Contacts of the helix formed by residues 69 - 84 (chain A) in PDB entry 4TVQ
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 LYS 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.3 17.0 - - - +
66A ILE 3.1 11.2 + - - +
68A GLU* 1.3 90.6 + - + +
70A LYS* 1.3 62.2 + - - +
71A SER 3.3 3.3 + - - -
72A VAL* 3.5 18.2 + - + +
73A GLU* 3.2 21.5 + - - +
24B ALA 5.2 4.0 - - - +
25B VAL* 4.3 33.1 - - + +
28B PRO* 4.8 15.4 - - - +
29B VAL* 5.4 4.7 - - + -
32B GLU* 4.6 16.4 + - - -
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Residues in contact with LYS 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 ILE 3.9 2.7 + - - -
67A LEU* 3.4 18.7 + - - +
68A GLU 3.1 4.7 + - - +
69A LYS* 1.3 76.7 - - - +
71A SER* 1.3 58.9 + - - +
73A GLU* 3.2 6.9 + - - +
74A VAL* 2.9 41.6 + - + +
186A LYS* 4.1 15.0 - - - +
188A ILE* 3.8 33.3 - - - +
67B LEU* 5.1 20.5 - - + +
70B LYS* 4.6 22.0 - - - +
186B LYS* 6.2 2.0 - - - +
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Residues in contact with SER 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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68A GLU 4.8 1.2 + - - -
69A LYS 3.3 0.6 - - - -
70A LYS* 1.3 79.4 - - - +
72A VAL* 1.3 60.5 + - - +
74A VAL* 3.3 6.9 + - - +
75A ASN* 2.9 30.9 + - - +
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Residues in contact with VAL 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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69A LYS* 3.5 24.9 + - + +
71A SER* 1.3 77.9 - - - +
73A GLU* 1.3 57.8 + - - +
75A ASN* 3.5 6.8 + - + +
76A PHE* 2.9 29.5 + - + +
20B MET* 5.2 7.4 - - + -
24B ALA* 4.2 30.5 - - + +
25B VAL* 4.9 4.3 - - + -
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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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66A ILE 5.8 1.3 - - - +
69A LYS 3.2 11.8 + - - +
70A LYS* 3.2 11.6 + - - +
71A SER 3.2 0.4 - - - -
72A VAL* 1.3 77.3 - - - +
74A VAL* 1.3 56.5 + - - +
76A PHE* 3.4 5.2 + - - +
77A THR* 2.7 37.5 + - - -
21B PRO* 4.0 5.8 - - - +
25B VAL* 3.6 13.0 - - + +
60B GLN* 2.8 28.3 + - - +
63B ILE* 3.5 44.7 - - + +
64B MET* 3.2 21.4 - - + +
67B LEU* 4.0 12.3 - - + -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 2.9 36.9 + - + +
71A SER* 3.7 6.3 - - - +
73A GLU* 1.3 73.0 - - + +
75A ASN* 1.3 62.3 + - - +
77A THR* 3.2 6.9 + - - -
78A GLU* 2.9 50.4 + - - +
188A ILE* 3.6 36.3 - - + -
191A PHE* 4.2 14.4 - - + -
64B MET* 6.1 0.2 - - - -
67B LEU* 5.6 2.5 - - + -
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Residues in contact with ASN 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 SER 2.9 17.5 + - - +
72A VAL* 3.5 9.3 - - + +
74A VAL* 1.3 76.8 - - - +
76A PHE* 1.3 58.1 + - - +
78A GLU* 3.2 19.2 + - - +
79A SER* 2.9 38.7 + - - -
82A ARG* 4.9 1.6 + - - +
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Residues in contact with PHE 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 VAL* 2.9 21.0 + - + +
73A GLU* 3.8 7.2 - - - +
75A ASN* 1.3 79.6 + - - +
77A THR* 1.3 59.0 + - - +
79A SER* 3.2 7.4 + - - -
80A LEU* 2.9 40.9 + - + +
17B MET* 3.2 47.1 - - + -
18B VAL* 3.8 12.1 - - - -
20B MET* 3.5 30.3 - - + -
21B PRO* 3.4 20.2 - - + -
24B ALA* 6.6 0.4 - - + -
60B GLN* 3.2 35.9 - - - -
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Residues in contact with THR 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* 2.7 23.2 + - - -
