Contacts of the helix formed by residues 56 - 72 (chain A) in PDB entry 2FY5
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLN 4.7 5.2 - - - -
51A PHE 4.5 2.0 - - - -
53A ALA* 2.8 20.2 + - - -
54A PRO 3.0 1.7 - - - -
55A GLY* 1.3 81.7 - - - +
57A LEU* 1.3 66.9 + - - -
58A GLY 3.3 2.5 - - - -
59A GLU* 3.7 4.0 + - - +
60A THR* 3.1 23.0 + - - -
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Residues in contact with LEU 57 (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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50A GLN* 4.9 2.7 + - - +
51A PHE* 3.8 14.7 + - + +
56A GLY* 1.3 69.9 - - - -
58A GLY* 1.3 67.2 + - - +
60A THR* 3.2 10.3 + - + -
61A LEU* 3.1 39.1 + - + +
513A ALA* 5.8 0.4 - - + -
516A MET* 4.2 23.6 - - + -
521A PRO* 3.3 39.9 - - + -
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Residues in contact with GLY 58 (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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21A LEU* 3.6 12.8 - - - +
51A PHE* 2.8 48.7 + - - -
57A LEU* 1.3 76.8 - - - +
59A GLU* 1.3 63.0 + - - +
61A LEU* 3.0 5.6 + - - +
62A GLN* 2.9 21.7 + - - +
509A LEU* 4.8 1.0 - - - +
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Residues in contact with GLU 59 (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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21A LEU* 3.6 17.8 - - + +
22A GLN* 4.7 5.7 + - - -
52A GLY 4.6 5.1 - - - +
53A ALA 4.0 11.0 - - - +
54A PRO* 3.7 14.6 - - - +
55A GLY* 2.8 28.8 + - - +
56A GLY 3.7 5.6 + - - +
57A LEU 3.4 0.6 - - - -
58A GLY* 1.3 75.1 - - - +
60A THR* 1.3 56.9 + - - +
62A GLN* 3.4 6.2 + - - +
63A GLN* 3.1 28.9 + - - +
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Residues in contact with THR 60 (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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55A GLY 4.9 2.3 + - - -
56A GLY 3.1 14.6 + - - -
57A LEU* 3.2 15.5 + - + +
58A GLY 3.1 0.8 - - - -
59A GLU* 1.3 74.9 - - - +
61A LEU* 1.3 65.3 + - - +
63A GLN* 3.3 8.6 + - - +
64A LYS* 3.2 31.0 + - + +
516A MET* 4.9 17.7 - - + -
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Residues in contact with LEU 61 (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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51A PHE* 3.8 31.4 - - + -
57A LEU* 3.3 19.7 - - + +
58A GLY 3.0 5.7 + - - +
60A THR* 1.3 73.2 - - - +
62A GLN* 1.3 61.7 + - - +
64A LYS* 3.0 11.8 + - + +
65A LEU* 2.8 27.5 + - - +
509A LEU* 3.7 33.7 - - + +
512A LEU* 3.7 10.9 - - + +
513A ALA* 3.8 30.7 - - + +
516A MET* 3.8 29.2 - - - -
521A PRO* 5.1 0.2 - - + -
524A PHE* 4.9 1.1 - - + -
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Residues in contact with GLN 62 (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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18A VAL* 3.6 16.0 + - - +
19A PRO 3.1 24.4 + - - -
20A PRO* 4.1 3.0 - - - +
21A LEU* 3.6 26.5 - - + +
58A GLY 2.9 12.4 + - - +
59A GLU* 3.6 13.5 - - - +
61A LEU* 1.3 76.4 - - - +
63A GLN* 1.3 58.3 + - - +
65A LEU* 3.1 5.8 + - - +
66A LEU* 2.9 40.0 + - + +
505A HIS* 3.0 24.6 + - - -
509A LEU* 3.8 10.4 - - + +
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Residues in contact with GLN 63 (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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59A GLU 3.1 14.1 + - - +
60A THR* 3.5 11.9 - - + +
61A LEU 3.2 0.2 - - - -
62A GLN* 1.3 77.1 - - - +
64A LYS* 1.3 61.5 + - + +
66A LEU* 3.3 22.5 + - - +
67A GLU* 2.9 44.4 + - - +
