Contacts of the strand formed by residues 82 - 88 (chain L) in PDB entry 1S5E
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 VAL 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L LEU* 3.8 5.0 - - + -
21L ASN* 2.8 27.8 + - - -
22L ASP 3.0 18.3 + - - +
24L ILE* 4.0 30.7 - - + -
42L PHE* 4.0 11.4 - - + -
75L ALA* 5.4 1.6 - - + -
80L ALA 3.9 9.4 - - - +
81L LYS* 1.3 71.9 - - - +
83L GLU* 1.3 60.5 + - - +
84L LYS 3.9 22.4 - - - +
85L LEU* 4.2 11.4 - - + -
99L ILE* 4.0 21.5 - - + -
100L SER 3.7 6.5 - - - +
101L MET* 4.3 4.0 - - + -
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Residues in contact with GLU 83 (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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5L ILE* 4.5 2.3 - - - +
19L THR* 3.7 3.6 - - + +
20L LEU 2.9 25.9 + - - -
21L ASN* 3.2 24.0 + - - +
81L LYS 3.8 3.2 + - - -
82L VAL* 1.3 73.2 - - - +
84L LYS* 1.3 84.0 + - + +
100L SER* 2.7 42.6 + - - +
102L ALA* 4.3 27.0 - - + +
103L ASN* 5.7 2.4 + - - +
26M SER* 6.0 1.2 - - - -
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Residues in contact with LYS 84 (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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5L ILE* 3.7 26.8 - - + +
6L THR* 4.0 12.2 + - - +
17L ILE* 3.7 21.7 - - + +
18L HIS 3.3 5.6 - - - +
19L THR* 2.8 38.0 + - - +
20L LEU 4.7 0.2 - - - +
82L VAL* 4.2 1.8 - - - -
83L GLU* 1.3 106.1 - - - +
85L LEU* 1.3 63.2 + - - +
99L ILE* 3.5 6.2 - - - +
100L SER* 2.9 34.7 + - - +
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Residues in contact with LEU 85 (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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5L ILE* 4.3 1.3 - - - -
16L GLN 3.7 0.7 - - - +
17L ILE* 3.4 4.4 - - - +
18L HIS* 2.8 35.4 + - + +
20L LEU* 3.9 17.7 - - + +
40L ILE* 4.3 6.7 - - + -
42L PHE* 4.0 10.1 - - + -
48L PHE* 3.6 44.2 - - + -
82L VAL* 4.2 3.1 - - + -
84L LYS* 1.3 73.2 - - - +
86L CYS* 1.3 58.8 + - - +
87L VAL* 4.0 11.5 + - + +
96L ILE* 4.2 19.3 - - + -
98L ALA 3.5 9.4 - - - +
99L ILE* 3.7 33.4 - - + -
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Residues in contact with CYS 86 (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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5L ILE* 3.8 14.3 - - + +
8L LEU* 5.0 3.1 - - - -
9L CYS* 2.1 51.8 - - + -
12L TYR* 5.8 2.7 - - - -
15L THR* 4.1 6.5 - - - -
16L GLN 3.5 4.3 - - - -
17L ILE* 4.1 1.1 - - + -
85L LEU* 1.3 71.9 - - - +
87L VAL* 1.3 62.1 + - - +
96L ILE* 3.8 0.7 - - - +
97L ALA* 2.8 38.2 + - - -
98L ALA* 2.9 29.5 + - + +
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Residues in contact with VAL 87 (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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15L THR* 3.2 9.4 + - - -
16L GLN* 2.9 42.2 + - + +
18L HIS* 3.4 33.0 - - + +
48L PHE* 3.7 26.9 - - + -
85L LEU* 4.1 10.8 - - + -
86L CYS* 1.3 80.4 - - - +
88L TRP* 1.3 62.2 + - - +
89L ASN 3.7 0.4 + - - +
94L HIS* 3.8 20.4 - - + -
95L ALA 3.1 13.0 - - - +
96L ILE* 4.3 6.5 - - + -
97L ALA 4.2 0.7 - - - +
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Residues in contact with TRP 88 (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 TYR* 4.6 13.5 - + - +
13L HIS* 3.8 16.0 + + - -
14L ASN* 3.2 13.5 - - + -
15L THR* 3.5 16.6 + - - -
51L GLU* 4.5 10.5 - - - +
57L HIS* 5.6 5.8 - + - -
61L GLN* 4.1 13.0 - - - -
87L VAL* 1.3 71.0 - - - +
89L ASN* 1.3 59.2 + - - +
90L ASN* 3.4 18.5 + - - +
91L LYS* 3.9 4.8 + - + -
94L HIS* 3.6 6.1 - - - -
95L ALA* 2.8 57.8 + - + +
96L ILE 3.5 20.4 - - - -
97L ALA* 3.5 23.6 - - + -
31M LEU* 3.6 19.3 - - + -
32M ALA* 4.2 15.0 - - + -
33M GLY 5.1 1.1 - - - -
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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