Contacts of the helix formed by residues 60 - 74 (chain Q) in PDB entry 4B2Q
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 ALA 60 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q ALA 3.5 11.1 + - - +
57Q LEU* 3.5 16.6 - - - +
58Q SER 3.1 0.2 - - - -
59Q GLU* 1.3 78.3 - - - +
61Q THR* 1.3 60.4 + - + +
63Q LEU* 2.9 26.0 + - - +
64Q PHE* 3.0 42.1 + - + -
59R GLU* 5.2 9.0 - - - +
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Residues in contact with THR 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q GLY 3.8 9.1 - - - +
19Q LEU* 3.6 2.3 - - - +
21Q GLY* 4.8 0.9 - - - -
22Q ALA* 3.7 10.7 + - - -
57Q LEU 5.4 1.6 - - - +
58Q SER 3.1 17.1 + - - +
60Q ALA* 1.3 78.7 - - + +
62Q GLY* 1.3 58.2 + - - +
63Q LEU 3.3 1.5 + - - -
64Q PHE* 4.4 6.7 - - + -
65Q CYS* 3.4 30.1 + - - +
19R LEU* 3.3 32.8 - - + +
22R ALA* 3.6 14.6 - - + +
23R GLY* 3.4 26.7 - - - +
26R ILE* 6.1 0.2 - - + -
62R GLY* 5.7 1.3 - - - -
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Residues in contact with GLY 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P THR* 5.7 0.9 - - - -
64P PHE* 5.0 4.9 - - - -
19Q LEU* 3.6 17.0 - - - +
22Q ALA* 3.8 19.0 - - - +
59Q GLU* 3.0 17.0 + - - +
60Q ALA 3.0 1.4 - - - -
61Q THR* 1.3 80.4 + - - +
63Q LEU* 1.3 61.6 + - - +
66Q LEU* 3.2 23.9 - - - +
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Residues in contact with LEU 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P PHE* 6.1 1.3 - - + -
56Q ALA 5.9 0.7 - - - +
59Q GLU* 3.1 42.2 - - + +
60Q ALA* 2.9 10.6 + - - +
62Q GLY* 1.3 82.1 - - - +
64Q PHE* 1.3 61.7 + - + +
65Q CYS 3.4 0.2 - - - -
66Q LEU* 3.1 15.0 + - + +
67Q MET* 2.9 46.4 + - + +
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Residues in contact with PHE 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q ALA* 3.0 44.4 + - + +
61Q THR* 4.3 5.2 - - + +
63Q LEU* 1.3 76.2 - - + +
65Q CYS* 1.3 63.2 + - - +
67Q MET* 3.1 36.3 + - + +
68Q VAL* 3.1 18.9 + - - +
19R LEU* 4.4 10.1 - - + -
59R GLU* 5.0 7.4 - - - -
62R GLY 5.0 6.7 - - - -
63R LEU* 6.1 1.6 - - + -
66R LEU* 3.6 49.8 - - + +
70R PHE* 5.6 3.8 - + - -
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Residues in contact with CYS 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q SER* 3.4 25.8 + - - +
16Q THR* 5.2 0.2 - - - -
18Q GLY* 3.5 17.5 - - - -
19Q LEU* 3.5 21.0 - - + +
61Q THR 3.4 13.9 + - - -
63Q LEU 3.4 0.2 - - - -
64Q PHE* 1.3 79.0 - - - +
66Q LEU* 1.3 61.2 + - - +
68Q VAL* 3.7 16.8 + - - +
69Q SER* 3.8 9.0 + - - -
16R THR* 3.6 17.7 - - - -
19R LEU* 3.4 31.4 - - - -
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Residues in contact with LEU 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P PHE* 3.6 59.9 - - + +
68P VAL* 5.8 2.9 - - + -
19Q LEU* 3.7 12.7 - - + +
62Q GLY 3.2 24.5 - - - +
63Q LEU* 3.1 17.2 + - + +
64Q PHE 3.0 0.4 - - - -
65Q CYS* 1.3 78.3 - - - +
67Q MET* 1.3 62.1 + - + +
69Q SER* 2.7 28.0 + - - +
70Q PHE* 3.1 33.8 - - + -
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Residues in contact with MET 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q LEU* 2.9 31.2 + - + +
64Q PHE* 3.1 37.9 + - + +
66Q LEU* 1.3 77.1 - - + +
68Q VAL* 1.3 65.6 + - - +