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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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60A THR* 3.2 23.3 + - + +
61A LEU* 3.0 14.7 + - + +
63A GLN* 1.3 78.0 - - + +
65A LEU* 1.3 56.1 + - - +
67A GLU* 3.2 20.9 + - - +
68A ARG* 2.8 28.8 + - - +
512A LEU* 4.2 25.1 - - + +
516A MET* 4.8 24.0 - - + +
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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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18A VAL* 4.0 18.6 - - + -
61A LEU 2.8 12.6 + - - +
62A GLN* 3.1 11.0 + - - +
64A LYS* 1.3 74.5 - - - +
66A LEU* 1.3 60.8 + - - +
68A ARG* 3.2 9.0 + - - +
69A GLN* 2.8 30.2 + - - +
75A TRP* 3.6 37.2 - - + -
505A HIS* 3.6 35.0 - - + +
508A ALA* 3.6 18.2 - - + -
509A LEU* 4.1 11.2 - - + -
512A LEU* 3.8 14.1 - - + +
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Residues in contact with LEU 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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18A VAL* 3.7 28.3 - - + +
62A GLN* 2.9 29.5 + - + +
63A GLN* 3.3 25.1 + - - +
65A LEU* 1.3 76.7 - - - +
67A GLU* 1.3 61.6 + - + +
69A GLN* 3.4 22.9 + - - +
70A GLU* 3.2 21.5 + - - +
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Residues in contact with GLU 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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63A GLN* 2.9 37.4 + - + +
64A LYS* 3.4 24.3 + - - +
66A LEU* 1.3 74.4 - - - +
68A ARG* 1.3 65.2 + - - +
70A GLU* 3.1 9.8 + - - +
71A LYS* 3.0 42.5 + - + +
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Residues in contact with ARG 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 2.8 16.2 + - - +
65A LEU* 3.6 12.3 - - - +
67A GLU* 1.3 74.8 - - - +
69A GLN* 1.3 63.9 + - - +
71A LYS* 3.1 6.4 + - - +
72A THR* 2.9 45.0 + - + +
75A TRP* 3.1 33.2 + - + +
78A GLU* 3.9 30.3 + - - +
79A TYR* 3.0 49.6 + - - -
512A LEU* 4.6 10.0 - - + +
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Residues in contact with GLN 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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15A LYS* 3.2 22.3 + - + +
16A LEU 3.2 23.6 + - - +
17A PRO* 4.2 2.8 - - - +
18A VAL* 3.4 30.2 - - + +
65A LEU 2.8 20.4 + - - +
66A LEU* 3.4 19.8 - - - +
67A GLU 3.2 0.2 - - - -
68A ARG* 1.3 74.0 - - - +
70A GLU* 1.3 58.6 + - + +
72A THR* 2.9 24.7 + - - +
73A ALA 5.3 0.3 - - - -
75A TRP* 3.9 19.9 + - + +
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Residues in contact with GLU 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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15A LYS* 3.3 17.1 + - - +
66A LEU 3.2 8.1 + - - +
67A GLU* 3.1 10.8 + - - +
69A GLN* 1.3 81.7 - - + +
71A LYS* 1.3 62.7 + - + +
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Residues in contact with LYS 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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15A LYS* 4.8 0.2 - - - -
67A GLU* 3.0 30.4 + - - +
68A ARG* 3.1 6.7 + - - +
70A GLU* 1.3 81.5 - - + +
72A THR* 1.3 64.4 + - + +
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Residues in contact with THR 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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15A LYS* 2.6 31.9 + - - -
68A ARG* 2.9 40.0 + - + +
69A GLN 2.9 7.6 + - - +
71A LYS* 1.3 86.3 - - + +
73A ALA* 1.3 57.8 + - - +
74A ASN 4.1 7.0 - - - +
75A TRP* 3.4 24.0 + - - -
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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