Contacts of the strand formed by residues 212 - 217 (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 PRO 212 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 4.0 19.1 - - + +
30A GLN* 3.4 21.3 - - - +
46A GLY 3.9 10.1 - - - +
47A SER* 4.2 8.5 - - - -
141A TRP 3.8 1.2 - - - +
142A VAL* 3.5 24.0 - - - +
143A THR* 3.6 18.6 + - - +
211A GLY* 1.3 85.1 - - - +
213A LEU* 1.3 59.6 + - - +
214A VAL* 3.9 16.6 + - + +
223A GLN* 3.5 25.8 - - - +
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Residues in contact with LEU 213 (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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140A CYS* 4.1 11.7 - - + -
141A TRP 3.4 16.6 - - - +
142A VAL* 3.9 7.2 - - + +
165A VAL* 3.6 29.2 - - + -
167A ILE* 4.4 8.3 - - + -
195A LEU* 3.6 31.2 - - + -
197A ALA* 4.2 7.4 - - + -
211A GLY 3.9 0.6 + - - -
212A PRO* 1.3 71.5 - - - +
214A VAL* 1.3 59.1 + - - +
223A GLN* 3.5 3.5 - - - -
224A ALA* 2.8 30.3 + - + -
225A GLY 2.9 21.2 + - - +
242A TYR* 3.7 30.9 - - + -
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.7 32.3 - - + -
29A TRP* 4.0 11.7 - - + +
125A VAL* 4.0 17.7 - - + -
140A CYS* 3.3 0.9 - - - -
141A TRP* 2.8 47.2 + - + +
143A THR* 6.0 1.6 - - + +
212A PRO* 3.9 20.2 - - + +
213A LEU* 1.3 79.6 - - - +
215A CYS* 1.3 63.9 + - - +
221A TRP* 3.7 15.6 - - + -
222A LEU 3.1 12.3 - - - +
223A GLN* 3.8 11.0 - - + -
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Residues in contact with CYS 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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134A PHE* 3.9 33.2 - - + -
138A MET* 4.0 9.0 - - + -
139A PRO 3.4 5.4 - - - +
140A CYS* 2.0 48.0 - - - -
167A ILE* 4.7 3.6 - - - -
213A LEU* 4.8 2.2 - - - -
214A VAL* 1.3 75.7 - - - +
216A LYS* 1.3 61.5 + - - +
217A VAL* 3.6 3.9 + - - +
220A THR 3.5 0.7 - - - +
221A TRP* 3.5 4.5 - - - -
222A LEU* 2.8 32.0 + - - +
224A ALA* 3.9 11.9 - - - -
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Residues in contact with LYS 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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138A MET* 4.5 2.8 - - - +
139A PRO* 3.2 33.9 + - + +
215A CYS* 1.3 68.5 - - - +
217A VAL* 1.3 65.0 + - - +
218A ASN 4.2 0.7 + - - -
219A GLY* 4.1 28.9 - - - +
220A THR 3.5 7.4 - - - +
221A TRP* 3.3 52.6 - - + +
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Residues in contact with VAL 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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132A GLU* 4.2 17.0 - - - +
134A PHE* 4.3 7.6 - - + -
138A MET* 3.7 29.2 - - + -
215A CYS 4.0 10.1 - - - +
216A LYS* 1.3 79.7 - - - +
218A ASN* 1.3 83.3 + - - +
219A GLY 3.2 0.2 - - - -
220A THR* 2.7 26.8 + - - +
222A LEU* 4.2 23.3 - - + +
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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