Contacts of the strand formed by residues 32 - 38 (chain B) in PDB entry 3ZXR
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 MET 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B ARG* 4.2 9.6 - - + +
25B PHE* 3.3 23.3 - - - +
26B CYS* 3.6 17.5 - - + +
30B GLY 3.8 0.8 + - - -
31B ILE* 1.3 76.0 - - - +
33B GLN* 1.3 60.4 + - - +
92B ASN* 3.7 35.9 - - - +
109B ARG* 5.1 1.6 - - - -
243B GLN* 3.5 48.7 - - + +
247B TYR* 6.4 0.9 - - + -
377B TYR* 4.3 4.9 - - - +
188C PRO* 3.3 6.8 - - - +
189C VAL* 2.9 46.4 + - + +
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Residues in contact with GLN 33 (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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24B ARG* 3.1 8.3 - - - +
25B PHE* 2.7 69.0 + - + +
27B ASP* 3.1 28.0 + - + +
31B ILE* 2.9 32.9 + - - +
32B MET* 1.3 79.5 + - - +
34B HIS* 1.3 65.0 + - - +
58B ILE* 3.7 10.7 - - + +
59B ARG* 5.1 0.2 - - - +
186C TYR 3.7 1.0 - - - +
187C PHE* 2.8 43.3 + - + -
188C PRO* 3.2 5.9 - - - +
189C VAL* 4.2 0.8 - - - +
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Residues in contact with HIS 34 (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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22B ASP* 2.7 40.8 + - - +
23B VAL 3.1 10.1 - - - +
24B ARG* 4.0 3.8 - - + -
25B PHE* 5.4 0.2 - - - -
33B GLN* 1.3 77.3 - - - +
35B PHE* 1.3 62.8 + - - +
36B THR* 4.3 4.0 + - - -
84B ARG* 4.6 5.4 - - - -
187C PHE* 2.9 38.2 + - + +
188C PRO 3.4 21.5 + - - -
189C VAL* 3.6 20.6 - - + -
190C ALA 5.1 0.9 - - - -
193C ASP* 2.9 30.2 + - - +
196C VAL* 4.0 15.5 - - + +
199C ARG* 4.2 7.4 + - - -
217C HIS* 4.4 2.1 - - - +
218C HIS 5.9 0.4 + - - -
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Residues in contact with PHE 35 (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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22B ASP* 3.4 2.9 - - - +
23B VAL* 2.8 59.4 + - + +
25B PHE* 4.8 0.9 - + - -
34B HIS* 1.3 76.8 - - - +
36B THR* 1.3 62.3 + - - +
37B ILE* 3.9 20.4 - - + -
51B LEU* 4.1 18.8 - - + -
52B ALA 4.0 18.6 - - - -
53B PHE* 4.4 1.1 - - + -
71B LEU* 3.7 23.3 - - + -
187C PHE* 3.5 26.5 - + + -
215C LYS* 3.7 29.8 - - + -
216C GLY 3.7 3.8 - - - +
217C HIS* 3.5 24.7 - + + +
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Residues in contact with THR 36 (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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20B TYR* 3.5 32.8 - - + -
21B VAL 3.5 6.7 - - - +
22B ASP* 2.8 20.3 + - - -
34B HIS* 4.3 4.3 + - - -
35B PHE* 1.3 73.4 - - - +
37B ILE* 1.3 65.7 + - - +
84B ARG* 3.0 29.3 + - - +
199C ARG* 5.5 2.6 + - - -
200C ASP* 4.9 0.2 - - - -
203C LEU* 4.3 14.0 - - + +
215C LYS* 3.1 5.2 - - - +
216C GLY 2.8 42.1 + - - -
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Residues in contact with ILE 37 (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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20B TYR* 3.5 3.0 - - - +
21B VAL* 2.8 46.9 + - + +
23B VAL* 4.5 6.7 - - + -
35B PHE* 3.9 24.2 - - + -
36B THR* 1.3 81.7 - - - +
38B PRO* 1.3 69.7 - - + +
41B ALA* 3.9 28.5 - - + +
42B PHE* 4.2 16.6 - - + -
46B VAL* 4.4 11.9 - - + -
51B LEU* 4.4 18.8 - - + -
214C GLU 3.2 19.5 - - - +
215C LYS* 4.0 2.0 - - + -
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Residues in contact with PRO 38 (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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19B GLU 4.5 0.4 - - - +
20B TYR* 3.7 15.2 - - + -
21B VAL 4.7 0.2 - - - -
36B THR 4.7 0.7 - - - +
37B ILE* 1.3 95.9 - - + +
39B ALA* 1.3 66.6 + - - +
40B SER* 3.7 17.3 - - - +
41B ALA* 3.0 18.2 + - + +
42B PHE* 3.5 6.6 + - - +
203C LEU* 5.9 2.9 - - + -
207C ILE* 4.3 16.6 - - + -
213C LEU* 3.4 37.7 - - + +
214C GLU 3.5 17.9 - - - +
215C LYS* 4.5 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