Contacts of the strand formed by residues 201 - 206 (chain A) in PDB entry 3ZJX
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 SER 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASN* 3.1 4.3 - - - +
61A ASP* 2.7 33.7 + - - +
62A PHE* 3.6 9.8 - - - -
200A GLY* 1.3 75.1 + - - -
202A GLU* 1.3 59.5 + - - +
203A TRP* 3.6 2.5 - - - -
218A LYS* 3.7 20.4 - - - -
219A PHE 3.3 17.0 - - - -
220A SER* 3.7 10.2 - - - -
1298A PO4 2.5 37.5 + - - -
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Residues in contact with GLU 202 (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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24A ILE* 3.7 8.5 - - - +
28A ARG* 2.8 42.2 + - - -
57A PRO* 3.7 8.1 - - + +
59A GLY 3.4 13.2 - - - +
60A ASN* 4.0 3.5 + - + +
62A PHE* 3.6 21.5 - - + -
201A SER* 1.3 73.5 - - - +
203A TRP* 1.3 70.6 + - - +
217A TYR* 2.8 26.5 + - - +
218A LYS* 3.2 3.6 - - - +
219A PHE* 3.0 52.4 + - + -
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Residues in contact with TRP 203 (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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57A PRO* 3.8 3.3 - - - +
58A GLN* 2.8 28.4 + - + +
59A GLY* 2.9 32.5 + - - +
60A ASN* 3.5 27.6 - - - -
61A ASP* 3.7 18.8 - - + -
201A SER 3.6 21.3 - - - -
202A GLU* 1.3 75.5 - - - +
204A GLY* 1.3 59.5 + - - +
217A TYR* 3.2 19.3 - - - +
218A LYS* 4.1 33.7 - - + -
1298A PO4 4.4 0.2 - - - -
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Residues in contact with GLY 204 (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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56A ASN 3.3 13.0 - - - -
58A GLN* 3.8 12.8 - - - -
203A TRP* 1.3 78.5 - - - +
205A GLU* 1.3 65.6 + - - +
214A ARG* 4.3 4.6 + - - -
216A GLY* 3.5 3.3 - - - -
217A TYR* 2.9 33.0 + - - +
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Residues in contact with GLU 205 (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 ILE* 3.7 0.2 - - - -
56A ASN* 2.8 57.6 + - + +
204A GLY* 1.3 76.8 - - - +
206A ILE* 1.3 60.3 + - - +
207A PRO* 3.6 20.3 - - - +
214A ARG* 2.8 42.2 + - - +
215A ASP 3.4 11.0 - - - +
217A TYR* 3.2 9.3 - - - -
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Residues in contact with ILE 206 (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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31A THR* 4.6 11.9 - - + -
32A LYS* 4.6 6.3 - - + -
35A TYR* 3.9 30.1 - - + -
53A VAL* 3.7 20.9 - - + -
54A THR 3.4 20.4 - - - +
55A ILE* 4.2 20.6 - - + -
205A GLU* 1.3 70.3 - - - +
207A PRO* 1.3 71.6 - - + +
213A PRO 4.3 0.2 - - - +
214A ARG* 3.4 2.8 - - - +
215A ASP* 2.9 47.1 + - + +
217A TYR* 4.2 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