Contacts of the strand formed by residues 32 - 38 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.3 9.4 - - + +
25A PHE* 3.3 22.4 - - - +
26A CYS* 3.5 20.0 - - + +
30A GLY 3.9 0.4 + - - -
31A ILE* 1.3 76.0 - - - +
33A GLN* 1.3 61.0 + - - +
92A ASN* 3.9 34.5 - - + +
109A ARG* 5.1 1.3 - - - -
243A GLN* 3.4 48.0 - - + +
247A TYR* 6.5 1.3 - - + -
377A TYR* 4.2 5.4 - - - +
188B PRO* 3.4 6.4 - - - +
189B VAL* 3.0 46.9 + - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.2 8.5 - - - +
25A PHE* 2.6 59.6 + - + +
27A ASP* 3.2 25.9 + - + +
31A ILE* 2.9 32.3 + - - +
32A MET* 1.3 80.8 + - - +
34A HIS* 1.3 64.9 + - - +
58A ILE* 3.6 12.6 - - + +
59A ARG* 5.2 0.2 - - - +
186B TYR 3.7 1.2 - - - +
187B PHE* 2.9 48.3 + - + -
188B PRO* 3.3 5.6 - - - +
189B VAL* 4.3 0.8 - - - +
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Residues in contact with HIS 34 (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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22A ASP* 2.7 41.9 + - - +
23A VAL 3.1 11.0 - - - +
24A ARG* 4.0 6.3 + - + -
25A PHE* 5.4 0.2 - - - -
33A GLN* 1.3 77.9 - - - +
35A PHE* 1.3 61.6 + - - +
36A THR* 4.4 3.1 + - - -
84A ARG* 4.5 5.2 - - - -
187B PHE* 2.9 50.4 + - + +
188B PRO 3.6 10.1 + - - -
189B VAL* 3.6 18.8 - - + +
190B ALA 5.1 0.9 - - - -
193B ASP* 2.9 29.2 + - - +
196B VAL* 4.0 15.7 - - + -
199B ARG* 4.2 8.0 + - - -
217B HIS* 4.4 1.7 - - - +
218B HIS* 5.9 0.4 + - - +
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Residues in contact with PHE 35 (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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22A ASP* 3.4 3.6 - - - +
23A VAL* 2.8 54.7 + - + +
25A PHE* 4.8 1.3 - + - -
34A HIS* 1.3 77.2 - - - +
36A THR* 1.3 64.7 + - - +
37A ILE* 3.8 24.2 - - + -
51A LEU* 4.0 18.6 - - + -
52A ALA 4.0 20.4 - - - -
53A PHE* 4.4 1.3 - - + -
71A LEU* 3.7 22.9 - - + -
187B PHE* 3.5 25.6 - + + -
215B LYS* 3.7 25.6 - - + -
216B GLY 3.8 3.1 - - - +
217B HIS* 3.5 24.5 - - + +
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Residues in contact with THR 36 (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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20A TYR* 3.5 31.9 - - + -
21A VAL 3.5 6.7 - - - +
22A ASP* 2.9 18.4 + - - -
34A HIS* 4.4 3.8 + - - -
35A PHE* 1.3 73.3 - - - +
37A ILE* 1.3 66.8 + - - +
84A ARG* 3.0 28.5 + - - +
199B ARG* 5.4 3.3 + - - -
200B ASP* 5.0 0.2 - - - -
203B LEU* 4.2 12.9 - - + +
215B LYS* 3.0 6.6 - - - +
216B GLY 2.8 42.0 + - - -
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Residues in contact with ILE 37 (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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20A TYR* 3.5 3.5 - - - +
21A VAL* 2.8 48.7 + - + +
23A VAL* 4.5 6.1 - - + -
35A PHE* 3.8 24.9 - - + -
36A THR* 1.3 81.9 - - - +
38A PRO* 1.4 68.6 - - + +
41A ALA* 3.8 28.7 - - + +
42A PHE* 4.1 20.4 - - + -
46A VAL* 4.3 9.9 - - + -
51A LEU* 4.4 17.0 - - + -
203B LEU* 6.1 0.2 - - - -
214B GLU 3.2 19.3 - - - +
215B LYS* 3.9 2.9 - - + -
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Residues in contact with PRO 38 (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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19A GLU 4.4 0.4 - - - +
20A TYR* 3.7 18.3 - - + -
21A VAL 4.6 0.4 - - - -
37A ILE* 1.4 91.0 - - + +
39A ALA* 1.3 66.8 + - - +
40A SER* 3.7 17.7 - - - +
41A ALA* 2.9 17.4 + - + +
42A PHE* 3.5 6.4 + - - +
203B LEU* 5.8 2.9 - - + -
207B ILE* 4.4 12.6 - - + -
213B LEU* 3.2 39.9 - - + +
214B GLU 3.3 22.0 - - - +
215B LYS* 4.3 1.3 - - - +
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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