Contacts of the strand formed by residues 77 - 82 (chain A) in PDB entry 5I4E
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLY* 3.0 31.9 + - - +
76A GLU* 1.3 79.5 - - + +
78A ALA* 1.3 69.3 + - - +
90A ARG* 3.1 43.3 + - + +
91A LEU 3.6 21.1 - - - +
92A PRO* 4.3 1.3 - - + -
93A ARG* 4.3 1.9 - - - +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.4 15.0 - - + -
72A ASP 3.8 12.1 - - - +
73A GLU* 4.9 2.7 - - - -
74A GLY 4.7 0.7 - - - +
77A GLU* 1.3 76.8 - - - +
79A GLU* 1.3 60.4 + - - +
80A VAL* 5.0 0.7 - - - -
89A LEU 3.7 0.7 - - - +
90A ARG* 3.4 3.8 - - - -
91A LEU* 2.9 39.6 + - + +
93A ARG* 4.2 22.0 - - + -
96A ILE* 4.4 11.4 - - + -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.8 1.4 - - - +
71A ARG* 2.9 58.1 + - + +
72A ASP* 3.2 24.7 + - + +
78A ALA* 1.3 74.3 - - - +
80A VAL* 1.3 69.7 + - - +
88A ARG* 4.7 13.2 + - - +
89A LEU 3.3 12.7 - - - +
90A ARG* 3.7 26.6 + - + +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 4.2 7.9 - - + -
58A VAL* 4.0 19.1 - - + -
68A ALA* 3.9 10.1 - - + -
69A ALA 3.3 9.9 - - - +
70A LEU* 4.0 12.6 - - + -
71A ARG* 4.0 4.3 - - - +
78A ALA 5.0 1.8 - - - +
79A GLU* 1.3 82.3 - - - +
81A GLU* 1.3 60.5 + - - +
82A LEU* 4.2 1.8 - - + +
87A ARG 4.0 0.2 - - - +
88A ARG* 3.4 5.4 - - - +
89A LEU* 2.9 62.7 + - + +
91A LEU* 4.3 2.5 - - + -
96A ILE* 3.7 28.0 - - + -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 3.2 2.6 - - - -
69A ALA* 2.7 50.9 + - + +
71A ARG* 5.3 13.2 + - + +
80A VAL* 1.3 75.9 - - - +
82A LEU* 1.3 68.5 + - - +
83A ALA* 4.5 3.5 - - - +
86A GLY* 3.4 30.4 - - - +
87A ARG 3.4 4.7 - - - -
88A ARG* 4.4 10.0 - - + +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.8 24.2 - - + -
66A GLU* 3.7 41.5 - - + +
67A ALA 3.9 5.6 - - - +
68A ALA* 4.1 3.8 - - + -
80A VAL* 4.2 2.2 - - + -
81A GLU* 1.3 74.8 - - - +
83A ALA* 1.3 61.5 + - - +
84A GLU 4.6 0.2 - - - +
85A SER* 3.9 25.4 - - - +
86A GLY* 2.9 26.9 + - - -
87A ARG* 2.8 49.8 + - + +
89A LEU* 5.0 12.8 - - + -
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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