Contacts of the helix formed by residues 63 - 79 (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 GLY 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LYS 3.5 2.6 + - - -
62B PHE* 1.3 69.1 - - - +
64B PHE* 1.3 64.6 + - - +
66B MET* 3.8 10.9 - - - +
67B ALA* 3.0 25.6 + - - +
103B TYR* 5.9 2.7 - - - -
104B PHE* 4.8 6.0 - - - -
115B TYR 5.7 0.2 - - - -
116B VAL* 2.8 30.7 + - - -
152B VAL* 4.0 8.6 - - - +
156B THR* 4.7 1.0 + - - -
196B TYR* 6.1 0.2 - - - -
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE 3.4 0.2 - - - -
63B GLY* 1.3 75.7 - - - +
65B PRO* 1.3 70.4 - - + +
67B ALA* 3.2 2.3 + - - +
68B PHE* 3.1 19.3 + - - +
116B VAL 4.6 0.8 + - - -
151B ASP* 3.9 28.9 - - + -
152B VAL* 3.8 22.7 - - + +
155B GLU* 4.0 6.7 - - + -
196B TYR* 3.4 44.4 + + + +
208B SER* 4.5 7.4 - - - -
215B GLU* 3.5 10.8 - - - -
260B TRP* 3.2 46.2 - + - -
261B ASP* 4.3 10.1 - - - -
263B LYS* 3.4 21.5 - - - -
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Residues in contact with PRO 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 3.5 22.2 - - - +
62B PHE* 3.3 26.0 - - + +
64B PHE* 1.3 96.3 - - + +
66B MET* 1.3 55.4 + - - +
68B PHE* 3.7 1.5 - - + +
69B THR* 2.8 34.9 + - - -
196B TYR* 4.9 0.4 - - - +
206B TYR* 3.7 37.2 - - + +
260B TRP* 4.1 18.6 - - + -
427B THR* 4.8 1.3 - - - +
428B ASP* 4.7 8.8 - - + +
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TRP* 3.4 60.9 - - + +
55B ASP* 5.8 0.2 - - - -
61B LYS* 3.8 27.1 - - + +
62B PHE 3.1 16.7 + - - +
63B GLY* 3.8 6.3 - - - +
65B PRO* 1.3 78.7 - - - +
67B ALA* 1.3 62.5 + - - +
69B THR* 3.4 6.7 + - - -
70B ALA* 3.2 20.3 + - - +
100B VAL* 3.8 17.5 - - + -
103B TYR* 3.8 31.9 - - + -
104B PHE* 4.1 6.1 - - + -
427B THR* 4.6 5.4 - - + +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.0 19.2 + - - +
64B PHE* 3.7 0.7 - - - +
66B MET* 1.3 73.6 - - - +
68B PHE* 1.3 67.1 + - - +
70B ALA* 3.0 5.4 + - - +
71B THR* 2.9 23.6 + - - -
104B PHE* 3.5 17.2 - - + -
155B GLU* 3.6 21.3 - - + -
156B THR* 3.7 29.2 - - - +
159B ALA* 3.5 1.5 - - + +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE 3.1 13.7 + - - +
65B PRO 3.7 5.2 - - - +
67B ALA* 1.3 75.5 - - - +
69B THR* 1.3 67.1 + - - +
71B THR* 3.1 1.9 + - - -
72B MET* 3.0 57.0 + - + +
155B GLU* 3.5 19.8 - - + +
218B TRP* 4.2 6.5 - + - -
258B ILE* 4.0 19.7 - - + -
259B ALA* 3.5 33.2 - - - -
260B TRP* 3.5 26.7 - - + +
263B LYS* 3.6 24.9 - - + -
321B ASN* 4.6 7.4 - - - -
428B ASP* 4.6 13.7 - - + -
431B ALA* 5.1 3.1 - - + -
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Residues in contact with THR 69 (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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17B TYR* 3.5 25.8 - - + +
53B TRP* 3.6 12.6 - - + -
65B PRO 2.8 21.5 + - - -
66B MET 3.5 6.3 - - - -
68B PHE* 1.3 76.9 - - - +
70B ALA* 1.3 63.0 + - - +
72B MET* 3.3 1.9 + - - +
73B LEU* 3.0 26.0 + - + +
427B THR* 3.2 35.8 + - - +
428B ASP* 3.3 14.4 + - - -
431B ALA* 4.1 11.8 - - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TRP* 4.4 4.0 - - - -
66B MET 3.2 9.1 + - - +
67B ALA 3.0 10.1 + - - +
69B THR* 1.3 80.4 - - - +
71B THR* 1.3 61.6 + - - +
73B LEU* 3.3 2.2 + - - +
74B ALA* 3.0 26.2 + - - +
97B LEU* 3.9 14.3 - - + +
100B VAL* 4.0 23.8 - - + -
101B ASN* 5.2 0.7 - - - +
104B PHE* 4.2 5.8 - - + -
159B ALA* 3.8 16.2 - - + -
163B SER* 5.0 3.6 - - - +
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Residues in contact with THR 71 (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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67B ALA 2.9 9.2 + - - -
68B PHE 3.1 4.2 + - - -
70B ALA* 1.3 75.5 - - - +
72B MET* 1.3 57.1 + - - +
74B ALA* 3.5 5.0 + - - +
75B TRP* 3.0 28.3 + - - +
155B GLU* 2.8 22.8 + - - -
158B ALA* 4.0 10.8 - - + +
159B ALA* 3.2 20.3 + - - +
162B ALA* 4.2 5.5 - - + +
218B TRP* 3.4 32.8 - - + +
222B TRP* 3.8 18.6 - - + +
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.0 52.7 + - + +
69B THR 3.7 0.2 - - - +
