Contacts of the strand formed by residues 72 - 79 (chain D) in PDB entry 3E5X
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 GLU 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D ASP* 2.4 36.6 - - + +
65D ILE 3.2 11.7 - - - +
66D ILE* 3.9 20.6 - - + +
67D PHE* 5.9 0.2 - - - -
70D GLY 4.0 7.2 - - - +
71D SER* 1.3 78.2 - - - +
73D LYS* 1.3 79.0 + - - +
95D TYR* 3.5 22.0 - - - -
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Residues in contact with LYS 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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142C ALA* 3.8 28.7 - - + +
145C ASN* 3.1 39.4 + - + +
146C THR* 3.2 26.3 + - - +
64D ASP* 3.1 7.2 - - - -
65D ILE* 2.8 38.8 + - + +
67D PHE* 4.9 3.3 - - + -
71D SER* 5.6 2.4 - - - -
72D GLU* 1.3 87.4 + - - +
74D LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 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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141C VAL* 6.0 2.4 - - - +
142C ALA* 5.2 0.9 - - - +
16D PRO* 4.6 18.6 - - + -
62D LYS* 3.7 32.5 - - + +
64D ASP* 3.3 11.0 + - - +
73D LYS* 1.3 76.4 - - - +
75D LEU* 1.3 66.3 + - - +
76D TYR 3.8 22.0 - - - +
77D TYR* 3.6 37.7 - - + -
185D GLU* 3.8 41.2 - - + +
186D ILE* 5.0 3.4 - - + +
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Residues in contact with LEU 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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138C ALA* 3.8 40.8 - - + +
141C VAL* 6.2 0.9 - - + -
142C ALA* 4.4 2.7 - - + -
16D PRO* 3.5 13.2 - - - +
63D LEU* 2.8 37.0 + - + +
65D ILE* 3.7 36.1 - - + +
73D LYS 3.5 0.6 + - - -
74D LEU* 1.3 81.9 - - - +
76D TYR* 1.3 60.6 + - + +
92D ASN* 5.8 0.2 - - - +
94D ILE* 3.9 20.4 - - + -
137D TYR* 2.7 30.7 + - + +
503D 3C4 4.3 13.0 - - + -
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Residues in contact with TYR 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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134C VAL* 6.2 0.4 - - + -
16D PRO* 3.4 14.4 - - - +
19D PHE* 3.6 20.9 - + + -
61D ILE 4.2 0.2 - - - +
62D LYS 3.8 0.2 - - - -
63D LEU* 2.9 50.5 + - + +
74D LEU* 3.8 9.5 - - - +
75D LEU* 1.3 86.1 - - + +
77D TYR* 1.3 73.6 + - - +
78D ALA* 4.0 19.1 - - + -
82D SER* 6.0 0.2 - - - -
83D LEU 3.7 2.1 + - - -
84D ILE* 3.5 22.3 - - + +
133D LYS* 3.7 14.3 + - + -
137D TYR* 3.4 20.4 - + - +
503D 3C4 2.4 50.3 + + - -
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Residues in contact with TYR 77 (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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16D PRO* 3.0 10.6 + - + +
17D ASP* 3.3 26.7 - - + +
18D ASN* 3.0 21.8 + - - -
19D PHE 4.8 1.2 + - - -
60D LYS* 4.3 12.8 - - - +
61D ILE 3.4 7.0 - - - -
62D LYS* 3.3 28.3 - - + -
74D LEU* 3.6 32.5 - - + -
76D TYR* 1.3 81.8 - - - +
78D ALA* 1.3 59.4 + - - +
99D MET* 3.5 41.2 - - + +
181D LYS* 5.3 2.8 + - - +
182D SER* 5.3 4.7 + - - -
185D GLU* 3.2 20.9 + - - -
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Residues in contact with ALA 78 (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 ASP* 5.1 0.9 - - - -
18D ASN* 3.7 1.1 - - - -
56D LEU* 3.4 12.8 - - + +
60D LYS* 3.3 9.2 - - - +
61D ILE* 2.9 42.0 + - + +
76D TYR* 4.0 19.3 - - + -
77D TYR* 1.3 75.3 - - - +
79D GLY* 1.3 57.7 + - - +
82D SER* 3.5 24.0 - - - -
84D ILE* 5.3 5.4 - - + -
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Residues in contact with GLY 79 (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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18D ASN* 2.8 21.9 + - - -
56D LEU* 3.5 11.4 - - - +
59D GLY 3.4 13.7 - - - -
60D LYS* 4.5 4.3 - - - -
78D ALA* 1.3 72.2 - - - +
80D GLY* 1.3 68.5 + - - -
81D ASN 3.3 0.3 + - - -
82D SER* 3.0 19.9 + - - -
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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