Contacts of the helix formed by residues 71 - 79 (chain T) 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 71 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15621 C 3.2 29.5 + - - -
15631 G 4.3 7.2 - - - -
69T GLY 3.8 1.6 + - - -
70T ALA* 1.3 76.4 - - - +
72T VAL* 1.3 67.1 + - - -
74T SER* 3.4 10.5 + - - -
75T MET* 3.2 21.5 + - - +
104T LEU* 4.9 4.9 - - - +
120T GLY* 4.8 1.3 - - - -
121T ARG* 4.6 2.6 + - - -
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Residues in contact with VAL 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15631 G 3.4 31.6 + - - +
15641 C 4.7 6.5 - - - +
71T GLY* 1.3 69.6 - - - -
73T GLY* 1.3 62.5 + - - +
74T SER 3.3 0.2 + - - -
75T MET* 3.3 6.2 + - - +
76T THR* 2.8 31.1 + - - +
97T LYS* 3.9 16.4 - - + +
100T ALA* 3.6 24.5 - - + +
101T ARG* 3.9 23.1 - - + +
104T LEU* 3.8 21.8 - - + -
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Residues in contact with GLY 73 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15611 A 5.6 2.0 - - - -
15621 C 3.5 17.9 + - - -
15631 G 4.8 0.4 + - - -
72T VAL* 1.3 79.5 - - - +
74T SER* 1.3 57.0 + - - +
76T THR* 3.3 11.7 + - - -
77T LYS* 2.9 37.6 + - - +
94T ARG* 5.2 0.5 - - - -
97T LYS* 5.2 11.2 - - - +
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Residues in contact with SER 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15611 A 3.8 5.7 + - - -
15621 C 2.7 22.3 + - - -
15841 G 4.4 11.1 + - - -
15871 G 4.8 15.1 + - - +
70T ALA* 4.4 9.6 - - - -
71T GLY 3.4 21.6 + - - -
72T VAL 3.1 0.6 - - - -
73T GLY* 1.3 77.4 - - - +
75T MET* 1.3 57.9 + - - +
77T LYS* 3.0 14.2 + - - +
78T ILE* 2.9 29.1 + - - +
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Residues in contact with MET 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T SER* 5.7 1.1 - - - -
60T THR* 3.5 23.8 - - + +
63T HIS* 5.4 2.9 - - + +
71T GLY 3.2 6.9 + - - +
72T VAL* 3.9 3.8 - - - +
74T SER* 1.3 74.7 - - - +
76T THR* 1.3 62.7 + - - +
78T ILE* 2.8 29.3 + - + +
79T TYR* 2.9 48.2 + - + +
100T ALA* 3.6 35.4 - - + +
103T VAL* 5.2 2.0 - - + -
104T LEU* 4.9 6.3 - - + -
121T ARG* 2.7 47.8 - - - +
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Residues in contact with THR 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T VAL 2.8 20.4 + - - -
73T GLY* 3.3 14.3 - - - -
75T MET* 1.3 76.8 - - - +
77T LYS* 1.3 58.6 + - - +
79T TYR* 3.7 22.8 + - + +
80T GLY 4.5 1.2 + - - -
92T PHE* 5.3 0.5 - - - -
93T SER 5.0 2.1 - - - +
94T ARG* 3.7 20.0 - - + -
95T GLY 3.3 42.4 + - - +
96T SER 4.4 0.9 + - - -
97T LYS* 3.9 20.3 - - + +
100T ALA* 4.0 11.3 - - - +
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Residues in contact with LYS 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15601 U 3.8 8.1 + - - -
15611 A 2.9 36.4 + - - -
15831 C 4.2 2.4 + - - +
15841 G 4.0 20.7 + - - +
15871 G 3.7 27.9 + - + +
15881 A 4.7 1.6 - - - +
73T GLY* 2.9 20.4 + - - +
74T SER* 3.0 12.1 + - - +
76T THR* 1.3 73.5 - - - +
78T ILE* 1.3 64.9 + - + +
79T TYR 3.2 0.9 - - - -
80T GLY* 3.2 10.0 + - - -
92T PHE* 3.6 20.4 - - + -
94T ARG* 3.4 43.4 - - - +
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Residues in contact with ILE 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15431 U 4.1 13.9 - - + +
15871 G 3.3 69.3 + - + +
63T HIS* 3.3 33.7 - - + +
67T ARG* 5.8 0.4 - - + -
70T ALA* 5.2 0.2 - - + -
74T SER* 2.9 14.7 + - - +
75T MET* 2.8 21.0 + - + +
77T LYS* 1.3 75.5 - - - +
79T TYR* 1.3 68.1 + - + +
80T GLY* 3.0 2.4 + - - -
121T ARG* 3.5 27.1 - - - +
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Residues in contact with TYR 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15411 G 4.6 8.7 - - - -
15421 C 5.5 3.5 + - - -
15431 U 5.0 3.1 - - - +
15891 A 4.5 0.7 + - - -
40T ALA* 6.0 3.6 - - + -
41T LYS* 6.5 1.1 - - + -
56T ARG* 3.7 37.5 + - - +
59T SER* 5.2 4.9 - - - -
60T THR* 4.9 1.7 + - - -
63T HIS* 6.5 1.3 - + - -
75T MET* 2.9 58.1 + - + +
76T THR* 3.7 22.7 - - - +
77T LYS 3.2 0.2 - - - -
78T ILE* 1.3 79.0 - - + +
80T GLY* 1.3 64.6 + - - +
81T GLY* 4.5 3.7 - - - +
95T GLY* 4.5 15.3 - - - +
96T SER 4.6 14.6 - - - -
99T VAL* 5.1 6.8 - - + +
100T ALA* 4.2 10.3 + - + +
103T VAL* 5.6 2.6 - - - +
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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