Contacts of the helix formed by residues 57 - 69 (chain B) 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 GLY 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B VAL* 3.5 30.3 - - - +
52B GLU* 2.9 13.4 + - - -
56B PRO* 1.3 72.6 - - - +
58B LEU* 1.3 61.8 + - - +
59B THR 3.6 1.3 - - - -
60B GLN* 3.6 7.8 - - - +
61B ASP* 3.1 30.1 + - - +
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Residues in contact with LEU 58 (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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33A LEU* 3.9 24.7 - - + -
36A VAL* 6.0 1.6 - - + -
37A ASN* 3.3 38.4 - - - +
40A ALA* 4.5 0.7 - - + -
44A LEU* 4.4 10.5 - - + -
51B ALA* 3.6 37.7 - - + +
52B GLU* 3.6 4.1 + - - +
55B ASN* 3.1 23.1 + - + +
56B PRO 3.3 0.2 - - - -
57B GLY* 1.3 76.0 - - - +
59B THR* 1.3 67.7 + - - +
60B GLN 3.2 0.4 - - - -
61B ASP* 3.0 10.2 + - + +
62B ILE* 2.9 33.8 + - + +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL 5.9 0.4 - - - -
19B SER* 6.1 0.2 - - - -
21B PRO* 3.9 5.2 - - - -
22B LEU* 3.8 28.6 - - - +
26B MET* 3.6 30.5 - - + -
48B PHE* 3.8 19.2 + - + -
52B GLU* 2.8 26.3 + - - +
58B LEU* 1.3 75.3 - - - +
60B GLN* 1.3 64.3 + - - +
62B ILE* 3.2 11.1 + - - +
63B ILE* 2.9 30.8 + - + +
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Residues in contact with GLN 60 (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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73A GLU* 2.8 20.4 - - - +
76A PHE* 3.2 12.8 - - - -
77A THR* 3.5 20.4 + - - +
80A LEU* 4.1 23.1 - - + +
195A ASN* 5.3 1.0 + - - +
18B VAL* 4.1 10.1 + - + +
21B PRO* 3.2 28.9 - - + +
57B GLY* 3.6 11.7 + - - +
59B THR* 1.3 79.4 - - - +
61B ASP* 1.3 66.3 + - - +
63B ILE* 3.1 3.4 + - - -
64B MET* 2.9 57.9 + - + +
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Residues in contact with ASP 61 (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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33A LEU* 4.2 27.2 - - + +
36A VAL* 5.9 2.3 - - - +
196A ARG* 4.1 18.2 + - - +
199A HIS* 5.3 9.2 + - - -
57B GLY 3.1 15.8 + - - +
58B LEU* 3.0 13.0 + - + +
60B GLN* 1.3 84.0 - - - +
62B ILE* 1.3 56.6 + - - +
64B MET* 3.5 6.8 + - - +
65B LYS* 2.9 35.1 + - - +
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Residues in contact with ILE 62 (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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26A MET* 4.4 11.0 - - + -
29A VAL* 3.9 20.9 - - + -
30A PHE* 4.1 8.3 - - + -
33A LEU* 3.8 17.5 - - + -
44A LEU* 3.7 28.9 - - + -
66A ILE* 6.1 0.7 - - + -
26B MET* 6.4 0.7 - - - -
48B PHE* 4.1 23.8 - - + -
58B LEU* 2.9 27.3 + - + +
59B THR* 3.4 10.3 - - - +
61B ASP* 1.3 77.0 - - - +
63B ILE* 1.3 59.3 + - + +
65B LYS* 3.2 4.0 + - - +
66B ILE* 2.9 45.8 + - + +
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Residues in contact with ILE 63 (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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66A ILE* 3.8 25.4 - - + +
73A GLU* 3.5 43.7 - - + +
21B PRO* 3.8 17.3 - - + -
25B VAL* 3.8 28.7 - - + -
26B MET* 4.5 8.5 - - - -
59B THR* 2.9 27.1 + - + +
60B GLN 3.7 3.4 - - - +
62B ILE* 1.3 77.7 - - + +
64B MET* 1.3 57.5 + - - +
66B ILE* 3.2 10.2 + - - +
67B LEU* 2.9 30.9 + - + +
