Contacts of the helix formed by residues 63 - 79 (chain A) in PDB entry 6T9L
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 ARG 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU 5.5 0.9 - - - +
61A LEU 3.8 5.4 + - - +
62A ILE* 1.3 90.1 - - - +
64A LYS* 1.3 66.4 + - - +
66A PRO* 4.1 17.6 - - + +
67A PHE* 3.7 10.2 + - - +
93A GLN* 3.8 2.2 + - - -
28B GLY 5.9 0.4 + - - -
30B THR* 4.9 7.5 + - - +
36B ARG* 4.6 5.2 - - - +
-14I A 2.9 23.1 + - - -
-13I A 2.6 49.2 + - - -
17J A 3.2 50.3 + - - -
18J G 3.2 13.9 - - - +
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Residues in contact with LYS 64 (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 ARG* 1.3 75.5 - - - +
65A LEU* 1.3 62.6 + - - +
67A PHE* 3.3 3.8 + - - +
68A GLN* 2.9 50.0 + - + +
86A SER* 4.5 20.1 - - - +
89A VAL* 5.6 10.2 - - + +
90A MET* 3.8 34.1 - - + +
93A GLN* 4.6 10.3 - - - +
18J G 4.1 10.0 + - - +
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Residues in contact with LEU 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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64A LYS* 1.3 79.6 - - - +
66A PRO* 1.3 63.5 - - + +
68A GLN* 3.3 17.0 + - - +
69A ARG* 2.9 53.6 + - + +
17J A 4.1 31.0 - - + +
18J G 3.9 14.0 + - - +
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Residues in contact with PRO 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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62A ILE* 6.4 0.4 - - + -
63A ARG* 4.1 22.0 - - + +
64A LYS 3.7 1.8 - - - +
65A LEU* 1.3 94.1 - - + +
67A PHE* 1.3 58.4 + - - +
69A ARG* 3.3 17.7 + - - +
70A LEU* 2.9 29.3 + - - +
25B ASN 4.4 4.2 - - - +
28B GLY* 3.9 34.3 - - - +
29B ILE* 5.6 2.5 - - + -
17J A 3.5 32.5 - - - +
18J G 5.0 0.2 - - - +
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Residues in contact with PHE 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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62A ILE* 4.1 20.4 - - + +
63A ARG 3.7 18.1 + - - +
64A LYS 3.3 3.2 + - - +
66A PRO* 1.3 79.0 - - - +
68A GLN* 1.3 59.6 + - - +
70A LEU* 3.3 7.9 + - + +
71A VAL* 2.9 54.4 + - + +
89A VAL* 4.0 15.9 - - + -
92A LEU* 4.1 5.2 - - + -
93A GLN* 3.6 39.5 - - + -
96A SER* 3.7 26.7 - - - -
29B ILE* 4.9 12.9 - - + +
58B LEU* 4.8 7.6 - - + -
62B LEU* 4.0 28.9 - - + -
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Residues in contact with GLN 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 LYS* 2.9 36.7 + - + +
65A LEU* 3.7 18.2 - - + +
67A PHE* 1.3 76.8 - - - +
69A ARG* 1.3 57.6 + - + +
71A VAL* 3.3 4.3 + - + +
72A ARG* 2.9 73.9 + - + +
89A VAL* 4.3 30.8 - - + +
-23I C 4.4 3.4 + - - -
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Residues in contact with ARG 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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65A LEU* 2.9 38.8 + - + +
66A PRO* 3.6 26.6 - - - +
68A GLN* 1.3 78.3 - - + +
70A LEU* 1.3 56.7 + - - +
72A ARG* 3.3 8.6 + - - +
73A GLU* 2.9 26.5 + - - +
22B LEU* 3.5 19.6 - - + +
25B ASN* 3.1 39.0 - - - +
28B GLY* 5.8 2.8 - - - -
17J A 3.3 34.9 + - - -
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Residues in contact with LEU 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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66A PRO 2.9 17.2 + - - +
67A PHE* 3.7 7.2 - - + +
69A ARG* 1.3 76.8 - - - +
71A VAL* 1.3 57.4 + - - +
73A GLU* 3.3 9.5 + - - +
74A ILE* 2.9 54.7 + - + +
25B ASN* 3.6 18.1 - - - +
26B ILE* 3.7 48.7 - - + +
29B ILE* 4.5 20.4 - - + -
58B LEU* 4.8 5.6 - - + -
59B LYS* 6.0 2.0 - - + -
62B LEU* 4.3 16.6 - - + -
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Residues in contact with VAL 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 PHE* 2.9 54.1 + - + +
