Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 1SR5
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 LYS 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ARG* 4.6 1.1 - - - -
68C ILE* 2.9 42.7 + - + +
78C ASN* 5.4 8.7 + - - +
79C ILE 4.5 6.7 + - - +
80C GLU* 1.3 82.5 + - - +
82C ILE* 1.3 67.4 + - - +
83C SER* 6.2 0.2 - - - -
112C VAL* 4.4 26.5 - - + -
113C ALA* 4.1 29.2 - - + +
118C ILE* 5.1 5.8 - - + -
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 4.1 27.1 - - + -
66C VAL 3.5 6.5 - - - +
67C ARG* 4.0 19.3 - - + +
76C TYR* 4.3 16.2 - - + +
80C GLU* 4.1 19.7 - - + +
81C LYS* 1.3 81.3 - - - +
83C SER* 1.3 73.6 + - - +
84C MET* 4.9 7.4 - - + -
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 3.6 3.5 - - - +
66C VAL* 3.1 36.1 + - - +
68C ILE* 4.4 9.0 - - - -
82C ILE* 1.3 83.9 - - - +
84C MET* 1.3 75.0 + - - +
108C LEU* 3.6 23.4 - - - +
109C LYS 4.4 0.9 + - - -
110C LYS* 3.8 18.2 + - - +
112C VAL* 6.0 3.1 - - - -
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Residues in contact with MET 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 3.5 35.2 - - - +
61C GLU 5.8 0.2 - - - +
62C ASN* 6.6 0.4 - - - -
64C LEU 5.2 2.0 - - - +
65C LEU* 4.4 22.4 - - - +
82C ILE* 4.9 6.5 - - + -
83C SER* 1.3 84.8 + - - +
85C LEU* 1.3 71.1 + - - +
108C LEU* 3.5 0.3 - - - -
109C LYS* 2.9 38.4 + - + +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 5.0 0.7 - - + -
61C GLU* 3.6 29.5 + - - +
62C ASN* 5.2 2.4 - - - +
64C LEU* 3.4 28.4 + - + +
65C LEU* 5.0 0.2 - - - -
66C VAL* 4.1 19.7 - - + -
84C MET* 1.3 86.6 - - - +
86C GLU* 1.3 61.9 + - - +
87C LYS 4.4 5.2 - - - +
88C ILE* 3.6 6.5 - - + -
106C MET* 3.1 47.1 - - + +
107C LYS 3.6 4.7 - - - +
108C LEU* 3.9 26.2 - - + +
109C LYS* 4.1 7.7 - - - +
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 3.7 8.0 - - - +
85C LEU* 1.3 74.4 - - - +
87C LYS* 1.3 73.1 + - + +
107C LYS* 2.6 30.4 + - + +
108C LEU 3.6 4.0 - - - +
109C LYS* 3.3 50.0 + - - +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 3.2 32.6 + - + -
85C LEU* 3.4 3.0 - - - +
86C GLU* 1.3 91.7 - - + +
88C ILE* 1.3 69.0 + - - +
89C TYR* 3.3 38.1 - - + +
106C MET* 3.4 3.8 - - - +
107C LYS* 2.8 31.9 + - + +
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 3.7 19.3 - - + -
60C THR* 3.8 15.7 - - + +
61C GLU* 3.5 30.9 + - + +
64C LEU* 4.7 0.2 - - + -
85C LEU* 3.6 12.8 - - + -
87C LYS* 1.3 78.7 - - - +
89C TYR* 1.3 81.6 + - - +
90C ILE* 3.6 30.7 - - + -
105C LEU 4.1 1.3 - - - +
106C MET* 3.4 39.3 - - + -
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Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 3.9 28.1 - + - -
87C LYS* 3.3 45.9 - - + +
88C ILE* 1.3 91.3 - - - +
90C ILE* 1.3 63.9 + - - +
104C ALA* 3.5 0.6 - - - -
105C LEU* 3.0 37.2 + - + +
107C LYS* 4.5 4.3 - - + +
237C TRP* 2.9 25.7 - - + -
241C VAL* 4.7 18.8 - - + -
244C GLN* 5.5 7.7 + - - -
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.3 7.9 - - + +
59C LEU* 3.4 42.6 - - + -
60C LEU* 4.6 18.8 - - + -
88C ILE* 3.6 11.7 - - + -
89C TYR* 1.3 75.3 - - - +
91C HIS* 1.3 78.3 + - - +
92C PRO* 3.5 2.9 - - - +
94C TYR* 3.8 27.6 - - + -
103C ILE 4.4 4.5 - - - +
104C ALA* 3.7 9.2 - - + -
237C TRP* 3.7 5.4 + - - -
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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