Contacts of the helix formed by residues 90 - 106 (chain B) in PDB entry 1TF4
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA* 4.6 9.2 - - + +
81B PRO* 3.9 39.5 - - + +
84B TYR* 3.0 25.8 + - + +
85B ILE* 4.3 16.6 - - + +
89B GLN* 1.3 75.3 - - - +
91B PRO* 1.3 70.2 - - + +
93B LEU* 3.2 21.2 + - - -
94B LYS* 3.0 55.5 + - - +
166B VAL* 5.1 2.7 - - + -
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Residues in contact with PRO 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY* 3.7 16.8 - - - +
89B GLN 3.4 1.8 - - - -
90B MET* 1.3 94.2 - - + +
92B TYR* 1.3 72.5 + - + +
94B LYS* 3.5 9.7 + - + +
95B ASP* 3.0 28.1 + - - +
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 4.1 18.8 - - + -
18B GLU* 4.9 2.9 - - - -
30B ARG* 3.8 49.4 + - + +
88B GLY 4.1 17.0 - - - -
89B GLN* 3.0 28.2 + - - +
91B PRO* 1.3 86.6 - - + +
93B LEU* 1.3 66.1 + - - +
95B ASP* 3.3 12.0 + - + +
96B ASN* 2.9 31.6 + - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 3.9 13.8 - - - -
73B LEU* 4.1 28.7 - - + +
77B ALA* 3.3 29.4 - - + -
84B TYR* 3.5 39.3 - - + +
89B GLN 3.0 12.2 + - - +
90B MET* 3.5 22.0 - - - +
92B TYR* 1.3 77.8 - - - +
94B LYS* 1.3 58.1 + - - +
96B ASN* 3.2 5.2 + - + +
97B LEU* 2.9 43.5 + - + +
166B VAL* 4.3 6.1 - - + -
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 3.0 49.0 + - + +
91B PRO* 3.8 7.6 - - + +
93B LEU* 1.3 78.9 - - - +
95B ASP* 1.3 55.7 + - - +
97B LEU* 4.5 1.8 - - - -
98B ARG* 2.9 33.3 + - - +
166B VAL* 3.9 30.4 + - + -
167B PHE* 3.3 25.7 - - + -
170B ASP* 2.7 32.8 + - - +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 5.3 4.3 - - - +
21B ARG* 2.9 26.7 + - - +
28B ASN* 5.2 8.8 + - - +
91B PRO 3.0 18.1 + - - +
92B TYR* 3.6 14.5 - - + +
93B LEU 3.2 0.2 - - - -
94B LYS* 1.3 77.4 - - - +
96B ASN* 1.3 57.0 + - - +
98B ARG* 3.9 10.1 - - - +
99B TRP* 3.0 29.1 + - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 3.2 41.8 + - - +
17B TYR* 3.7 21.7 - - + +
18B GLU* 3.9 11.8 + - - +
21B ARG* 3.7 17.4 + - - +
53B TRP* 3.5 23.1 + - + +
73B LEU* 5.4 5.6 - - + -
92B TYR* 2.9 20.8 + - - +
93B LEU* 3.5 5.6 - - + +
95B ASP* 1.3 74.8 - - - +
97B LEU* 1.3 64.7 + - + +
99B TRP* 3.2 5.6 + - - +
100B VAL 3.2 17.3 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.9 28.0 - - - +
73B LEU* 4.2 18.4 - - + -
74B ALA* 4.1 26.9 - - + +
93B LEU* 2.9 38.5 + - + +
94B LYS* 3.9 3.1 - - - +
96B ASN* 1.3 72.8 - - - +
98B ARG* 1.3 60.2 + - - +
100B VAL* 3.2 9.2 - - + +
101B ASN* 2.7 39.4 + - - +
163B SER* 4.1 14.6 - - - +
166B VAL* 4.3 16.4 - - + -
167B PHE* 4.0 11.2 - - + -
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS 2.9 18.2 + - - +
95B ASP* 3.9 11.0 - - - +
97B LEU* 1.3 75.8 - - - +
99B TRP* 1.3 64.0 + - - +
102B ASP* 2.9 44.2 + - - +
167B PHE* 3.7 32.7 - - + -
170B ASP* 5.7 1.4 - - - +
171B ASP* 3.3 31.5 + - - +
174B TYR* 3.6 38.1 - - - +
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 3.7 40.2 - - + +
22B SER 3.1 21.7 + - - -
23B GLY* 5.0 0.4 - - - -
24B LYS 3.4 23.6 - - - -
25B LEU* 4.2 4.7 - - + -
26B PRO* 3.8 28.9 - - + -
51B GLY* 4.4 6.2 - - - -