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Residues in contact with MET 64 (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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73A GLU* 3.2 30.1 - - + +
74A VAL* 6.1 0.2 - - - -
77A THR* 3.6 17.0 - - + +
188A ILE* 4.3 7.2 - - + -
192A VAL* 3.5 37.0 - - + +
196A ARG* 4.1 13.2 - - - +
60B GLN* 2.9 37.8 + - + +
61B ASP* 3.8 5.2 - - - +
63B ILE* 1.3 78.6 - - - +
65B LYS* 1.3 58.1 + - - +
67B LEU* 3.2 25.7 + - + +
68B GLU* 2.9 35.5 + - - +
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Residues in contact with LYS 65 (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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29A VAL* 3.6 26.5 - - + +
32A GLU* 2.7 51.3 + - + +
33A LEU* 5.0 7.9 - - + -
196A ARG* 4.0 21.0 - - - +
61B ASP 2.9 21.3 + - - +
62B ILE* 3.4 6.1 - - - +
64B MET* 1.3 76.7 - - - +
66B ILE* 1.3 60.7 + - - +
68B GLU* 3.4 20.7 + - - +
69B LYS* 3.2 35.0 + - - +
8C MET* 6.1 0.2 - - - +
12C ALA* 4.5 9.5 - - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.5 9.7 - - + +
26A MET* 4.0 24.9 - - + -
29A VAL* 4.4 13.9 - - + -
63A ILE* 4.1 27.1 - - + -
66A ILE* 3.7 35.7 - - + -
67A LEU* 4.2 14.6 - - + +
62B ILE* 2.9 32.0 + - + +
63B ILE* 3.4 9.4 - - - +
64B MET 3.2 0.2 - - - -
65B LYS* 1.3 74.6 - - - +
67B LEU* 1.3 64.6 + - - +
69B LYS* 3.2 20.1 + - - +
70B LYS* 3.5 3.3 + - - -
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Residues in contact with LEU 67 (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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66A ILE* 5.1 4.5 - - + +
67A LEU* 3.6 33.2 - - + -
70A LYS* 5.1 24.5 - - + +
73A GLU* 4.0 20.2 - - + -
74A VAL* 5.6 2.2 - - + -
186A LYS* 3.6 19.1 + - - +
188A ILE* 4.4 15.5 - - + -
189A ASN* 5.8 0.4 - - - -
63B ILE* 2.9 19.7 + - + +
64B MET* 3.2 34.5 + - + +
66B ILE* 1.3 76.7 - - + +
68B GLU* 1.3 60.7 + - + +
70B LYS* 3.3 21.7 - - + +
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Residues in contact with GLU 68 (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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186A LYS* 5.5 0.2 - - - +
189A ASN* 4.2 22.8 + - - +
192A VAL* 3.3 31.0 - - + +
196A ARG* 3.8 12.5 + - - -
64B MET 2.9 19.3 + - - +
65B LYS* 3.7 30.6 + - - +
66B ILE 3.2 0.4 - - - -
67B LEU* 1.3 78.9 - - + +
69B LYS* 1.3 62.6 + - + +
70B LYS 3.3 3.2 + - - -
71B SER* 4.9 3.1 + - - -
15C THR* 5.8 0.9 - - - +
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Residues in contact with LYS 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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24A ALA 4.7 2.5 - - - +
25A VAL* 4.1 22.7 - - + +
28A PRO* 3.9 21.3 - - + +
29A VAL* 3.7 25.6 - - + -
32A GLU* 3.2 33.9 + - - -
65B LYS* 3.2 17.5 + - - +
66B ILE 3.2 10.0 + - - +
68B GLU* 1.3 80.7 - - + +
70B LYS* 1.3 61.6 + - - +
71B SER* 3.2 5.2 - - - +
72B VAL* 3.3 30.0 + - + +
73B GLU* 3.7 4.3 + - - +
11C GLU 4.7 0.8 + - - -
12C ALA* 3.9 18.8 + - - +
15C THR* 4.5 14.5 - - + +
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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
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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