Contacts of the helix formed by residues 82 - 94 (chain A) in PDB entry 1TF5
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 PHE 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE 3.2 9.6 + - - -
81A PRO* 1.3 79.3 - - - +
83A LYS* 1.3 88.6 + - - +
84A VAL* 3.9 10.5 - - + -
85A GLN* 2.7 37.4 + - + +
86A LEU* 3.2 11.1 + - - +
104A GLU 5.4 1.3 - - - -
395A ASN* 3.5 42.2 - - + +
529A GLN* 4.0 20.6 - - - -
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 3.9 10.3 - - + +
24A ASN* 6.1 1.3 - - - +
27A ASP* 5.5 8.7 - - + +
70A ARG* 4.3 16.1 - - - +
80A PHE* 5.5 0.8 + - - -
81A PRO 5.0 0.2 + - - -
82A PHE* 1.3 105.8 - - - +
84A VAL* 1.3 67.2 + - + +
85A GLN 3.1 2.0 - - - -
86A LEU* 3.1 21.6 + - + +
87A MET* 3.0 36.3 + - + +
395A ASN* 4.0 12.3 - - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.9 11.7 - - + -
83A LYS* 1.3 80.1 - - + +
85A GLN* 1.3 65.2 + - + +
87A MET* 3.3 21.9 + - + +
88A GLY* 3.0 21.3 + - - -
100A MET* 5.2 0.7 - - - +
104A GLU* 4.1 6.5 - - - +
392A ILE* 3.3 15.9 - - + +
393A PRO* 3.0 35.7 - - + +
394A THR 3.9 8.5 - - - +
395A ASN* 3.8 33.7 - - + +
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Residues in contact with GLN 85 (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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80A PHE 4.6 0.2 - - - +
81A PRO* 3.3 16.7 - - + +
82A PHE* 2.7 50.4 + - + +
83A LYS 3.1 0.2 - - - -
84A VAL* 1.3 81.6 - - + +
86A LEU* 1.3 60.1 + - - +
88A GLY 3.1 0.3 + - - -
89A GLY 2.9 24.6 + - - -
100A MET* 5.4 2.9 - - - -
104A GLU 3.1 19.1 + - - +
105A GLY* 3.0 30.1 + - - -
108A LEU* 4.3 15.8 - - - +
109A THR* 3.1 29.7 + - - +
112A LEU* 3.7 4.6 - - + +
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Residues in contact with LEU 86 (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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23A ALA* 4.0 23.8 - - + +
26A ILE* 4.2 27.1 - - + -
27A ASP* 5.2 0.2 - - + -
66A PHE* 3.9 3.3 - - - -
70A ARG* 3.7 44.9 - - + +
81A PRO* 4.1 8.1 - - + -
82A PHE 3.2 12.0 + - - +
83A LYS* 3.1 22.0 + - + +
85A GLN* 1.3 76.0 - - - +
87A MET* 1.3 63.5 + - - +
89A GLY* 3.2 2.3 + - - -
90A VAL* 3.0 27.4 + - - +
112A LEU* 4.0 26.9 - - + -
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Residues in contact with MET 87 (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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17A ASN* 6.0 0.7 - - - -
19A TYR* 3.4 43.0 - - + +
20A GLU* 4.3 21.1 - - + +
23A ALA* 3.9 7.4 - - + -
83A LYS* 3.0 32.5 + - + +
84A VAL* 3.4 29.4 - - + +
86A LEU* 1.3 78.2 - - - +
88A GLY* 1.3 62.2 + - - +
90A VAL* 3.1 15.2 + - - +
91A ALA* 3.1 13.2 + - - +
392A ILE* 4.1 10.9 - - + +
393A PRO* 4.5 20.4 - - + -
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Residues in contact with GLY 88 (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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84A VAL 3.0 14.4 + - - -
85A GLN 3.1 3.1 + - - -
87A MET* 1.3 76.5 - - - +
89A GLY* 1.3 63.0 + - - +
91A ALA* 3.0 4.7 + - - +
