Contacts of the helix formed by residues 60 - 74 (chain l) 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 l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56l ALA 3.5 9.4 + - - +
57l LEU* 3.5 16.4 - - - +
58l SER 3.1 0.4 - - - -
59l GLU* 1.3 77.9 - - - +
61l THR* 1.3 61.0 + - + +
63l LEU* 2.9 25.8 + - - +
64l PHE* 3.0 41.0 + - + -
55m PHE* 6.5 0.2 - - + -
59m GLU* 5.1 9.6 - - - +
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Residues in contact with THR 61 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18l GLY 3.8 8.8 - - - +
19l LEU* 3.6 1.9 - - - +
21l GLY 4.8 0.9 - - - -
22l ALA* 3.7 10.4 + - - -
57l LEU 5.4 1.1 - - - +
58l SER 3.1 17.0 + - - +
60l ALA* 1.3 77.2 - - + +
62l GLY* 1.3 58.4 + - - +
63l LEU 3.3 0.8 + - - -
64l PHE* 4.4 7.2 - - + -
65l CYS* 3.4 30.5 + - - +
19m LEU* 3.3 22.7 - - + +
22m ALA* 3.5 16.2 - - + +
23m GLY* 3.2 37.2 - - - +
26m ILE* 6.0 0.2 - - + -
62m GLY* 5.7 0.9 - - - -
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Residues in contact with GLY 62 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61k THR* 5.8 0.4 - - - -
64k PHE* 5.0 4.9 - - - -
19l LEU* 3.6 17.6 - - - +
22l ALA* 3.8 19.6 - - - +
59l GLU* 3.0 17.0 + - - +
60l ALA 3.0 1.0 - - - -
61l THR* 1.3 80.0 + - - +
63l LEU* 1.3 63.3 + - - +
66l LEU* 3.2 24.3 - - - +
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Residues in contact with LEU 63 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64k PHE* 6.1 1.6 - - + -
56l ALA 5.9 0.7 - - - +
59l GLU* 3.1 41.5 - - + +
60l ALA* 2.9 10.0 + - - +
62l GLY* 1.3 82.6 - - - +
64l PHE* 1.3 62.7 + - + +
65l CYS 3.4 0.4 - - - -
66l LEU* 3.1 14.8 + - + +
67l MET* 2.9 44.5 + - + +
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Residues in contact with PHE 64 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60l ALA* 3.0 46.0 + - + +
61l THR* 4.3 4.3 - - + +
63l LEU* 1.3 76.0 - - + +
65l CYS* 1.3 63.0 + - - +
67l MET* 3.1 35.4 + - + +
68l VAL* 3.1 18.5 + - - +
19m LEU* 4.3 11.2 - - + -
59m GLU* 4.8 11.2 - - - -
62m GLY 4.9 5.6 - - - -
63m LEU* 5.9 2.2 - - + -
66m LEU* 3.6 46.6 - - + +
70m PHE* 5.8 2.2 - + - -
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Residues in contact with CYS 65 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15l SER* 3.4 26.9 + - - +
18l GLY* 3.5 17.7 - - - -
19l LEU* 3.5 21.5 - - + +
61l THR 3.4 13.9 + - - -
63l LEU 3.4 0.4 - - - -
64l PHE* 1.3 77.3 - - - +
66l LEU* 1.3 59.7 + - - +
68l VAL* 3.7 16.0 + - - +
69l SER* 3.8 9.4 + - - -
16m THR* 3.5 18.6 - - - -
19m LEU* 3.3 30.1 - - - -
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Residues in contact with LEU 66 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64k PHE* 3.6 59.5 - - + +
68k VAL* 5.9 3.1 - - + -
19l LEU* 3.7 11.6 - - + +
62l GLY 3.2 24.2 - - - +
63l LEU* 3.1 17.6 + - + +
64l PHE 3.0 1.0 - - - -
65l CYS* 1.3 79.4 - - - +
67l MET* 1.3 60.5 + - + +
69l SER* 2.7 27.7 + - - +
70l PHE* 3.1 35.1 - - + -
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Residues in contact with MET 67 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63l LEU* 2.9 31.9 + - + +
64l PHE* 3.1 37.7 + - + +
66l LEU* 1.3 77.2 - - + +
68l VAL* 1.3 65.4 + - + +
