Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 1TFZ
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 HIS 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER 3.6 4.2 - - - +
56A ASP* 3.8 0.7 - - - -
61A ASN* 3.0 51.9 + - - -
63A VAL* 1.3 82.1 - - + +
65A ALA* 1.3 59.0 + - - +
66A SER* 2.7 30.3 + - - -
79A THR* 3.6 10.1 - - + +
80A ALA 3.4 13.7 - - - +
82A TYR* 3.4 13.6 - - - -
97A ALA* 3.6 17.2 - - + +
98A SER* 3.3 27.2 + - - -
99A ILE* 3.4 23.7 + - + +
102A PHE* 3.8 24.0 - + + -
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Residues in contact with ALA 65 (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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36A ALA* 3.6 7.5 - - + +
37A THR* 5.8 0.4 - - - +
55A SER 3.7 3.4 - - - -
56A ASP* 4.0 0.7 - - - -
64A HIS* 1.3 71.8 - - - +
66A SER* 1.3 60.3 + - - +
67A TYR* 4.0 21.1 - - + +
78A PHE 3.5 2.1 - - - +
79A THR* 3.2 4.2 - - - +
80A ALA* 2.8 37.2 + - + +
82A TYR* 3.5 32.0 - - + +
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Residues in contact with SER 66 (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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54A LYS* 3.4 4.0 - - - -
55A SER 2.7 41.1 + - - +
64A HIS* 2.7 31.3 + - - -
65A ALA* 1.3 70.1 - - - +
67A TYR* 1.3 66.2 + - - +
77A LEU* 4.0 2.7 - - - -
78A PHE 3.2 4.5 - - - -
79A THR* 2.8 19.6 + - - +
99A ILE* 4.2 1.9 - - - +
185A PHE* 3.6 27.1 - - - -
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Residues in contact with TYR 67 (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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36A ALA* 3.8 26.2 - - + -
37A THR* 3.7 31.6 + - + -
40A ALA* 4.3 16.6 - - + -
51A PHE* 3.8 23.6 - + + -
53A ALA 3.7 2.0 - - - -
54A LYS* 3.7 21.1 - - + -
56A ASP* 2.6 38.6 + - + +
65A ALA* 4.0 14.4 - - + +
66A SER* 1.3 78.9 - - - +
68A LEU* 1.3 60.0 + - - +
69A LEU* 5.7 0.2 - - + -
77A LEU* 3.9 4.5 - - - +
78A PHE* 2.9 38.7 + - - +
82A TYR* 4.5 1.2 + - - -
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Residues in contact with LEU 68 (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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28A HIS* 5.3 0.2 - - + -
51A PHE* 3.6 7.8 - - - -
52A SER* 2.9 41.0 + - - +
53A ALA* 2.9 28.2 + - + +
66A SER 4.3 0.2 - - - -
67A TYR* 1.3 72.9 - - - +
69A LEU* 1.3 63.8 + - - +
70A THR* 4.0 8.7 - - + -
75A ARG* 4.0 20.0 - - + +
76A PHE 3.6 15.9 - - - +
77A LEU* 4.1 9.6 - - + +
180A GLU* 4.3 5.2 - - - +
181A PHE* 3.8 57.4 - - + -
185A PHE* 4.9 1.1 - - + -
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Residues in contact with LEU 69 (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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40A ALA* 3.3 31.0 - - + +
43A PHE* 4.0 3.1 - - + -
44A SER* 3.6 32.3 - - - +
49A MET* 3.6 21.3 - - + +
50A ARG 3.1 5.2 - - - +
51A PHE* 3.8 24.7 - - + -
67A TYR 5.3 0.2 - - - +
68A LEU* 1.3 83.5 - - - +
70A THR* 1.3 62.7 + - - +
75A ARG* 3.4 3.8 - - - -
76A PHE 2.8 35.4 + - - +
78A PHE* 3.5 30.5 - - + -
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Residues in contact with THR 70 (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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48A GLY 4.7 0.2 - - - +
49A MET* 3.4 2.8 - - - -
50A ARG* 2.7 45.9 + - - +
52A SER* 3.0 34.0 + - - +
68A LEU* 4.0 13.0 - - + -
69A LEU* 1.3 78.3 - - - +
71A SER* 1.3 63.3 + - - +
72A GLY 4.8 7.6 - - - +
74A LEU 3.2 5.8 - - - -
75A ARG* 4.0 18.2 - - + +
180A GLU* 5.7 0.9 - - - +
196A LEU 5.2 0.2 - - - +
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Residues in contact with SER 71 (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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47A LEU 5.0 0.2 + - - -
48A GLY 3.9 12.9 + - - -
49A MET* 3.9 23.6 - - - -
70A THR* 1.3 78.5 - - - +
72A GLY* 1.3 64.6 + - - +
73A ASP 3.2 0.5 + - - -
74A LEU* 3.0 24.4 + - - +
196A LEU 6.0 0.9 - - - -
197A ASP* 4.2 5.3 + - - +
198A TYR 5.1 0.3 + - - -
199A GLY 5.1 0.2 + - - -
200A ILE* 2.7 43.6 + - - +
201A ARG* 3.5 5.1 + - - +
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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