Contacts of the helix formed by residues 63 - 76 (chain D) in PDB entry 5FLX
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 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.5 13.7 + - - -
61D GLU 3.3 5.1 + - - -
62D LYS* 1.3 77.5 - - - +
64D ARG* 1.3 65.4 + - - +
65D ARG 3.8 0.7 - - - -
66D ILE* 4.4 10.1 - - - -
67D ARG* 3.4 31.7 - - - +
93K THR* 3.6 9.0 - - - +
94K LEU* 5.1 2.0 - - - -
97K SER* 6.5 0.7 - - - -
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Residues in contact with ARG 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU 3.7 2.6 + - - -
61D GLU* 3.8 17.2 + - - +
62D LYS 3.5 2.8 - - - +
63D GLY* 1.3 75.8 - - - +
65D ARG* 1.3 105.9 + - + +
68D GLU* 3.3 9.4 + - - +
59K LYS* 5.8 0.8 - - - +
70K TYR* 2.9 44.5 + - - +
71K LEU 3.9 7.7 + - - +
72K THR* 3.4 24.9 + - - +
73K ASN* 3.1 49.3 + - - +
76K ILE* 5.8 2.2 - - + -
93K THR* 3.3 27.4 - - + +
94K LEU* 4.7 12.6 - - + -
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 6.4 2.0 - - + -
57D ASN* 3.1 38.8 + - - +
58D VAL* 3.5 11.4 - - - +
59D LEU 4.2 3.4 + - - -
60D GLY* 3.5 14.0 - - - -
61D GLU* 3.4 33.5 + - - -
64D ARG* 1.3 102.6 - - - +
66D ILE* 1.3 59.4 + - - +
68D GLU* 3.3 2.1 + - - +
69D LEU* 2.9 40.8 + - + +
70K TYR* 3.0 26.9 + - + +
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 6.4 1.3 - - + -
58D VAL* 3.0 24.1 + - + +
59D LEU* 3.7 44.9 - - + +
63D GLY* 4.4 7.2 - - - +
65D ARG* 1.3 76.2 - - - +
67D ARG* 1.3 73.2 + - + +
69D LEU* 3.4 10.4 + - + +
70D THR* 2.9 34.0 + - - +
86D LEU* 4.5 16.8 - - + +
87D TYR* 5.1 0.9 - - - -
88D ALA* 3.8 27.6 - - + +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS 5.6 0.7 - - - -
63D GLY* 3.4 23.1 + - - +
64D ARG 3.8 1.4 + - - -
65D ARG 3.3 0.4 - - - -
66D ILE* 1.3 85.7 - - + +
68D GLU* 1.3 60.4 + - - +
70D THR* 3.3 10.6 - - - +
71D ALA* 2.9 24.3 + - - +
85D GLU* 4.8 11.7 + - - -
92K ALA* 5.0 11.7 + - - +
93K THR* 3.0 32.1 + - + +
96K ARG* 3.0 47.3 + - - +
97K SER* 3.9 10.6 + - - +
98K ARG* 3.8 25.1 - - - +
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG* 3.3 19.7 + - - +
65D ARG 3.9 2.2 - - - +
67D ARG* 1.3 76.5 - - - +
69D LEU* 1.3 60.0 + - - +
71D ALA* 3.1 3.6 + - - +
72D VAL* 2.9 30.1 + - + +
19K GLY 4.5 4.1 - - - +
20K VAL* 4.1 13.9 - - + +
69K TRP 4.2 3.6 - - - +
70K TYR* 3.1 31.5 + - + -
71K LEU* 2.4 60.1 + - - +
93K THR* 3.3 19.4 - - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 5.3 0.4 - - + -
25D LEU* 4.6 7.4 - - + -
28D GLU* 3.2 38.1 - - + +
29D LEU* 3.6 32.3 - - + -
50D ILE* 5.5 4.7 - - + -
58D VAL* 5.3 9.2 - - + +
65D ARG* 2.9 30.4 + - + +
66D ILE* 3.5 9.4 - - + +
68D GLU* 1.3 77.2 - - - +
70D THR* 1.3 61.0 + - - +
72D VAL* 3.3 10.6 + - + +
