Contacts of the strand formed by residues 81 - 90 (chain S) in PDB entry 5JBA
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 GLN 81 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66S VAL 3.6 0.9 - - - +
67S VAL* 3.4 3.6 - - - -
68S ALA* 2.9 40.0 + - + +
79S THR 4.2 5.1 + - - +
80S GLU* 1.4 77.2 - - - +
82S LYS* 1.3 60.3 + - - +
83S ARG* 3.3 24.1 + - - +
112S LEU* 3.5 16.5 - - + +
113S VAL* 2.8 53.7 + - - +
115S ASN* 3.4 18.2 - - - +
118S VAL* 3.6 13.5 - - + +
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Residues in contact with LYS 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S THR* 3.8 29.5 + - - +
66S VAL 3.3 9.4 - - - +
67S VAL* 4.4 14.1 - - + +
80S GLU* 4.2 1.0 - - + -
81S GLN* 1.3 73.2 - - - +
83S ARG* 1.3 84.6 + - - +
84S ASN* 4.9 5.8 - - - +
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Residues in contact with ARG 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S THR* 3.4 7.1 - - - -
66S VAL* 2.9 35.0 + - + +
81S GLN* 3.3 31.0 + - - +
82S LYS* 1.3 101.6 + - - +
84S ASN* 1.3 64.5 + - - +
108S LEU* 4.1 23.6 - - + -
109S ASP* 3.7 11.2 - - - +
110S GLU* 3.0 36.1 + - - +
111S PRO 3.0 20.2 + - - -
112S LEU* 3.7 19.9 - - + +
113S VAL* 4.1 9.3 - - - +
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Residues in contact with ASN 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S LYS* 5.8 4.4 - - - -
64S ILE 4.1 4.2 - - - +
65S THR* 3.5 18.9 - - - +
82S LYS* 4.9 5.8 - - - +
83S ARG* 1.3 75.3 - - - +
85S VAL* 1.3 64.9 - - - +
86S ILE* 5.0 2.2 - - + -
108S LEU* 3.4 5.7 - - - -
109S ASP* 2.8 59.2 + - + +
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Residues in contact with VAL 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S LYS* 5.7 5.0 - - - +
64S ILE* 3.1 39.0 + - + +
66S VAL* 3.8 28.7 - - + -
84S ASN* 1.3 76.3 - - - +
86S ILE* 1.3 63.9 + - - +
87S ARG 3.5 21.8 - - - +
88S ILE* 3.6 25.1 - - + -
106S LEU* 4.0 17.5 - - + -
107S GLU 3.4 6.1 - - - +
108S LEU* 4.3 2.9 - - + -
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Residues in contact with ILE 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50S LYS* 4.3 6.1 - - - +
84S ASN* 4.3 3.1 - - + +
85S VAL* 1.3 76.1 - - - +
87S ARG* 1.3 62.7 + - + +
107S GLU* 2.9 37.8 + - - +
108S LEU 3.8 15.9 - - - +
109S ASP* 3.5 32.8 - - + +
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Residues in contact with ARG 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S TRP* 3.6 24.7 - - - -
85S VAL* 3.5 3.9 - - - +
86S ILE* 1.3 83.4 - - + +
88S ILE* 1.3 68.7 + - - +
89S ILE* 4.3 24.2 - - + +
105S LEU 3.9 0.3 - - - +
106S LEU* 3.4 4.2 - - - -
107S GLU* 2.8 67.2 + - + +
241S LYS 5.1 1.4 + - - -
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Residues in contact with ILE 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59S VAL* 3.7 38.4 - - + +
60S THR 4.5 13.5 - - - +
61S GLY* 5.2 4.3 - - - -
62S VAL 4.6 8.3 - - - +
64S ILE* 4.3 21.5 - - + -
85S VAL* 3.6 21.8 - - + -
87S ARG* 1.3 80.4 - - - +
89S ILE* 1.3 66.5 + - - +
90S PRO* 3.5 18.4 - - + +
105S LEU 3.4 3.8 - - - +
106S LEU* 3.9 8.1 - - + -
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Residues in contact with ILE 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S TRP* 3.8 28.9 - - + -
87S ARG* 4.3 25.8 - - + +
88S ILE* 1.3 76.2 - - - +
90S PRO* 1.3 76.5 - - + +
104S ALA* 3.3 2.9 - - - -
105S LEU* 2.8 40.0 + - + +
237S TRP* 3.5 21.0 - - + +
241S LYS* 4.3 32.1 - - + +
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Residues in contact with PRO 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56S ALA* 4.3 16.6 - - + +
59S VAL* 5.1 6.1 - - + +
60S GLU* 6.5 0.4 - - - -
88S ILE* 3.5 21.3 - - + +
89S ILE* 1.3 97.4 - - + +
91S HIS* 1.3 72.0 + - - +
92S HIS* 3.3 3.8 + - - -
94S TYR* 4.8 7.9 - - + -
104S ALA* 3.7 12.5 - - + -
237S TRP* 4.0 0.4 - - - -
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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