Contacts of the strand formed by residues 45 - 54 (chain D) in PDB entry 3ZWG
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 TRP 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ILE* 3.5 24.7 - - + -
38D ASP 3.8 2.2 - - - -
39D ASN* 3.0 40.8 + - + -
41D SER* 2.8 21.5 + - - -
43D LYS 3.5 10.3 - - - -
44D THR* 1.3 72.1 - - - +
46D THR* 1.3 65.7 + - - +
64D LYS* 3.6 5.7 - - - +
65D VAL* 2.8 43.3 + - + +
71D LEU* 4.4 15.9 - - + -
92D TYR* 3.9 20.8 - + + -
93D SER 3.3 6.1 - - - +
94D MET* 3.8 25.9 - - + -
100D LEU* 3.5 29.6 - - + -
176D VAL* 3.6 34.1 - - + -
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 4.3 5.0 + - - +
45D TRP* 1.3 76.0 + - - +
47D ALA* 1.3 66.7 + - - +
48D MET* 4.4 0.2 - - - +
63D HIS* 3.2 32.8 - - + +
64D LYS* 2.9 32.7 + - - +
92D TYR* 3.4 3.5 - - - -
93D SER* 2.7 54.6 + - - -
94D MET 6.1 0.2 - - - -
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR* 1.3 75.9 - - - +
48D MET* 1.3 63.9 + - - +
61D LEU* 3.6 27.4 - - + +
62D PRO 3.5 11.9 - - - +
63D HIS* 2.9 29.9 + - - +
91D ALA 4.2 0.2 - - - -
92D TYR* 3.3 27.2 - - + -
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Residues in contact with MET 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR 3.6 0.4 + - - +
47D ALA* 1.3 77.1 - - - +
49D ASN* 1.3 71.9 + - - +
61D LEU* 4.5 1.9 - - - +
91D ALA* 2.9 21.4 + - + +
92D TYR 3.6 5.6 - - - -
93D SER* 3.5 37.0 - - - +
99D THR* 3.5 27.4 - - + +
125D GLN* 4.3 12.1 - - - +
126D LYS 3.5 30.7 - - - +
127D ARG* 3.7 31.1 + - + +
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Residues in contact with ASN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D MET* 1.3 85.4 - - - +
50D THR* 1.3 81.1 + - - +
51D TYR* 4.3 1.2 - - - +
61D LEU* 3.7 11.3 - - - +
89D VAL 3.8 0.9 - - - +
90D ILE* 3.6 1.6 - - - -
91D ALA* 2.9 29.3 + - - +
127D ARG* 3.6 31.1 - - - +
128D ALA* 3.0 43.9 + - - +
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Residues in contact with THR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN* 1.3 86.9 + - - +
51D TYR* 1.3 68.7 + - - +
52D PHE* 3.4 40.1 + - + -
61D LEU* 3.8 12.6 - - - +
73D TYR* 3.2 32.9 + - + +
89D VAL 3.2 15.5 - - - +
90D ILE* 3.9 7.0 - - + +
104D PHE* 4.5 3.1 - - + -
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN* 3.8 3.4 - - - +
50D THR* 1.3 73.6 - - - +
52D PHE* 1.3 65.6 + - - +
53D ARG* 4.0 24.6 - - + -
88D GLY* 3.1 5.9 - - - -
89D VAL* 2.8 34.2 + - + +
128D ALA* 3.6 27.3 - - + +
129D ASP* 3.7 17.3 - - + +
130D GLN* 2.8 55.8 + - + +
133D TYR* 4.0 15.9 - - + -
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Residues in contact with PHE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR* 3.4 30.1 + - + -
51D TYR* 1.3 83.9 - - - +
53D ARG* 1.3 62.5 + - - +
54D SER 3.7 13.7 - - - +
55D GLY 3.2 28.5 - - - +
56D THR* 3.8 13.2 - - - -
57D SER* 3.7 31.2 - - - -
73D TYR* 3.9 17.0 - + - -
75D GLY* 4.5 3.1 - - - -
86D VAL* 4.1 10.5 - - + -
87D VAL 3.6 4.9 - - - -
104D PHE* 3.9 20.0 - + - -
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Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TYR* 3.6 21.9 + - + -
52D PHE* 1.3 73.6 - - - +
54D SER* 1.3 72.5 + - - +
87D VAL* 2.8 26.0 + - + +
88D GLY* 5.2 0.2 - - - -
130D GLN* 3.4 31.0 + - - +
133D TYR* 3.8 32.2 + - + +
138D TYR* 5.5 4.2 + - - -
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Residues in contact with SER 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PHE* 3.7 5.5 - - - -
53D ARG* 1.3 95.3 + - - +
55D GLY* 1.3 64.4 + - - +
78D ASN* 4.5 2.2 - - - -
84D THR* 4.4 16.0 - - - +
85D GLY 3.5 22.2 + - - -
86D VAL* 3.2 2.3 - - - -
87D VAL* 2.9 36.7 + - - +
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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