Contacts of the strand formed by residues 51 - 61 (chain L) in PDB entry 4FAO
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 THR 51 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46L ARG 4.0 0.3 - - - +
47L ASN* 3.7 2.0 - - - +
48L SER* 2.7 48.0 + - - +
49L SER 3.2 5.1 + - - +
50L GLY* 1.3 77.1 - - - +
52L ILE* 1.3 60.9 + - - +
53L GLU* 3.7 3.6 + - - +
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Residues in contact with ILE 52 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45L TRP* 3.7 33.4 - - + +
46L ARG 3.7 3.1 - - - -
47L ASN* 3.4 16.2 - - - +
50L GLY 3.5 8.7 + - - +
51L THR* 1.3 71.2 - - - +
53L GLU* 1.3 63.0 - - - +
54L LEU* 4.0 2.7 + - + +
95L PHE* 4.3 17.9 - - + -
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Residues in contact with GLU 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ALA* 5.6 3.3 - - + +
45L TRP* 3.3 3.1 - - - +
46L ARG* 2.8 70.7 + - + +
51L THR 3.7 3.7 + - - +
52L ILE* 1.3 73.0 - - - +
54L LEU* 1.3 71.5 - - - +
55L VAL* 4.1 2.4 - - - +
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Residues in contact with LEU 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L TYR* 4.0 33.9 + - + -
16L ALA* 3.5 17.2 - - - +
43L ALA* 5.4 0.2 - - + -
44L SER 3.2 16.6 - - - +
45L TRP* 4.0 6.3 - - + -
52L ILE* 4.0 4.2 + - + +
53L GLU* 1.3 81.6 - - - +
55L VAL* 1.3 72.9 + - - +
56L LYS* 3.8 15.3 - - - +
57L LYS* 3.5 36.3 - - + +
95L PHE* 4.5 15.7 - - + -
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Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H LEU* 6.1 0.2 - - + -
93H PRO* 4.2 29.8 - - + +
14L TYR* 4.5 0.9 - - - -
15L ASN* 4.0 1.0 - - - +
16L ALA* 3.3 25.1 + - + +
17L ASN* 4.5 2.1 + - + +
44L SER* 2.9 24.3 + - - +
45L TRP* 4.1 1.3 - - - -
46L ARG* 3.9 42.8 - - + +
53L GLU* 4.1 11.0 - - - +
54L LEU* 1.3 79.8 - - - +
56L LYS* 1.3 81.9 + - + +
81L VAL* 5.4 3.8 - - + -
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Residues in contact with LYS 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H LEU* 4.4 14.1 - - + -
93H PRO 3.6 19.9 + - - +
94H THR* 4.1 8.3 - - - +
95H LEU* 4.2 11.0 - - + +
13L TYR* 6.1 0.2 - - - -
14L TYR* 3.2 12.6 - - - +
15L ASN* 2.7 32.7 + - + +
17L ASN* 4.1 4.6 - - - +
21L GLU* 3.0 33.7 + - - -
42L TYR* 3.7 21.3 - - + +
43L ALA* 3.3 1.9 - - - -
44L SER* 2.9 41.7 + - - +
54L LEU* 3.8 1.8 - - - +
55L VAL* 1.3 90.1 + - + +
57L LYS* 1.3 64.7 - - - +
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Residues in contact with LYS 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ILE* 3.2 30.9 - - + +
13L TYR* 3.5 7.8 - - - -
14L TYR* 2.7 38.6 + - + +
42L TYR* 3.3 15.5 + - - +
43L ALA* 3.8 12.1 - - + -
54L LEU* 3.5 31.0 - - + +
56L LYS* 1.3 78.7 - - - +
58L GLY* 1.3 58.9 + - - +
92L ASN* 3.4 20.6 + - - +
93L GLU* 3.2 26.3 + - - -
95L PHE* 4.1 18.5 - - - -
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Residues in contact with GLY 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L CYS* 3.8 7.4 - - - -
12L ILE 3.1 14.7 + - - -
13L TYR* 4.4 3.6 - - - -
29L GLU* 3.9 7.6 - - - -
41L CYS* 3.4 4.3 - - - -
42L TYR* 2.9 45.5 + - - +
57L LYS* 1.3 75.3 - - - +
59L CYS* 1.3 60.6 + - - -
92L ASN* 3.7 1.6 + - - -
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Residues in contact with CYS 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H SER* 4.6 0.2 + - - -
95H LEU* 4.6 2.1 - - - +
97H TYR* 3.3 34.6 - - + +
11L CYS* 3.8 6.1 - - - -
29L GLU* 2.8 40.5 + - - +
31L CYS* 2.0 52.3 - - + -
40L HIS 3.6 4.5 - - - -
42L TYR* 3.5 10.9 - - - -
58L GLY* 1.3 73.6 - - - -
60L TRP* 1.3 63.3 + - - +
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Residues in contact with TRP 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ALA 3.6 17.3 - - - -
29H PRO* 3.8 16.2 - - + -
83H SER* 3.3 45.5 - - - +
84H VAL* 3.8 1.1 - - - -
85H LEU* 3.9 11.4 - - + -
95H LEU* 4.1 10.5 - - + -
97H TYR* 3.6 5.1 - - - -
39L LEU* 3.9 4.0 - - - +
40L HIS* 2.9 45.6 + - + +
41L CYS 4.4 0.7 - - - -
42L TYR* 4.1 26.9 - + + -
59L CYS* 1.3 76.8 - - - +
61L LEU* 1.3 72.9 + - - +
63L ASP* 3.2 28.7 + - + +
66L CYS* 4.0 20.7 - - - -
83L PHE* 3.7 37.2 - + - -
85L CYS* 4.4 1.1 - - + -
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Residues in contact with LEU 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H PRO* 3.4 40.8 - - + +
82H ILE* 4.0 6.9 - - + +
83H SER* 3.4 23.7 + - - +
97H TYR* 3.6 33.4 - - + +
98H HIS* 4.6 7.9 - - + +
32L GLU 4.1 7.0 - - - +
33L GLY* 4.8 4.9 - - - -
34L GLU 5.5 1.3 - - - +
38L ARG 4.9 0.9 - - - +
39L LEU* 3.7 25.6 - - + -
40L HIS* 3.7 1.8 - - - -
60L TRP* 1.3 80.4 + - - +
62L ASP* 1.3 56.8 + - + +
63L ASP* 2.6 31.8 + - - +
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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