Contacts of the strand formed by residues 77 - 82 (chain E) in PDB entry 6H7L
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 77 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E VAL 3.6 1.6 - - - +
26E ASP* 3.6 1.7 - - - +
27E PHE* 3.1 37.8 + - + -
72E ILE* 3.4 37.3 - - + +
73E ARG 5.2 0.2 + - - -
74E GLY 3.1 20.1 + - - -
75E ILE* 3.9 1.0 - - - +
76E PRO* 1.3 70.8 - - - +
78E LEU* 1.3 63.8 + - - +
79E LEU* 4.0 20.4 - - + -
89E THR* 4.1 2.7 - - - +
90E LYS 3.5 4.5 - - - +
91E VAL* 3.4 28.0 - - + +
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Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 4.1 15.9 - - + -
25E VAL 3.3 6.1 - - - +
26E ASP* 3.7 35.2 - - + +
38E ILE* 5.3 13.9 - - + -
42E LEU* 4.2 19.7 - - + -
76E PRO* 5.4 4.9 - - + +
77E THR* 1.3 72.9 - - - +
79E LEU* 1.3 62.5 + - - +
80E LEU 3.9 1.2 + - - -
88E ALA 4.1 0.2 - - - +
89E THR* 3.6 2.9 - - - -
90E LYS* 2.7 42.8 + - + +
92E GLY 5.5 4.0 - - - +
94E LEU* 4.6 13.7 - - + -
99E LEU* 3.7 31.6 - - + -
102E PHE* 4.5 5.8 - - + -
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Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE 3.6 1.9 - - - +
24E LEU* 4.2 1.3 - - - -
25E VAL* 2.9 36.4 + - + +
27E PHE* 3.7 21.1 - - + -
70E TYR* 4.1 22.4 - - + +
72E ILE* 4.1 13.0 - - + -
77E THR* 3.9 15.2 - - + -
78E LEU* 1.3 70.8 - - - +
80E LEU* 1.3 60.2 + - - +
81E PHE* 3.4 29.7 - - + -
86E VAL* 4.0 15.0 - - + -
88E ALA 3.7 2.0 - - - -
89E THR* 3.2 32.1 - - - +
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Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA* 4.2 17.7 - - + -
23E ILE 3.6 20.0 - - - +
24E LEU* 4.1 20.4 - - + +
53E LEU* 4.7 8.7 - - + -
78E LEU 3.9 1.6 + - - -
79E LEU* 1.3 70.3 - - - +
81E PHE* 1.3 62.0 + - - +
82E LYS* 4.5 14.8 - - - -
86E VAL* 4.0 1.2 - - - -
87E ALA* 3.1 26.5 + - + +
88E ALA 3.0 18.8 + - - +
102E PHE* 4.5 9.6 - - + -
103E LEU* 4.6 13.5 - - + -
106E ASN* 3.6 36.8 - - + +
107E LEU* 4.9 5.6 - - + -
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Residues in contact with PHE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 4.1 6.7 - + - -
16E VAL* 3.4 28.3 - - + +
17E LEU* 3.8 27.4 - - + -
21E GLY 4.2 0.8 - - - +
22E ALA* 3.3 3.8 - - - +
23E ILE* 2.7 40.8 + - + +
25E VAL* 4.0 11.4 - - + -
70E TYR* 3.7 29.2 - + - -
79E LEU* 3.4 39.5 - - + -
80E LEU* 1.3 76.4 - - - +
82E LYS* 1.3 69.0 + - - +
83E ASN 4.4 0.2 - - - -
84E GLY 4.6 7.0 - - - +
85E GLU 3.4 13.9 - - - +
86E VAL* 3.9 20.4 - - + -
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Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLY 4.6 4.9 - - - -
22E ALA* 4.2 17.7 - - + +
80E LEU* 4.2 15.5 + - + +
81E PHE* 1.3 79.6 - - - +
83E ASN* 1.3 76.2 + - - +
84E GLY 3.3 1.1 - - - -
85E GLU* 2.9 26.8 + - - +
87E ALA* 4.2 25.2 - - + +
106E ASN* 2.7 32.6 + - - +
107E LEU* 4.5 5.1 - - - +
109E GLU* 3.6 23.7 + - - +
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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