Contacts of the strand formed by residues 220 - 229 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B THR* 4.1 13.9 - - + +
215B CYS 3.4 0.3 - - - +
216B LYS* 4.2 2.2 - - - +
217B VAL* 2.6 48.7 + - - +
218B ASN* 3.9 5.6 + - - +
219B GLY* 1.3 77.0 + - - +
221B TRP* 1.3 68.7 - - - +
222B LEU* 3.5 26.4 + - + +
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Residues in contact with TRP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS* 6.2 3.1 - - + -
27B TRP* 3.9 20.4 - + - -
29B TRP* 3.7 30.7 - + + -
125B VAL* 4.0 2.3 - - + +
126B THR* 3.6 25.8 + - - +
139B PRO* 4.4 1.8 - - + -
141B TRP* 3.8 27.4 - + - -
214B VAL* 3.7 32.3 - - + -
215B CYS* 3.3 22.9 - - - -
216B LYS* 3.6 42.8 - - + +
219B GLY 5.7 1.1 - - - -
220B THR* 1.3 74.3 - - - +
222B LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.6 0.2 - - - -
126B THR* 3.4 23.8 - - + +
127B LEU 3.9 7.4 - - - +
128B PRO* 4.3 7.2 - - + -
129B PRO* 4.2 22.9 - - + -
132B GLU* 4.8 3.1 - - + -
134B PHE* 4.2 17.3 - - + -
214B VAL* 3.3 3.9 - - - -
215B CYS* 2.7 36.9 + - - +
217B VAL* 3.7 32.1 - - + +
220B THR* 3.7 30.1 - - + +
221B TRP* 1.3 73.8 - - - +
223B GLN* 1.3 59.3 + - - +
224B ALA* 3.1 5.0 + - - +
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER* 2.7 30.0 + - - -
49B ILE* 4.1 0.9 - - - +
55B LEU* 3.8 13.7 + - + +
125B VAL* 3.5 20.4 - - + +
126B THR 3.0 16.7 + - - +
127B LEU* 4.5 7.2 - - + -
128B PRO* 3.0 27.1 - - - +
210B GLY 5.2 1.0 + - - -
211B GLY 4.4 1.0 + - - -
212B PRO* 3.3 24.5 - - + +
213B LEU 3.7 6.3 - - - +
214B VAL* 4.1 4.0 - - + -
222B LEU* 1.3 70.1 - - - +
224B ALA* 1.3 58.6 + - - +
225B GLY 2.8 31.3 + - - +
226B VAL* 3.9 12.9 - - - +
245B VAL* 3.7 9.9 - - + +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 3.8 35.8 - - + -
195B LEU* 4.2 17.3 - - + +
213B LEU* 2.8 18.4 + - + +
215B CYS* 3.8 23.3 - - - -
222B LEU 3.1 3.8 + - - -
223B GLN* 1.3 72.8 - - - +
225B GLY* 1.3 56.1 + - - +
243B THR 3.9 0.5 - - - +
244B ARG* 4.0 5.7 - - - +
245B VAL* 3.2 21.1 + - - +
246B THR 4.8 0.5 + - - -
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 5.4 0.4 - - - -
213B LEU* 2.9 31.3 + - - +
223B GLN* 2.8 26.0 + - - -
224B ALA* 1.3 81.2 - - - +
226B VAL* 1.3 62.2 + - - -
242B TYR* 4.2 8.3 - - - -
243B THR 3.1 11.2 - - - -
245B VAL* 3.7 2.9 - - - -
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.0 18.2 - - + -
56B THR 3.6 19.1 - - - +
57B ALA* 3.6 7.9 - - + +
106B ASP 4.7 1.3 - - - +
107B ILE* 4.8 4.9 - - + -
210B GLY* 3.3 36.3 - - - +
211B GLY 3.4 3.1 - - - -
223B GLN* 3.9 11.7 - - - +
225B GLY* 1.3 78.4 - - - +
227B VAL* 1.3 65.0 + - - +
228B SER* 3.1 1.6 + - - -
242B TYR* 3.2 4.1 - - - -
243B THR* 2.8 41.3 + - - +
245B VAL* 3.9 14.6 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 2FF 3.7 17.5 - - + -
57B ALA* 3.7 7.6 - - - +
142B VAL* 3.7 19.1 - - + -
143B THR 5.3 0.2 - - - +
204B SER* 3.5 22.0 - - - +
208B ASP* 3.4 22.0 - - + +
209B SER* 3.6 19.0 - - - +
210B GLY* 2.9 24.3 + - - +
211B GLY 2.9 22.1 + - - +
226B VAL* 1.3 69.6 - - - +
228B SER* 1.3 62.2 + - - +
241B ILE 5.2 0.9 - - - +
242B TYR* 3.6 26.2 - - + -
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 2FF 4.8 3.6 - - - +
59B HIS* 3.1 22.4 + - - -
101B ALA* 3.8 2.1 + - - +
106B ASP* 2.6 30.7 + - - +
209B SER* 4.2 3.0 + - - -
226B VAL 3.8 7.9 - - - -
227B VAL* 1.3 80.8 - - - +
229B TRP* 1.3 82.5 + - - +
241B ILE* 3.1 16.0 + - - -
242B TYR* 4.1 1.3 - - - -
243B THR* 3.8 16.1 + - - -
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Residues in contact with TRP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 2FF 3.3 61.2 - + + -
101B ALA* 3.3 24.9 + - + -
102B GLN* 3.3 52.9 - - + +
177B TYR* 4.1 7.0 - + - -
189B ILE* 3.9 26.7 - - + -
194B MET* 4.0 13.8 - - + +
228B SER* 1.3 105.3 - - - +
230B GLY* 1.3 84.0 + - - +
241B ILE* 2.9 65.8 + - + +
99D TYR* 5.5 0.4 - + - -
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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