Contacts of the strand formed by residues 51 - 57 (chain A) in PDB entry 5T5W
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 THR 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 4.8 6.7 - - - +
50A LEU* 1.3 78.6 - - - +
52A PHE* 1.3 65.1 + - - +
68A GLN* 4.1 28.3 - - + +
69A THR 3.5 15.0 - - - +
70A THR* 4.2 13.5 - - + -
91A ALA* 3.4 5.2 - - - +
92A GLU* 2.7 54.0 + - - +
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Residues in contact with PHE 52 (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 PRO* 4.3 7.6 - - + -
40A TRP* 3.4 43.7 - + + -
42A SER* 3.5 31.2 - - - -
43A PRO* 4.3 10.8 - - + -
50A LEU* 4.2 14.6 - - + -
51A THR* 1.3 83.3 - - - +
53A THR* 1.3 61.9 + - - +
54A ALA 4.3 0.2 - - - -
66A CYS* 4.1 1.3 - - - +
67A MET 3.9 0.3 - - - -
68A GLN* 2.9 22.3 + - - -
69A THR* 3.1 23.7 + - - +
70A THR 4.7 6.7 - - - -
71A LEU 3.5 23.6 - - - -
72A THR* 5.0 2.9 - - + -
89A VAL* 4.3 2.7 - - + -
90A ARG 3.3 8.5 - - - +
91A ALA* 3.7 27.4 - - + -
92A GLU* 4.7 2.0 - - - +
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Residues in contact with THR 53 (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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52A PHE* 1.3 76.1 + - - +
54A ALA* 1.3 64.3 + - - +
55A GLN* 4.5 0.4 - - + +
64A ASP* 3.9 22.2 - - - +
66A CYS 3.2 11.4 - - - +
67A MET* 4.4 5.6 - - + -
68A GLN* 3.2 17.8 + - - +
89A VAL* 4.0 2.7 - - - -
90A ARG* 3.1 29.0 + - - +
92A GLU* 3.3 31.7 + - - +
100A TRP* 3.4 22.2 - - + -
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Residues in contact with ALA 54 (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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38A LEU* 4.1 9.2 - - + -
40A TRP* 4.8 2.4 - - + -
52A PHE 4.3 0.4 - - - -
53A THR* 1.3 73.9 - - - +
55A GLN* 1.3 65.0 + - - +
64A ASP* 3.9 0.9 - - - -
65A LYS 3.0 21.4 + - - -
66A CYS* 2.9 13.7 + - + +
74A CYS* 4.0 20.6 - - + -
76A PHE* 3.8 26.5 - - + -
88A ARG 3.5 8.1 - - - +
89A VAL* 4.2 8.3 - - + -
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Residues in contact with GLN 55 (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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53A THR* 4.5 1.3 - - + +
54A ALA* 1.3 79.0 - - - +
56A TYR* 1.3 61.1 + - - +
62A PHE* 3.5 27.7 + - + +
63A GLN 3.3 11.9 - - - +
64A ASP* 2.9 31.8 + - - +
65A LYS 4.4 0.9 - - - +
76A PHE* 3.9 10.1 - - - -
87A LEU* 3.5 4.2 - - - -
88A ARG* 2.8 69.9 + - + +
100A TRP* 3.4 23.0 - - + -
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Residues in contact with TYR 56 (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 GLN* 1.3 73.5 - - - +
57A LEU* 1.3 61.6 + - - +
58A SER* 3.3 29.6 + - - -
62A PHE* 3.4 4.7 - - - -
63A GLN* 2.6 81.5 + - + -
64A ASP 4.2 2.5 - - - -
65A LYS* 4.1 36.2 + - + -
76A PHE* 3.6 7.2 - + + -
79A LEU* 3.8 23.6 - - + -
85A HIS* 5.4 2.5 - - + -
86A THR 3.5 4.7 - - - -
87A LEU* 3.6 20.6 - - + -
87C ASP* 5.2 1.2 + - - -
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Residues in contact with LEU 57 (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 TYR* 1.3 74.2 - - - +
58A SER* 1.3 73.1 + - - +
60A ARG 4.9 2.0 - - - +
61A ILE* 3.6 8.3 - - - +
62A PHE* 3.5 51.3 - - + +
84A ASP 5.7 0.2 - - - +
85A HIS* 4.6 12.0 + - - +
86A THR* 2.9 42.9 + - + +
91C HIS* 5.7 2.8 + - - -
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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