52B GLY 3.0 36.4 + - - +
53B TRP* 3.9 15.7 - + - +
95B ASP* 3.0 16.1 + - - +
96B ASN* 3.4 10.8 - - - +
97B LEU 3.2 0.2 - - - -
98B ARG* 1.3 79.9 - - - +
100B VAL* 1.3 62.5 + - - +
102B ASP* 3.5 7.2 + - - +
103B TYR* 3.5 15.8 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY* 4.9 1.6 - - - -
53B TRP* 3.8 32.5 - - + -
66B MET* 3.8 27.8 - - + +
70B ALA* 4.0 13.0 - - + -
96B ASN 3.2 8.4 + - - +
97B LEU* 3.2 15.3 - - + +
99B TRP* 1.3 82.2 - - - +
101B ASN* 1.3 74.0 + - - +
103B TYR* 3.2 7.9 + - - +
104B PHE* 3.1 44.3 + - + -
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 5.2 1.0 - - - +
97B LEU* 2.7 32.1 + - - +
100B VAL* 1.3 79.0 - - - +
102B ASP* 1.3 65.1 + - - +
103B TYR 3.0 2.0 - - - -
104B PHE* 3.1 13.3 + - - +
105B ILE* 3.0 27.0 + - - +
159B ALA 4.0 1.4 - - - +
160B MET* 3.7 34.7 - - - +
163B SER* 3.1 29.6 + - - -
167B PHE* 4.9 1.0 - - - -
174B TYR* 3.3 21.3 - - + +
178B LEU* 4.0 12.8 - - + +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 2.9 36.3 + - - +
99B TRP* 3.7 8.2 - - - +
100B VAL 3.3 0.2 - - - -
101B ASN* 1.3 76.8 - - - +
103B TYR* 1.3 60.9 + - - +
105B ILE* 3.6 10.1 + - - +
106B LYS* 3.3 31.1 + - - +
174B TYR* 3.0 29.3 + - - -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.4 29.5 - - + +
50B THR 3.8 9.4 - - - +
51B GLY* 3.8 14.4 - - - -
52B GLY* 3.6 19.3 - - - +
61B LYS* 3.6 21.2 + - - +
63B GLY* 5.9 2.9 - - - -
66B MET* 3.8 34.3 - - + +
99B TRP 3.5 3.9 + - - +
100B VAL 3.2 7.8 + - - +
101B ASN 3.0 0.6 - - - -
102B ASP* 1.3 76.8 - - - +
104B PHE* 1.3 74.2 + + - +
105B ILE 3.1 1.6 - - - -
106B LYS* 3.1 11.1 + - + +
107B ALA* 2.8 39.1 + - + +
115B TYR* 4.7 9.7 + - - +
116B VAL 5.5 1.0 - - - -
117B GLN 5.1 2.3 + - - -
118B VAL* 3.5 23.6 + - - +
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY* 4.8 5.6 - - - -
66B MET* 4.1 19.5 - - + -
67B ALA* 3.5 32.3 - - + -
70B ALA* 4.2 5.2 - - + -
100B VAL* 3.1 32.8 + - + -
101B ASN* 3.1 23.6 + - - +
103B TYR* 1.3 86.6 - + - +
105B ILE* 1.3 61.2 + - - +
107B ALA* 3.4 7.3 + - + +
108B HIS* 3.2 25.1 + - - +
114B LEU* 4.7 3.9 - - + +
156B THR* 3.9 23.1 - - + +
159B ALA* 4.0 20.2 - - + -
160B MET* 3.9 22.9 - - + +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASN 3.0 18.7 + - - +
102B ASP* 3.6 12.8 - - - +
104B PHE* 1.3 74.3 - - - +
106B LYS* 1.3 68.7 + - + +
108B HIS 3.1 21.7 + - - +
109B PRO* 5.0 0.2 - - - +
160B MET* 3.7 15.7 - - + -
174B TYR* 4.3 15.0 - - + -
177B THR* 4.1 22.9 - - + -
178B LEU* 4.2 13.2 - - + -
181B HIS* 4.0 25.0 - - + +
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.9 4.0 - - - +
48B ASP* 3.3 38.9 + - + +
49B LEU* 3.9 12.5 - - + +
50B THR* 2.8 47.2 + - - +
51B GLY* 4.9 1.2 - - - -
102B ASP* 3.3 17.7 + - - +
103B TYR* 3.1 10.5 + - + +
105B ILE* 1.3 83.1 - - + +
107B ALA* 1.3 59.9 + - - +
108B HIS 3.2 4.5 + - - -
109B PRO* 4.0 11.8 - - - +
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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
------------------------------------------------------------
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