92A LEU* 3.0 26.7 + - - +
98A ALA* 3.8 6.9 - - - +
100A MET* 4.2 4.3 - - - -
109A THR* 3.9 10.5 - - - -
392A ILE* 3.9 20.1 - - - +
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Residues in contact with GLY 89 (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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66A PHE* 3.7 11.7 - - - -
85A GLN 2.9 14.2 + - - -
86A LEU 3.2 3.8 + - - -
88A GLY* 1.3 76.1 - - - +
90A VAL* 1.3 55.5 + - - +
92A LEU* 3.3 2.1 + - - +
93A HIS* 2.8 29.6 + - - +
109A THR* 3.5 9.1 - - - +
112A LEU* 4.3 1.3 - - - -
113A PRO* 3.6 26.9 - - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.9 18.6 - - - +
19A TYR* 3.9 15.9 - - + +
22A ILE* 3.8 37.5 - - + -
23A ALA 5.6 0.2 - - - +
26A ILE* 5.2 0.2 - - + -
62A LEU* 4.1 8.5 - - + -
66A PHE* 3.9 13.7 - - + -
86A LEU 3.0 19.0 + - - +
87A MET* 3.1 8.9 + - - +
89A GLY* 1.3 76.8 - - - +
91A ALA* 1.3 56.6 + - - +
93A HIS* 3.1 5.6 + - - +
94A ASP* 2.9 42.0 + - - +
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Residues in contact with ALA 91 (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 TYR* 4.1 10.7 - - + -
87A MET 3.1 10.2 + - - +
88A GLY* 3.0 11.2 + - - +
90A VAL* 1.3 75.3 - - - +
92A LEU* 1.3 62.7 + - - +
94A ASP* 3.2 14.9 + - - +
95A GLY 3.5 0.2 + - - -
96A ASN* 3.2 22.4 + - + +
97A ILE 4.6 1.1 - - - +
98A ALA* 3.9 17.5 - - + -
390A VAL* 3.9 33.2 - - + -
392A ILE* 4.6 0.4 - - + -
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Residues in contact with LEU 92 (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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88A GLY 3.0 20.5 + - - +
89A GLY* 3.6 7.9 - - - +
91A ALA* 1.3 74.6 - - - +
93A HIS* 1.3 65.5 + - - +
95A GLY* 2.9 12.0 + - - -
96A ASN 3.8 4.3 - - - +
98A ALA* 3.6 15.9 - - + +
100A MET* 4.6 4.7 - - + -
109A THR* 4.6 1.8 - - + -
110A SER* 4.3 10.8 - - - -
113A PRO* 3.8 23.8 - - + -
203A PHE* 3.9 5.1 - - + -
205A VAL* 4.6 4.9 - - + -
368A ALA* 3.3 21.7 - - + +
369A GLY 3.0 42.2 - - - +
370A MET* 3.8 26.0 - - + -
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Residues in contact with HIS 93 (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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58A THR* 3.2 24.2 + - - -
59A ASP* 2.9 32.7 - - - -
62A LEU* 3.6 28.1 - - + +
66A PHE* 4.5 1.8 - - + -
89A GLY 2.8 14.3 + - - +
90A VAL 3.1 6.7 + - - +
92A LEU* 1.3 77.9 - - - +
94A ASP* 1.3 64.1 + - - +
113A PRO* 3.8 12.7 - - + +
116A LEU* 3.6 11.2 - - + -
117A ASN* 2.9 31.4 + - - +
203A PHE* 4.9 0.2 - - - -
366A LYS* 2.9 40.4 + - - +
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Residues in contact with ASP 94 (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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18A ARG* 2.9 44.0 + - - -
19A TYR* 3.9 11.6 + - - -
59A ASP* 4.8 2.1 - - - +
90A VAL* 2.9 21.9 + - - +
91A ALA 3.6 8.5 - - - +
92A LEU 3.1 0.8 - - - -
93A HIS* 1.3 85.8 + - - +
95A GLY* 1.3 60.4 + - - +
96A ASN* 3.6 17.7 + - - +
366A LYS* 4.7 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