + - - -
219A GLY* 1.3 77.8 - - - +
221A TRP* 1.3 76.6 + - - +
222A LEU* 3.6 14.1 + - + +
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Residues in contact with TRP 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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26A LYS* 6.4 0.7 - - + -
27A TRP* 4.0 18.3 - + - -
29A TRP* 3.7 33.1 - + + -
125A VAL* 4.1 2.0 - - - +
126A THR* 3.7 14.7 + - - +
139A PRO* 4.5 1.3 - - + -
141A TRP* 3.6 36.6 - + - -
214A VAL* 3.7 24.9 - - + -
215A CYS 3.5 5.8 - - - -
216A LYS* 3.3 68.7 - - + +
219A GLY 4.9 2.7 - - - -
220A THR* 1.3 80.3 - - - +
222A LEU* 1.3 66.4 + - - +
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Residues in contact with LEU 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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126A THR* 3.3 31.4 - - + +
127A LEU 4.0 4.7 - - - +
128A PRO* 3.8 10.1 - - + -
129A PRO* 3.7 27.4 - - + -
132A GLU* 4.6 3.6 - - + +
134A PHE* 4.1 16.4 - - + -
214A VAL* 3.1 5.6 - - - -
215A CYS* 2.8 37.6 + - - +
217A VAL* 4.2 25.4 - - + -
220A THR* 4.0 17.7 - - + +
221A TRP* 1.3 82.1 - - - +
223A GLN* 1.3 60.1 + - - +
224A ALA* 3.2 3.3 + - - +
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Residues in contact with GLN 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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47A SER* 2.6 33.1 + - - -
49A ILE* 4.1 3.0 - - - +
55A LEU* 3.9 15.8 - - - +
125A VAL* 3.5 19.3 - - + +
126A THR 3.1 9.9 + - - -
127A LEU* 4.3 11.4 - - + +
128A PRO* 3.2 21.0 - - - +
134A PHE* 4.5 0.2 - - - -
210A GLY 5.1 1.0 - - - +
211A GLY 4.3 1.6 - - - +
212A PRO* 3.5 17.3 - - - +
213A LEU 3.5 7.0 - - - +
214A VAL* 3.8 8.7 - - + -
222A LEU* 1.3 70.0 - - - +
224A ALA* 1.3 61.2 + - - +
225A GLY 3.1 27.4 - - - +
226A VAL* 3.9 12.0 - - - +
245A VAL* 3.5 11.0 - - + +
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Residues in contact with ALA 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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134A PHE* 3.5 48.9 - - + -
195A LEU* 4.0 17.2 - - + +
213A LEU* 2.8 13.4 + - + +
215A CYS* 3.9 14.1 - - - -
222A LEU 3.2 3.4 + - - -
223A GLN* 1.3 73.7 - - - +
225A GLY* 1.3 59.3 + - - +
243A THR 3.9 0.3 - - - +
244A ARG* 4.0 4.9 - - - +
245A VAL* 3.1 21.7 + - - +
246A THR 4.7 0.5 + - - -
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Residues in contact with GLY 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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195A LEU* 5.2 0.9 - - - -
213A LEU* 2.9 39.2 + - - +
223A GLN* 3.1 14.6 - - - +
224A ALA* 1.3 80.5 - - - +
226A VAL* 1.3 64.7 + - - -
242A TYR* 4.2 7.6 - - - -
243A THR 3.1 11.7 - - - -
245A VAL* 3.9 3.6 - - - -
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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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55A LEU* 3.9 32.8 - - + -
56A THR 3.9 4.7 - - - +
57A ALA* 3.8 18.2 - - + +
106A ASP 4.5 2.9 - - - +
107A ILE* 4.8 6.1 - - + -
210A GLY* 3.6 30.7 - - - +
211A GLY 3.5 3.4 - - - -
223A GLN* 3.9 4.5 - - - +
225A GLY* 1.3 76.1 - - - -
227A VAL* 1.3 69.9 + - - +
228A SER* 3.1 1.6 + - - -
242A TYR* 3.2 5.0 - - - -
243A THR* 2.8 45.4 + - - +
245A VAL* 4.0 7.2 - - + -
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Residues in contact with VAL 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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4A 2FF 3.7 26.0 - - + -
57A ALA* 3.9 4.0 - - - +
59A HIS* 4.2 0.2 - - - -
142A VAL* 3.6 29.4 - - + -
143A THR 5.3 0.4 - - - +
204A SER* 3.8 11.4 - - - +
208A ASP* 3.3 21.8 - - + +
209A SER* 3.4 23.3 - - - +
210A GLY 3.0 17.9 + - - +
211A GLY 3.0 19.8 + - - +
226A VAL* 1.3 73.3 - - - +
228A SER* 1.3 60.4 + - - +
242A TYR* 3.6 16.9 - - + -
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Residues in contact with SER 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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4A 2FF 4.8 4.4 - - - +
59A HIS* 3.0 23.4 + - - -
101A ALA* 3.7 2.8 + - - +
106A ASP* 2.5 31.4 + - - +
194A MET* 6.5 0.7 - - - -
209A SER* 4.5 2.4 + - - -
226A VAL 3.1 9.0 + - - -
227A VAL* 1.3 80.6 - - - +
229A TRP* 1.3 79.3 + - - +
241A ILE 3.2 13.5 + - - -
242A TYR* 4.2 0.9 - - - -
243A THR* 3.8 16.6 + - - -
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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
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4A 2FF 3.4 60.9 - + + -
101A ALA* 3.4 23.2 + - + -
102A GLN* 3.4 51.6 - - + +
177A TYR* 4.4 4.5 - + - -
189A ILE* 3.9 35.0 - - + -
194A MET* 4.0 8.7 - - + -
228A SER* 1.3 103.2 - - - +
230A GLY* 1.3 83.0 + - - +
241A ILE* 2.9 69.4 + - + +
99C TYR* 5.0 1.1 - + - -
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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