68A GLN* 3.7 7.0 - - + +
70A LEU* 1.3 74.7 - - - +
72A ARG* 1.3 61.7 + - + +
74A ILE* 3.3 3.3 + - - -
75A ALA* 2.9 27.8 + - + +
84A PHE* 5.5 10.8 - - + -
89A VAL* 5.4 10.8 - - + -
92A LEU* 4.4 18.4 - - + -
62B LEU* 4.3 15.7 - - + -
66B ILE* 3.3 21.0 - - + +
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Residues in contact with ARG 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 GLN* 2.9 54.1 + - + +
69A ARG* 3.7 9.4 - - - +
71A VAL* 1.3 80.0 - - + +
73A GLU* 1.3 56.5 + - - +
75A ALA* 3.3 6.3 + - - +
76A GLN* 2.9 29.1 + - - +
82A LEU 4.4 5.9 + - - -
84A PHE* 3.4 44.0 + - + +
89A VAL* 5.7 1.8 - - - +
22B LEU* 3.7 15.0 - - + +
-23I C 2.8 47.2 + - - -
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Residues in contact with GLU 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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69A ARG 2.9 17.1 + - - +
70A LEU* 3.7 12.5 - - - +
72A ARG* 1.3 76.3 - - - +
74A ILE* 1.3 65.1 + - + +
76A GLN* 3.3 20.3 + - - +
77A ASP* 3.9 11.9 + - - +
22B LEU* 3.5 34.2 - - + +
23B ARG* 3.4 19.3 - - - +
24B ASP 3.8 3.3 + - - -
25B ASN* 3.2 31.6 + - - +
26B ILE* 4.1 3.2 + - - +
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Residues in contact with ILE 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 LEU* 2.9 36.9 + - + +
71A VAL* 3.8 4.9 - - - +
72A ARG 3.3 0.2 - - - -
73A GLU* 1.3 77.4 - - + +
75A ALA* 1.3 61.1 + - - +
76A GLN 3.4 0.7 + - - -
77A ASP* 3.5 18.7 + - - +
78A PHE* 3.7 12.6 - - + -
59B LYS* 4.3 27.1 - - + +
62B LEU* 3.8 34.1 - - + -
63B GLU* 3.7 32.8 - - + +
66B ILE* 3.7 17.0 - - + -
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Residues in contact with ALA 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 VAL* 2.9 18.0 + - + +
72A ARG 3.9 2.9 - - - +
73A GLU 3.3 0.2 - - - -
74A ILE* 1.3 74.4 - - - +
76A GLN* 1.3 63.8 + - - +
77A ASP 3.2 0.4 + - - -
78A PHE* 3.4 4.5 + - - +
79A LYS 3.1 22.3 + - - +
82A LEU* 4.2 6.3 - - + +
84A PHE* 3.6 33.2 - - + -
66B ILE* 3.6 25.8 - - + +
70B VAL* 5.1 1.1 - - + -
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Residues in contact with GLN 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 ARG 2.9 16.8 + - - +
73A GLU* 3.5 9.7 - - - +
74A ILE 3.2 0.8 - - - -
75A ALA* 1.3 77.2 - - - +
77A ASP* 1.3 64.4 + - - +
78A PHE 3.5 0.3 + - - -
79A LYS* 3.7 14.1 + - - +
80A THR* 3.7 29.2 - - + +
20B LYS 3.8 8.2 + - - -
21B VAL* 3.4 37.1 - - - +
22B LEU* 3.3 28.7 + - + +
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Residues in contact with ASP 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 GLU* 4.0 14.8 - - - +
74A ILE* 3.5 12.4 + - - +
75A ALA 3.2 0.6 - - - -
76A GLN* 1.3 83.9 - - - +
78A PHE* 1.3 65.7 + - + +
59B LYS* 5.9 0.7 + - - -
63B GLU* 5.8 0.2 - - - +
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Residues in contact with PHE 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 ILE* 3.7 20.6 - - + -
75A ALA* 3.4 4.4 + - - +
76A GLN 3.3 0.6 - - - -
77A ASP* 1.3 84.8 - - + +
79A LYS* 1.3 62.4 + - - +
63B GLU* 3.8 28.3 - - + -
66B ILE* 3.7 17.5 - - + -
67B ARG* 3.5 57.4 - - + -
70B VAL* 4.2 20.7 - - + +
74B GLU* 4.8 3.3 - - - +
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Residues in contact with LYS 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 ALA 3.1 15.8 + - - +
76A GLN* 3.7 8.1 - - - +
77A ASP 3.5 0.8 - - - -
78A PHE* 1.3 82.7 - - - +
80A THR* 1.3 72.7 + - - +
82A LEU* 3.3 42.4 - - + +
70B VAL* 4.4 5.2 - - + -
74B GLU* 3.3 36.1 + - + +
78B ARG 5.5 6.3 - - - -
79B LYS* 4.8 15.2 - - - +
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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