Contacts of the strand formed by residues 67 - 76 (chain Y) 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 67 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136J ARG* 5.1 11.9 - - - +
139J LYS 5.9 0.9 - - - -
27Y VAL 4.0 0.9 - - - +
28Y LEU* 3.9 18.4 - - - -
29Y HIS* 3.5 29.6 + - - +
63Y HIS* 5.0 0.4 - - - -
66Y GLY* 1.3 72.5 - - - -
68Y LYS* 1.3 67.6 + - - +
69Y THR* 4.3 3.8 - - - +
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Residues in contact with LYS 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J LYS* 5.8 11.4 - - - +
8Y ARG* 3.4 31.7 - - - +
10Y ARG* 4.3 16.8 - - - +
26Y ASP* 4.5 26.2 - - + +
27Y VAL 3.5 7.2 - - - +
28Y LEU* 4.2 11.4 - - + +
61Y ARG 4.5 0.2 - - - +
63Y HIS* 2.5 50.2 + - + +
66Y GLY 4.3 0.7 - - - +
67Y GLY* 1.3 76.3 - - - +
69Y THR* 1.3 62.8 + - - +
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Residues in contact with THR 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y ILE 3.3 3.1 - - - +
26Y ASP* 3.2 5.4 - - - -
27Y VAL* 2.9 43.7 + - - +
29Y HIS* 3.8 23.1 + - + +
34Y THR* 4.9 15.6 - - + +
40Y ILE* 5.6 1.7 - - - +
60Y PHE* 4.9 16.2 - - - -
61Y ARG 3.7 17.7 - - - +
62Y THR* 5.4 4.0 - - + +
63Y HIS* 4.5 0.2 - - - -
67Y GLY 4.3 2.5 - - - +
68Y LYS* 1.3 79.2 - - - +
70Y THR* 1.3 61.8 + - - +
71Y GLY 3.8 0.2 + - - -
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Residues in contact with THR 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y VAL* 4.6 12.8 - - + -
26Y ASP* 3.2 23.2 + - - +
59Y GLY 4.2 0.2 - - - -
60Y PHE* 3.2 10.5 + - - +
61Y ARG* 3.1 60.0 + - - +
63Y HIS* 4.0 16.0 + - - -
69Y THR* 1.3 71.5 - - - +
71Y GLY* 1.3 62.9 + - - +
72Y PHE* 5.3 9.4 - - + -
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Residues in contact with GLY 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y VAL* 3.6 5.2 - - - +
25Y ILE* 2.6 45.9 + - - -
57Y VAL* 5.1 3.1 - - - -
59Y GLY 3.6 17.0 - - - -
60Y PHE* 5.0 4.7 - - - -
69Y THR 3.8 0.2 + - - -
70Y THR* 1.3 79.3 - - - +
72Y PHE* 1.3 64.6 + - - -
73Y GLY 4.1 0.2 - - - -
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Residues in contact with PHE 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LYS* 5.3 9.2 - - - -
56E LEU* 6.1 6.3 - - + -
23Y MET 3.8 4.7 - - - +
24Y VAL* 3.7 35.4 - - + -
57Y VAL* 3.4 3.2 - - - +
58Y PHE* 3.0 71.6 + + + -
59Y GLY* 5.9 1.8 - - - -
61Y ARG* 5.4 11.9 - - - -
70Y THR* 5.3 9.2 - - + -
71Y GLY* 1.3 76.3 - - - -
73Y GLY* 1.3 60.6 + - - +
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Residues in contact with GLY 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Y LYS 5.1 0.7 - - - -
22Y GLN* 4.1 1.0 - - - +
23Y MET* 3.1 31.6 + - - +
25Y ILE* 3.7 26.1 - - - +
44Y LEU* 5.4 2.0 - - - -
56Y PHE 3.6 6.3 - - - -
57Y VAL* 4.0 4.3 - - - -
72Y PHE* 1.3 74.1 - - - +
74Y MET* 1.3 74.4 - - - +
75Y ILE* 5.4 0.9 - - - -
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Residues in contact with MET 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y ARG* 3.4 34.3 - - + +
21Y LYS 4.4 1.6 - - - +
22Y GLN* 3.6 31.9 - - + +
54Y VAL 4.3 0.3 - - - +
55Y ILE* 3.5 0.2 - - - -
56Y PHE* 2.5 58.0 + - + +
58Y PHE* 3.5 31.0 - - + -
72Y PHE* 6.0 0.2 - - - -
73Y GLY* 1.3 87.2 - - - +
75Y ILE* 1.3 65.2 + - - +
76Y TYR* 4.1 7.2 - - + +
86Y GLU* 3.3 22.7 - - - +
90Y ARG* 3.6 11.4 - - - +
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Residues in contact with ILE 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y ARG* 3.5 4.3 - - - +
21Y LYS* 3.1 41.1 + - + +
23Y MET* 3.6 27.6 - - + -
44Y LEU* 3.8 26.9 - - + -
48Y TYR* 3.6 49.1 - - + +
50Y THR* 4.9 0.7 - - - +
54Y VAL 4.4 2.9 - - - -
55Y ILE* 3.7 24.5 - - + -
73Y GLY 5.4 0.4 - - - -
74Y MET* 1.3 81.6 - - - +
76Y TYR* 1.3 72.6 - - - +
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Residues in contact with TYR 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Y GLN 3.6 9.6 - - - +
20Y ARG* 3.0 40.7 + - + -
48Y TYR* 5.5 1.0 - - - -
50Y THR* 5.9 1.7 - - - +
54Y VAL* 3.2 40.7 + - + +
56Y PHE* 4.4 6.7 - + - -
74Y MET* 4.6 8.7 - - + -
75Y ILE* 1.3 83.6 - - - +
77Y ASP* 1.3 62.7 + - - +
78Y SER 3.4 16.6 - - - +
81Y TYR* 3.6 6.7 - - + -
82Y ALA* 3.5 25.4 - - + -
85Y ASN* 3.3 30.3 - - + +
86Y GLU* 2.3 49.5 + - + +
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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