Contacts of the helix formed by residues 63 - 79 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS 3.5 2.6 + - - -
62A PHE* 1.3 69.2 - - - +
64A PHE* 1.3 63.0 + - - +
66A MET* 3.9 11.1 - - - +
67A ALA* 3.0 25.8 + - - +
103A TYR* 5.9 2.5 - - - -
104A PHE* 4.9 5.7 - - - -
115A TYR 5.7 0.2 - - - -
116A VAL* 2.8 31.5 + - - -
152A VAL* 4.0 8.5 - - - +
156A THR* 4.7 0.9 + - - -
196A TYR* 6.1 0.2 - - - -
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 1.3 76.4 - - - +
65A PRO* 1.3 71.3 - - + +
67A ALA* 3.2 2.2 + - - +
68A PHE* 3.1 19.1 + - - +
116A VAL 4.6 1.0 + - - -
151A ASP* 3.9 29.2 - - + -
152A VAL* 3.8 21.4 - - + +
155A GLU* 4.1 7.3 - - + +
196A TYR* 3.4 43.5 + + + +
206A TYR* 5.0 0.2 - - + -
208A SER* 4.5 7.4 - - - -
215A GLU* 3.5 11.9 - - - -
260A TRP* 3.3 44.9 - + - -
261A ASP* 4.3 9.6 - - - -
263A LYS* 3.4 21.1 - - - -
3001A CA 4.7 0.9 - - - -
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Residues in contact with PRO 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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55A ASP* 3.5 22.2 - - - +
62A PHE* 3.3 24.5 - - + +
64A PHE* 1.3 96.3 - - + +
66A MET* 1.3 57.0 + - - +
68A PHE* 3.3 1.3 + - + +
69A THR* 2.8 34.3 + - - -
206A TYR* 3.7 36.8 - - + -
260A TRP* 4.0 19.1 - - + -
427A THR* 4.7 2.0 - - - +
428A ASP* 4.7 9.0 - - + +
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Residues in contact with MET 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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53A TRP* 3.4 61.3 - - + +
55A ASP* 5.8 0.4 - - - -
61A LYS* 3.8 29.4 - - + -
62A PHE 3.1 18.4 + - - +
63A GLY* 3.9 5.8 - - - +
64A PHE 3.2 0.2 - - - -
65A PRO* 1.3 77.7 - - - +
67A ALA* 1.3 63.8 + - - +
69A THR* 3.4 6.9 + - - -
70A ALA* 3.2 20.3 + - - +
100A VAL* 3.8 17.3 - - + -
103A TYR* 3.8 28.9 - - + -
104A PHE* 4.1 6.3 - - + -
427A THR* 4.6 5.4 + - - +
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Residues in contact with ALA 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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63A GLY 3.0 19.5 + - - +
64A PHE* 3.7 0.7 - - - +
66A MET* 1.3 74.3 - - - +
68A PHE* 1.3 67.0 + - - +
70A ALA* 3.0 5.2 + - - +
71A THR* 2.9 23.8 + - - -
104A PHE* 3.6 16.7 - - + -
152A VAL 5.0 0.2 - - - +
155A GLU* 3.6 20.6 - - + +
156A THR* 3.8 29.4 - - - +
159A ALA* 3.5 0.9 - - + +
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Residues in contact with PHE 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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64A PHE 3.1 12.4 + - - +
65A PRO 3.7 6.3 - - - +
67A ALA* 1.3 75.6 - - - +
69A THR* 1.3 67.3 + - - +
71A THR* 3.1 2.3 + - - -
72A MET* 3.0 56.0 + - + +
155A GLU* 3.5 20.0 - - + +
218A TRP* 4.2 6.1 - + - -
258A ILE* 3.9 18.4 - - + -
259A ALA* 3.5 33.0 - - - -
260A TRP* 3.5 27.4 - - + +
263A LYS* 3.5 25.8 - - + -
321A ASN* 4.7 7.2 - - - -
428A ASP* 4.6 12.6 - - + -
431A ALA* 5.1 3.8 - - + -
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Residues in contact with THR 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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17A TYR* 3.6 25.6 - - + +
53A TRP* 3.6 13.7 - - + -
65A PRO 2.8 21.9 + - - -
66A MET 3.5 5.8 - - - -
68A PHE* 1.3 77.7 - - - +
70A ALA* 1.3 64.1 + - - +
72A MET* 3.3 1.9 + - - +
73A LEU* 3.0 25.9 + - + +
427A THR* 3.2 34.0 + - - +
428A ASP* 3.4 14.4 + - - -
431A ALA* 4.1 11.4 - - + -
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Residues in contact with ALA 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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53A TRP* 4.4 4.0 - - - -
66A MET 3.2 9.6 + - - +
67A ALA 3.0 9.3 + - - +
69A THR* 1.3 79.4 - - - +
71A THR* 1.3 62.8 + - - +
73A LEU* 3.3 2.4 + - - +
74A ALA* 3.0 25.3 + - - +
97A LEU* 3.9 13.8 - - + +
100A VAL* 4.0 24.5 - - + -
101A ASN* 5.2 0.7 - - - +
104A PHE* 4.2 5.6 - - + -
159A ALA* 3.8 15.9 - - + -
163A SER* 5.0 3.6 - - - +
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Residues in contact with THR 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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67A ALA 2.9 9.4 + - - -
68A PHE 3.1 4.7 + - - -
70A ALA* 1.3 75.3 - - - +
72A MET* 1.3 57.5 + - - +
74A ALA* 3.8 5.0 - - - +
75A TRP* 3.0 27.7 + - - +
155A GLU* 2.8 23.1 + - - -
158A ALA* 4.1 11.0 - - + +