70l PHE* 3.2 13.6 + - + +
71l LEU* 3.1 35.3 + - + +
70m PHE* 6.4 2.2 - - + -
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Residues in contact with VAL 68 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15l SER* 3.7 17.3 - - - -
64l PHE* 3.1 18.4 + - + +
65l CYS* 3.8 7.4 - - - +
66l LEU 3.3 0.4 - - - -
67l MET* 1.3 79.3 - - + +
69l SER* 1.3 60.2 + - - +
71l LEU* 3.4 15.7 + - + +
72l LEU* 3.2 28.4 - - + +
12m ALA 4.2 9.9 - - - +
16m THR* 3.7 24.9 - - + -
19m LEU* 6.1 0.7 - - + -
66m LEU* 5.7 4.3 - - + -
69m SER* 4.5 13.9 - - - +
70m PHE* 6.5 2.0 - - + -
73m LEU* 4.6 14.4 - - + -
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Residues in contact with SER 69 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68k VAL* 4.7 17.6 - - - +
12l ALA* 4.1 15.0 - - - +
15l SER* 3.6 19.5 + - - -
16l THR* 4.9 3.4 - - - -
65l CYS 3.8 4.8 + - - -
66l LEU* 2.7 27.9 + - - +
68l VAL* 1.3 80.3 - - - +
70l PHE* 1.3 69.9 + - - +
72l LEU* 3.3 3.6 + - - +
73l LEU* 3.2 31.7 + - - +
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Residues in contact with PHE 70 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64k PHE* 5.8 2.9 - + - -
67k MET* 6.4 1.3 - - + -
68k VAL* 6.6 0.4 - - + -
71k LEU* 5.1 8.7 - - + -
66l LEU* 3.1 52.0 - - + -
67l MET* 3.2 12.6 + - + +
69l SER* 1.3 77.7 + - - +
71l LEU* 1.3 54.1 + - + +
72l LEU 3.0 6.2 + - - -
73l LEU* 4.8 2.2 - - + -
74l PHE* 2.9 43.5 + + + +
75l GLY* 2.7 31.9 + - - -
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Residues in contact with LEU 71 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67l MET* 3.1 30.1 + - + +
68l VAL* 3.8 10.1 - - + +
69l SER 3.3 0.6 - - - -
70l PHE* 1.3 78.0 - - + +
72l LEU* 1.3 69.0 + - - +
75l GLY* 4.8 7.2 - - - -
76l VAL* 3.0 28.1 + - - +
70m PHE* 4.9 11.2 - - + -
73m LEU* 4.4 19.3 - - + +
74m PHE* 3.6 38.8 - - + -
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Residues in contact with LEU 72 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8l LYS* 3.3 38.3 - - - +
9l TYR* 5.2 0.9 - - - -
11l GLY* 3.4 38.6 - - - +
12l ALA* 3.6 5.6 - - + +
68l VAL* 3.2 26.7 - - + +
69l SER 3.3 7.3 + - - +
70l PHE 3.0 0.4 - - - -
71l LEU* 1.3 86.9 - - + +
73l LEU* 1.3 64.7 + - - +
76l VAL* 3.7 12.6 - - - +
9m TYR* 3.5 42.6 - - + +
12m ALA* 5.4 0.4 - - + -
13m GLY* 5.0 1.8 - - - +
73m LEU* 3.7 14.8 - - + -
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Residues in contact with LEU 73 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68k VAL* 4.6 14.6 - - + -
71k LEU* 4.4 31.6 - - + +
72k LEU* 3.8 9.4 - - + -
76k VAL* 5.5 2.4 - - - +
8l LYS 4.2 0.4 - - - +
9l TYR* 3.6 34.7 - - + -
12l ALA* 3.8 22.4 - - + -
69l SER* 3.2 22.5 + - - +
70l PHE* 5.8 1.6 - - + -
72l LEU* 1.3 86.2 - - - +
74l PHE* 1.3 80.8 + - + +
75l GLY 3.5 1.3 + - - -
76l VAL* 5.2 2.0 - - - +
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Residues in contact with PHE 74 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71k LEU* 3.7 42.8 - - + -
76k VAL* 5.3 11.7 - - - -
70l PHE* 2.9 37.2 + + + +
73l LEU* 1.3 92.3 - - + +
75l GLY* 1.3 58.0 + - - +
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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