70Q PHE* 3.2 13.1 + - + +
71Q LEU* 3.1 36.4 + - + +
70R PHE* 6.3 2.0 - - + -
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Residues in contact with VAL 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q SER* 3.7 19.7 - - - -
64Q PHE* 3.1 19.2 + - + +
65Q CYS 3.8 7.4 - - - +
66Q LEU 3.3 0.2 - - - -
67Q MET* 1.3 80.0 - - + +
69Q SER* 1.3 59.8 + - - +
71Q LEU* 3.4 16.1 + - + +
72Q LEU* 3.2 28.8 - - + +
12R ALA 4.2 9.6 - - - +
16R THR* 3.8 23.6 - - + -
19R LEU* 6.3 0.4 - - + -
66R LEU* 5.9 3.4 - - + -
69R SER* 4.6 13.7 - - - +
70R PHE* 6.5 1.6 - - + -
73R LEU* 4.5 15.5 - - + -
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Residues in contact with SER 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P VAL* 4.6 17.9 - - - +
12Q ALA* 4.1 15.5 - - - -
15Q SER* 3.6 18.9 + - - -
16Q THR* 4.9 3.4 - - - -
65Q CYS 3.8 5.2 + - - -
66Q LEU* 2.7 27.2 + - - +
68Q VAL* 1.3 79.6 - - - +
70Q PHE* 1.3 68.2 + - - +
72Q LEU* 3.3 3.5 + - - +
73Q LEU* 3.2 33.4 + - - +
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Residues in contact with PHE 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P PHE* 5.7 3.6 - + - -
67P MET* 6.4 1.3 - - + -
68P VAL* 6.5 1.6 - - + -
71P LEU* 5.1 8.5 - - + -
66Q LEU* 3.1 50.9 - - + -
67Q MET* 3.2 13.3 + - + +
69Q SER* 1.3 78.3 + - - +
71Q LEU* 1.3 54.1 + - + +
72Q LEU 3.0 5.6 + - - -
73Q LEU* 3.8 2.5 - - + -
74Q PHE* 2.9 43.0 + + + +
75Q GLY* 2.7 32.4 + - - -
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Residues in contact with LEU 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Q MET* 3.1 28.2 + - + +
68Q VAL* 3.8 10.5 - - + +
69Q SER 3.3 0.8 - - - -
70Q PHE* 1.3 78.4 - - + +
72Q LEU* 1.3 66.3 + - - +
75Q GLY* 4.8 7.9 - - - -
76Q VAL* 3.0 28.5 + - - +
9R TYR* 5.2 0.2 - - - -
70R PHE* 5.1 8.3 - - + -
73R LEU* 4.4 19.6 - - + +
74R PHE* 3.6 39.0 - - + -
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Residues in contact with LEU 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q LYS* 3.3 38.2 - - - +
9Q TYR* 5.2 0.9 - - - -
11Q GLY* 3.4 38.8 - - - +
12Q ALA* 3.6 4.5 - - + +
68Q VAL* 3.2 28.7 - - + +
69Q SER 3.3 6.9 + - - +
70Q PHE 3.0 0.4 - - - -
71Q LEU* 1.3 87.1 - - - +
73Q LEU* 1.3 64.4 + - - +
76Q VAL* 3.7 12.8 - - + +
9R TYR* 3.5 43.1 - - + +
12R ALA* 5.5 0.2 - - + -
13R GLY* 5.1 1.3 - - - +
73R LEU* 3.8 14.6 - - + -
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Residues in contact with LEU 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P VAL* 4.5 15.5 - - + -
71P LEU* 4.4 31.4 - - + +
72P LEU* 3.7 11.7 - - + -
76P VAL* 5.5 2.9 - - - +
8Q LYS 4.2 0.4 - - - +
9Q TYR* 3.6 34.8 - - + -
12Q ALA* 3.8 19.5 - - + -
69Q SER* 3.2 22.3 + - - +
70Q PHE* 5.5 2.0 - - + -
72Q LEU* 1.3 86.9 - - - +
74Q PHE* 1.3 81.7 + - + +
75Q GLY 3.5 0.9 - - - -
76Q VAL* 5.2 2.2 - - - +
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Residues in contact with PHE 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P LEU* 3.6 44.2 - - + -
76P VAL* 5.3 10.8 - - - -
70Q PHE* 2.9 38.0 + + + +
73Q LEU* 1.3 89.8 - - + +
75Q GLY* 1.3 57.2 + - - +
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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