71B THR* 1.3 73.5 - - - +
73B LEU* 1.3 65.3 + - - +
75B TRP* 3.3 31.6 + - + +
76B GLY 3.1 10.7 + - - -
218B TRP* 4.6 2.2 - - + -
258B ILE* 4.4 9.6 - - + -
321B ASN* 4.2 18.6 - - + +
324B PHE* 3.9 18.2 - - + -
431B ALA* 3.6 22.7 - - + -
432B GLY* 3.7 25.4 - - - +
435B SER* 2.8 19.4 + - - -
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Residues in contact with LEU 73 (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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14B MET* 4.4 6.5 - - + -
17B TYR* 4.0 32.1 - - + +
53B TRP* 3.9 28.7 - - + -
69B THR* 3.0 19.3 + - + +
70B ALA 3.8 3.1 - - - +
72B MET* 1.3 73.5 - - - +
74B ALA* 1.3 66.8 + - - +
76B GLY* 3.4 2.3 + - - -
77B ALA* 3.2 21.0 + - - +
84B TYR* 4.2 10.8 + - - +
93B LEU* 4.1 15.4 - - + +
96B ASN* 5.4 4.9 - - + -
97B LEU* 4.2 13.5 - - + -
431B ALA* 4.2 8.1 - - - +
434B SER* 3.8 31.4 - - - +
435B SER* 4.1 3.7 + - - +
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Residues in contact with ALA 74 (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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70B ALA 3.0 17.0 + - - +
71B THR 3.8 4.0 - - - +
73B LEU* 1.3 75.8 - - - +
75B TRP* 1.3 64.9 + - - +
77B ALA* 3.1 5.0 + - - +
78B ILE* 2.9 28.2 + - - +
97B LEU* 4.1 20.5 - - + +
162B ALA* 3.8 34.8 - - + +
163B SER* 4.0 5.4 - - - +
166B VAL* 4.0 4.4 - - + +
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Residues in contact with TRP 75 (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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71B THR 3.0 17.7 + - - +
72B MET* 3.5 24.0 - - - +
74B ALA* 1.3 75.6 - - - +
76B GLY* 1.3 62.7 + - - +
78B ILE* 3.1 6.6 + - + +
79B GLU* 2.9 49.7 + - + +
218B TRP* 3.7 27.4 - + - -
222B TRP* 3.7 28.2 - + + -
258B ILE* 4.3 7.9 - - + -
266B GLY* 4.4 9.2 - - - -
269B VAL* 5.0 2.9 - - + -
270B LEU* 3.5 34.6 - - + +
324B PHE* 3.6 21.1 - + + -
325B VAL* 4.1 22.4 - - + -
328B VAL* 4.4 19.3 - - + -
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Residues in contact with GLY 76 (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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72B MET 3.1 10.9 + - - -
73B LEU 3.8 1.3 - - - -
74B ALA 3.3 0.2 - - - -
75B TRP* 1.3 76.4 - - - +
77B ALA* 1.3 56.3 + - - +
79B GLU* 3.3 1.4 + - - +
80B SER* 2.8 33.4 + - - +
84B TYR* 4.2 7.2 - - - -
324B PHE* 3.8 9.6 - - - -
435B SER* 3.4 31.1 + - - +
438B ALA* 4.6 1.9 - - - +
439B MET* 5.4 0.2 - - - +
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Residues in contact with ALA 77 (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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73B LEU 3.2 9.1 + - - +
74B ALA 3.1 9.9 + - - +
76B GLY* 1.3 76.1 - - - +
78B ILE* 1.3 60.7 + - - +
80B SER 4.1 0.9 - - - -
81B PRO* 3.3 25.6 - - - +
84B TYR* 3.8 15.8 - - + -
90B MET* 4.6 5.1 - - + +
93B LEU* 3.3 34.5 - - + -
166B VAL* 4.3 13.5 - - + -
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Residues in contact with ILE 78 (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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74B ALA 2.9 20.9 + - - +
75B TRP* 3.1 8.3 + - + +
77B ALA* 1.3 76.5 - - - +
79B GLU* 1.3 69.7 + - + +
81B PRO* 3.4 10.6 - - - +
162B ALA 3.6 20.9 - - - +
165B ILE* 4.0 26.9 - - + -
166B VAL* 4.1 12.6 - - + +
222B TRP* 3.8 31.0 - - + -
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 2.9 47.5 + - + +
76B GLY* 3.8 4.9 - - - +
78B ILE* 1.3 82.5 - - + +
80B SER* 1.3 59.4 + - - +
81B PRO* 3.6 3.3 - - - +
270B LEU* 4.9 1.2 - - - +
273B LYS* 3.5 32.6 + - - +
324B PHE* 4.2 2.5 - - + -
328B VAL* 3.7 27.6 - - + +
331B LYS* 5.1 10.4 + - - +
439B MET* 4.1 19.5 - - - +
442B GLU* 4.4 3.5 - - - +
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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
------------------------------------------------------------
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