74A VAL* 3.7 6.7 - - - -
76A PHE* 1.3 75.3 - - - +
78A GLU* 1.3 60.9 + - - +
80A LEU* 3.3 7.0 + - - +
81A LEU* 2.9 27.5 + - - +
188A ILE* 5.2 1.6 - - + +
191A PHE* 3.6 26.9 - - + -
192A VAL* 4.4 4.3 - - + +
195A ASN* 3.3 19.4 - - - +
60B GLN* 3.5 22.0 + - - +
64B MET* 3.6 19.2 - - + +
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Residues in contact with GLU 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 VAL* 2.9 28.3 + - - +
75A ASN* 3.4 18.4 + - - +
77A THR* 1.3 77.3 - - - +
79A SER* 1.3 57.3 + - - +
81A LEU* 3.0 4.8 + - - +
82A ARG* 2.9 62.1 + - - +
118A PRO* 3.9 20.7 - - + +
191A PHE* 3.7 32.7 - - + -
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Residues in contact with SER 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 ASN* 2.9 25.3 + - - -
76A PHE* 3.5 12.6 - - - -
78A GLU* 1.3 76.4 - - - +
80A LEU* 1.3 57.6 + - - +
82A ARG* 3.3 19.5 + - - +
83A MET* 2.9 28.8 + - - +
17B MET* 3.8 20.7 - - - +
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Residues in contact with LEU 80 (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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76A PHE* 2.9 45.8 + - + +
77A THR 3.5 6.3 - - - +
78A GLU 3.2 0.2 - - - -
79A SER* 1.3 75.8 - - - +
81A LEU* 1.3 62.9 + - - +
83A MET* 3.5 31.1 + - + +
84A ALA* 3.6 10.7 + - - +
195A ASN* 3.7 24.2 + - + +
17B MET* 4.4 2.7 - - + +
18B VAL* 3.6 31.6 - - + +
60B GLN* 4.1 23.3 - - + +
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Residues in contact with LEU 81 (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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77A THR 2.9 13.2 + - - +
78A GLU 3.0 8.5 + - - +
80A LEU* 1.3 77.9 - - - +
82A ARG* 1.3 61.0 + - - +
83A MET 3.4 0.5 + - - -
84A ALA* 3.5 9.4 + - - +
114A LEU* 3.3 25.1 - - + +
115A SER* 3.3 18.9 - - - -
117A ILE* 3.9 7.0 - - + -
118A PRO* 3.7 27.4 - - + -
191A PHE* 3.9 23.8 - - + -
194A ALA* 3.7 24.9 - - + -
195A ASN* 3.6 10.7 - - - +
198A ILE* 3.6 24.7 - - + -
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Residues in contact with ARG 82 (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 ASN* 4.9 1.6 + - - +
78A GLU* 2.9 45.7 + - - +
79A SER* 3.3 33.4 + - - +
81A LEU* 1.3 76.1 - - - +
83A MET* 1.3 62.7 + - - +
84A ALA 3.3 0.5 + - - -
85A ALA* 3.4 19.1 + - - +
86A ASP* 5.2 1.9 - - - +
115A SER* 3.7 21.4 - - - +
118A PRO* 3.9 11.8 + - + +
119A ASP* 3.0 38.8 + - - +
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Residues in contact with MET 83 (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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79A SER 2.9 18.0 + - - +
80A LEU* 3.6 33.2 - - + +
81A LEU 3.2 0.6 - - - -
82A ARG* 1.3 73.1 - - - +
84A ALA* 1.3 58.5 + - - +
85A ALA 3.1 9.7 + - - -
86A ASP* 3.3 26.0 + - + +
17B MET* 3.9 31.4 - - + -
18B VAL* 4.3 12.6 - - + -
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Residues in contact with ALA 84 (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 LEU 3.6 6.0 + - - +
81A LEU 3.5 9.6 + - - +
82A ARG 3.2 1.0 - - - -
83A MET* 1.3 77.6 - - - +
85A ALA* 1.3 59.5 + - - +
86A ASP 3.1 11.2 + - - +
111A LYS* 3.2 36.3 - - + +
115A SER* 5.6 0.2 - - - -
198A ILE* 3.6 44.2 - - + -
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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