159A ALA* 3.2 19.7 + - - +
162A ALA* 4.3 2.4 - - + +
218A TRP* 3.4 33.2 - - + +
222A TRP* 3.8 20.9 - - + +
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Residues in contact with MET 72 (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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68A PHE* 3.0 53.1 + - + +
69A THR 3.7 0.2 - - - +
71A THR* 1.3 72.7 - - - +
73A LEU* 1.3 65.9 + - - +
75A TRP* 3.3 31.0 + - + +
76A GLY 3.1 11.1 + - - -
218A TRP* 4.6 1.8 - - - -
258A ILE* 4.3 9.9 - - + -
321A ASN* 4.2 18.4 - - + +
324A PHE* 3.9 16.9 - - + -
325A VAL* 5.1 0.2 - - + -
431A ALA* 3.6 23.3 - - + -
432A GLY* 3.7 25.8 - - - +
435A SER* 2.8 18.7 + - - -
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Residues in contact with LEU 73 (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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14A MET* 4.4 6.3 - - + -
17A TYR* 4.0 32.5 - - + +
53A TRP* 3.9 28.7 - - + -
69A THR* 3.0 19.7 + - + +
70A ALA 3.8 3.6 - - - +
72A MET* 1.3 73.7 - - - +
74A ALA* 1.3 65.9 + - - +
76A GLY* 3.4 2.4 + - - -
77A ALA* 3.2 21.5 + - - +
84A TYR* 4.2 9.2 + - - +
93A LEU* 4.1 16.0 - - + +
96A ASN* 5.4 5.4 - - + -
97A LEU* 4.2 13.0 - - + -
431A ALA* 4.2 7.6 - - - +
434A SER* 3.8 31.2 - - - +
435A SER* 4.0 2.4 + - - +
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Residues in contact with ALA 74 (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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70A ALA 3.0 16.4 + - - +
71A THR 3.8 4.3 - - - +
73A LEU* 1.3 76.4 - - - +
75A TRP* 1.3 64.5 + - - +
77A ALA* 3.1 4.4 + - - +
78A ILE* 2.9 29.0 + - - +
97A LEU* 4.1 21.7 - - + +
162A ALA* 3.8 34.8 - - + +
163A SER* 4.0 4.9 - - - +
166A VAL* 4.0 4.4 - - + +
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Residues in contact with TRP 75 (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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71A THR 3.0 18.6 + - - +
72A MET* 3.5 23.8 - - - +
74A ALA* 1.3 76.2 - - - +
76A GLY* 1.3 57.3 - - - +
78A ILE* 3.1 5.8 + - + +
79A GLU* 2.9 55.5 + - + +
162A ALA* 5.0 0.2 - - - +
218A TRP* 3.7 27.1 - + - -
222A TRP* 3.7 28.9 - + + -
258A ILE* 4.3 3.8 - - + -
266A GLY* 4.4 9.4 - - - -
269A VAL* 5.1 1.8 - - + -
270A LEU* 3.5 34.7 - - + +
324A PHE* 3.5 21.5 - + + -
325A VAL* 4.1 26.7 - - + -
328A VAL* 4.4 19.3 - - + -
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Residues in contact with GLY 76 (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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72A MET 3.1 11.3 + - - -
73A LEU 3.4 1.1 + - - -
74A ALA 3.3 0.4 - - - -
75A TRP* 1.3 76.2 - - - +
77A ALA* 1.3 56.0 + - - +
79A GLU* 3.3 1.7 + - - +
80A SER* 2.8 33.3 + - - +
84A TYR* 4.2 7.1 - - - -
324A PHE* 3.8 10.0 - - - -
435A SER* 3.4 31.1 + - - +
438A ALA* 4.5 1.9 - - - +
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Residues in contact with ALA 77 (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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73A LEU 3.2 9.5 + - - +
74A ALA 3.1 10.2 + - - +
76A GLY* 1.3 74.6 - - - +
78A ILE* 1.3 62.4 + - - +
80A SER 4.1 0.7 - - - -
81A PRO* 3.3 25.9 - - - +
84A TYR* 3.8 16.0 - - + -
90A MET* 4.6 5.1 - - + +
93A LEU* 3.3 34.5 - - + -
166A VAL* 4.2 12.8 - - + -
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Residues in contact with ILE 78 (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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74A ALA 2.9 21.6 + - - +
75A TRP* 3.4 7.9 - - + +
77A ALA* 1.3 76.5 - - - +
79A GLU* 1.3 71.5 + - + +
81A PRO* 3.4 10.4 - - - +
162A ALA* 3.6 20.4 - - - +
165A ILE* 4.0 27.4 - - + -
166A VAL* 4.1 12.1 - - + +
222A TRP* 3.8 30.1 - - + -
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Residues in contact with GLU 79 (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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75A TRP* 2.9 47.0 + - + +
76A GLY* 3.8 5.4 - - - +
78A ILE* 1.3 84.2 - - - +
80A SER* 1.3 59.6 + - - +
81A PRO* 3.6 3.6 - - - +
270A LEU* 5.0 0.9 - - - +
273A LYS* 3.5 30.5 + - - +
324A PHE* 4.2 2.2 - - + -
328A VAL* 3.6 28.9 - - + +
331A LYS* 5.0 13.7 + - - +
439A MET* 4.1 17.8 - - - +
442A GLU* 4.4 3.3 - - - +
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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