Contacts of the helix formed by residues 65 - 75 (chain A) in PDB entry 2XFN
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 GLN 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TYR 4.1 1.6 + - - +
61A VAL* 3.1 18.2 - - - +
62A GLY 3.1 33.6 + - - +
64A THR* 1.3 74.3 - - - +
66A ASN* 1.3 62.8 + - - +
68A ILE* 3.4 5.4 - - + +
69A LEU* 3.2 25.0 + - + +
205A GLY* 4.2 10.9 + - - -
432A TRP* 3.3 57.0 - - + +
435A TYR* 3.8 14.6 - - - -
437A GLU* 3.1 32.9 + - + +
1500A FAD 4.9 1.6 - - - +
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Residues in contact with ASN 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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64A THR* 3.2 27.2 + - - +
65A GLN* 1.3 78.3 + - - +
67A ARG* 1.3 58.2 + - - +
69A LEU* 3.6 6.6 + - - +
70A ARG* 2.9 30.1 + - - +
437A GLU* 3.5 2.8 + - - -
466A GLU* 3.6 18.1 + - + +
467A PRO 3.5 15.5 + - - +
468A GLU* 3.7 21.9 + - - +
469A SER* 2.9 35.5 + - - +
472A VAL 4.7 1.6 - - - +
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Residues in contact with ARG 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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66A ASN* 1.3 75.2 - - - +
68A ILE* 1.3 61.4 + - - +
70A ARG* 3.2 10.3 + - - +
71A LEU* 2.9 30.3 + - - +
431A HIS* 4.5 15.6 + - - +
437A GLU* 3.0 23.0 + - - +
440A VAL* 3.8 18.6 - - + -
441A GLU* 3.6 49.8 + - - +
444A GLU* 5.0 3.3 + - - -
448A ARG* 6.0 1.0 - - - +
464A GLN 2.9 28.1 + - - -
465A SER* 3.9 3.8 - - - +
466A GLU* 3.7 42.9 + - + +
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Residues in contact with ILE 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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14A ILE* 4.4 7.6 - - + -
61A VAL* 3.9 20.2 - - + -
65A GLN* 3.4 19.1 - - + +
67A ARG* 1.3 73.1 - - - +
69A LEU* 1.3 61.1 + - + +
71A LEU* 4.5 2.2 - - + -
72A ALA* 2.9 28.4 + - - +
210A PHE* 4.1 15.0 - - + -
217A VAL* 4.3 28.5 - - + -
436A MET* 4.1 22.0 - - + -
437A GLU* 2.8 38.4 + - + +
440A VAL* 3.8 21.2 - - + +
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Residues in contact with LEU 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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61A VAL* 3.9 28.5 - - + -
62A GLY 4.0 12.6 - - - +
63A PRO* 5.3 0.4 - - + -
65A GLN* 3.2 24.8 + - + +
66A ASN* 3.8 6.5 - - - +
67A ARG 3.2 0.2 - - - -
68A ILE* 1.3 79.7 - - + +
70A ARG* 1.3 58.2 + - - +
72A ALA* 4.0 3.5 - - - +
73A LYS* 2.9 31.4 + - - +
79A THR* 4.1 14.1 - - + -
210A PHE* 4.8 3.1 - - + -
469A SER* 3.9 20.6 - - - +
472A VAL* 3.8 40.8 - - + +
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Residues in contact with ARG 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 ASN 2.9 18.8 + - - +
67A ARG* 3.2 20.1 + - - +
69A LEU* 1.3 74.8 - - - +
71A LEU* 1.3 82.7 + - - +
73A LYS* 3.3 7.1 + - - +
74A GLU* 3.0 37.0 + - + +
440A VAL* 4.5 0.2 - - - +
444A GLU* 2.8 43.4 + - - -
464A GLN* 6.1 1.0 - - - +
466A GLU* 2.9 39.8 + - - +
467A PRO 5.9 0.2 - - - +
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Residues in contact with LEU 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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14A ILE* 4.7 1.8 - - + -
18A ALA* 4.2 14.1 - - + -
21A LYS* 4.1 30.5 - - + +
67A ARG 2.9 16.4 + - - +
68A ILE* 4.0 3.8 - - + +
70A ARG* 1.3 95.3 - - - +
72A ALA* 1.3 63.2 + - - +
74A GLU* 3.3 7.4 + - + +
75A LEU* 3.1 43.0 + - + +
217A VAL* 4.0 21.1 - - + -
221A ILE* 4.1 11.0 - - + -
440A VAL* 3.8 26.2 - - + -
444A GLU* 5.0 2.5 - - - +
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Residues in contact with ALA 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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68A ILE* 2.9 17.8 + - - +
69A LEU 4.0 2.2 - - - +
71A LEU* 1.3 76.1 - - - +
73A LYS* 1.3 61.2 + - - +
75A LEU* 3.2 12.3 + - - +
76A GLY 3.3 0.2 + - - -
77A LEU* 3.0 44.6 + - + +
210A PHE* 3.2 38.6 - - + -
217A VAL* 4.3 5.8 - - + -
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Residues in contact with LYS 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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69A LEU 2.9 19.8 + - - +
70A ARG* 3.7 6.7 - - - +
72A ALA* 1.3 75.1 - - - +
74A GLU* 1.3 59.1 + - - +
76A GLY* 2.9 21.7 + - - -
77A LEU 3.9 12.7 - - - +
470A VAL* 4.0 13.9 - - - +
471A ASP* 2.8 34.4 + - - +
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Residues in contact with GLU 74 (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 LYS* 2.8 37.3 + - - -
70A ARG* 3.0 31.7 + - + +
71A LEU* 3.7 8.0 - - + +
73A LYS* 1.3 76.9 - - - +
75A LEU* 1.3 61.8 + - + +
76A GLY* 3.4 1.4 + - - -
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Residues in contact with LEU 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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21A LYS* 4.4 9.9 - - - -
71A LEU* 3.1 30.3 + - + +
72A ALA* 3.7 9.0 - - - +
73A LYS 3.1 0.8 - - - -
74A GLU* 1.3 80.5 - - + +
76A GLY* 1.3 55.4 + - - +
77A LEU* 3.5 4.5 - - + -
217A VAL* 3.6 37.5 - - + +
220A ARG* 2.8 44.0 + - + -
221A ILE* 3.8 16.6 - - + -
224A LEU* 3.8 28.9 - - + -
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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