Contacts of the strand formed by residues 87 - 92 (chain E) in PDB entry 6S1M
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 ILE 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E ARG* 3.6 51.6 - - + +
6E LEU 3.7 13.2 - - - +
7E VAL* 4.2 28.0 - - + +
85E GLU 4.9 3.1 - - - +
86E ASP* 1.3 72.8 - - - +
88E ILE* 1.3 63.1 + - - +
89E THR* 4.4 1.1 + - - +
102E VAL 3.4 2.3 - - - +
103E PHE* 3.3 4.0 - - - -
104E GLU* 2.7 49.2 + - + +
105E ALA 6.2 0.2 - - - +
106E PRO* 5.8 7.0 - - + -
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Residues in contact with ILE 88 (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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4E ALA 3.9 0.2 - - - +
5E ARG* 3.7 0.3 - - - -
6E LEU* 2.8 40.1 + - + +
9E GLY* 3.2 39.7 - - - +
12E LEU* 4.0 23.8 - - + -
13E LYS* 4.6 2.0 - - + -
79E LEU* 4.1 19.7 - - + -
82E ALA* 4.4 10.8 - - + -
83E GLY 5.6 0.7 - - - +
86E ASP 4.0 5.8 - - - +
87E ILE* 1.3 75.6 - - - +
89E THR* 1.3 71.1 + - - +
90E LEU* 4.3 8.7 - - + -
101E LEU* 5.0 0.9 - - + -
102E VAL 3.5 3.1 - - - +
103E PHE* 3.5 31.6 - - + -
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Residues in contact with THR 89 (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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3E GLU* 4.3 20.2 - - + +
4E ALA 3.2 16.6 - - - +
5E ARG* 3.7 26.6 + - + +
87E ILE* 4.4 1.9 + - - +
88E ILE* 1.3 79.6 + - - +
90E LEU* 1.3 69.4 + - - +
91E ARG* 3.7 8.4 + - + +
100E ALA 3.1 13.7 - - - +
101E LEU* 3.6 1.2 - - - -
102E VAL* 2.9 38.6 + - + +
104E GLU* 4.1 7.2 + - - -
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Residues in contact with LEU 90 (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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2E PHE* 3.5 31.6 - - + -
3E GLU* 3.3 0.9 - - - -
4E ALA* 2.8 36.5 + - + +
12E LEU* 3.6 33.2 - - + -
28E TRP* 5.3 9.9 - - + -
30E ILE* 5.7 1.3 - - + -
35E VAL* 4.9 10.8 - - + -
52E LEU* 6.5 0.9 - - + -
57E PHE* 5.2 10.8 - - + -
68E MET* 6.3 0.4 - - + -
75E MET* 4.9 9.2 - - + -
88E ILE* 4.3 4.3 - - + -
89E THR* 1.3 78.1 - - - +
91E ARG* 1.3 61.1 + - - +
99E LEU* 4.5 15.5 - - + -
100E ALA 3.5 2.7 - - - -
101E LEU* 4.3 20.9 - - + -
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Residues in contact with ARG 91 (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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1E MET* 5.4 3.4 - - + -
2E PHE* 3.1 15.9 - - - +
3E GLU* 2.8 37.8 + - - +
89E THR* 4.6 8.7 - - + +
90E LEU* 1.3 76.9 - - - +
92E ALA* 1.3 65.0 + - - +
93E GLU* 4.7 7.6 - - - +
98E THR 4.8 0.2 - - - +
99E LEU* 3.7 3.3 - - - +
100E ALA* 2.9 47.6 + - + +
102E VAL* 3.7 29.1 - - + +
113E ASP* 4.3 7.9 + - - -
115E GLU* 5.1 1.2 + - - -
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Residues in contact with ALA 92 (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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1E MET* 3.6 0.7 - - - +
2E PHE* 2.8 33.0 + - + +
66E LEU* 3.8 24.9 - - + -
68E MET* 4.2 9.9 - - - -
91E ARG* 1.3 75.4 - - - +
93E GLU* 1.3 80.0 + - - +
96E ALA 5.8 0.2 - - - +
98E THR 4.4 9.6 - - - +
99E LEU* 3.8 16.4 - - + -
118E LEU* 5.8 1.3 - - + -
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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