73D VAL* 3.1 28.2 + - - +
86D LEU* 3.9 11.0 - - + -
70K TYR* 5.3 12.8 - - + -
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ILE* 2.9 17.6 + - - +
67D ARG* 3.3 16.2 - - - +
69D LEU* 1.3 76.8 - - - +
71D ALA* 1.3 61.7 + - - +
73D VAL* 3.4 4.3 + - - +
74D GLN* 3.1 30.8 + - - +
84D VAL 4.2 13.9 - - - +
85D GLU* 4.4 10.0 + - - +
86D LEU* 3.2 47.2 + - + +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG 2.9 13.7 + - - +
68D GLU* 3.1 12.3 + - - +
70D THR* 1.3 73.5 - - - +
72D VAL* 1.3 60.2 + - - +
74D GLN* 2.8 17.8 + - - +
75D LYS* 2.8 46.9 + - - +
18K GLU 4.8 3.6 - - - +
20K VAL* 3.7 16.4 - - + -
92K ALA 5.0 4.9 - - - +
93K THR* 4.6 7.2 - - - +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 3.6 36.6 - - + -
28D GLU* 5.7 0.7 - - - +
68D GLU* 2.9 24.9 + - + +
69D LEU* 3.3 15.2 + - + +
71D ALA* 1.3 75.3 - - - +
73D VAL* 1.3 61.7 + - + +
74D GLN 3.2 1.2 + - - -
75D LYS* 3.7 7.3 + - - +
76D ARG 4.2 9.5 + - - +
77D PHE* 4.2 7.7 - - + -
20K VAL* 3.7 30.3 - - + -
68K TYR* 4.0 20.7 - - + -
69K TRP 4.9 5.6 - - - +
70K TYR* 6.0 2.9 - - + -
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PHE* 4.7 1.6 - - + -
21D LEU* 3.8 20.2 - - + -
24D PHE* 6.1 3.6 - - + -
25D LEU* 5.6 7.4 - - + -
48D ILE* 3.7 17.9 - - + -
69D LEU 3.1 15.3 + - - +
70D THR 3.7 7.2 - - - +
72D VAL* 1.3 77.7 - - + +
74D GLN* 1.3 59.9 + - - +
77D PHE* 2.9 43.0 - - + +
79D PHE* 4.9 0.5 - - - +
84D VAL* 3.6 29.9 - - + +
86D LEU* 3.9 18.4 - - + -
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Residues in contact with GLN 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D THR* 3.1 22.2 + - - +
71D ALA* 2.8 19.8 + - - +
73D VAL* 1.3 79.0 - - - +
75D LYS* 1.3 81.8 + - + +
76D ARG 3.4 1.2 + - - -
77D PHE 3.5 8.1 + - - -
79D PHE* 3.5 34.1 + - - +
80D PRO* 5.1 3.7 - - + +
81D GLU 6.1 0.2 - - - -
82D GLY* 3.9 22.2 - - - -
84D VAL* 3.5 29.2 + - + +
85D GLU* 5.2 1.8 + - - -
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA* 2.8 39.7 + - - +
72D VAL 3.7 3.9 + - - +
74D GLN* 1.3 84.1 + - + +
76D ARG* 1.3 61.8 + - - +
77D PHE 4.1 0.2 + - - -
78D GLY* 4.2 5.7 + - - -
79D PHE 4.9 0.5 + - - -
80D PRO* 6.1 0.3 - - - +
18K GLU* 2.4 73.7 + - + +
20K VAL* 3.6 32.3 - - + +
22K VAL* 5.4 8.5 - - + -
92K ALA 5.9 0.2 + - - -
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15541 C 2.5 49.8 + - - +
15551 U 5.1 8.1 + - - +
20D GLU* 5.7 1.4 + - - -
72D VAL 4.2 7.4 + - - +
75D LYS* 1.3 81.3 - - - +
77D PHE* 1.3 73.6 + - - +
78D GLY* 3.6 5.8 - - - +
22K VAL* 4.1 32.7 - - + +
66K HIS* 3.1 43.6 + - - -
68K TYR* 4.7 15.1 + - - -
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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