Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 1C9T
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C VAL 3.0 13.5 - - - +
66C ARG* 3.2 2.0 - - - -
67C LEU* 3.0 46.1 + - + +
70C GLU* 4.6 1.0 + - - -
79C ASN* 5.4 6.9 + - - +
80C GLU* 1.3 82.5 - - - +
82C PHE* 1.3 65.0 + - - +
83C ILE* 3.8 7.9 - - + +
112C ALA* 4.3 5.4 - - - +
113C SER* 2.8 38.2 + - - -
115C ASN* 6.1 0.4 - - - +
118C VAL* 3.1 28.1 - - - +
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Residues in contact with PHE 82 (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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34C ASN* 5.8 5.8 - - - -
64C GLN* 5.6 15.9 - - + +
65C VAL 3.3 5.8 - - - +
66C ARG* 3.4 43.3 - - + -
70C GLU* 4.2 1.8 - - - -
76C VAL* 6.3 0.2 - - + -
80C GLU* 3.4 34.1 - - + -
81C GLN* 1.3 77.1 - - - +
83C ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 83 (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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64C GLN* 3.5 3.5 - - - -
65C VAL* 2.8 42.0 + - - +
67C LEU* 3.7 24.2 - - + -
81C GLN* 4.5 10.1 - - + +
82C PHE* 1.3 77.9 - - - +
84C SER* 1.3 79.3 + - - +
85C ALA 3.8 0.2 + - - -
108C LEU* 3.7 20.4 - - + -
109C LYS* 4.4 1.1 - - + -
110C SER* 3.7 43.3 - - - +
111C ALA 4.7 1.6 - - - +
112C ALA* 4.1 14.1 - - + -
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Residues in contact with SER 84 (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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63C ILE 4.1 5.6 - - - -
64C GLN* 4.6 13.4 + - - +
82C PHE 4.3 0.4 + - - -
83C ILE* 1.3 82.0 - - - +
85C ALA* 1.3 56.3 + - - +
108C LEU* 3.6 1.3 - - - -
109C LYS* 2.7 64.9 + - - +
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Residues in contact with ALA 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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62C GLY* 5.7 3.3 - - - -
63C ILE* 3.3 28.5 + - + +
65C VAL* 4.9 3.1 - - + -
83C ILE 3.8 0.2 + - - -
84C SER* 1.3 74.8 - - - +
86C SER* 1.3 64.7 + - - +
87C LYS 4.8 0.2 - - - +
88C SER* 3.9 16.2 + - - +
106C ILE* 3.6 28.5 - - + -
107C LYS 3.4 4.5 - - - +
108C LEU* 4.4 2.2 - - - +
109C LYS* 5.8 0.8 - - - -
109F LYS* 4.8 2.0 + - - -
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Residues in contact with SER 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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85C ALA* 1.3 75.3 - - - +
87C LYS* 1.3 76.1 + - - +
88C SER* 4.2 0.3 + - - -
107C LYS* 2.6 18.2 + - - -
108C LEU 4.3 3.1 - - - -
109C LYS* 3.6 21.4 - - - +
64F GLN* 4.1 2.9 - - - +
84F SER* 2.7 23.7 + - - -
109F LYS* 3.0 36.7 + - - +
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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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51C TRP* 5.0 1.0 - - + -
86C SER* 1.3 100.2 - - - +
88C SER* 1.3 62.6 + - - +
89C ILE* 3.7 23.3 + - + -
105C LEU 4.0 0.2 - - - +
106C ILE* 3.6 2.3 - - - +
107C LYS* 2.8 52.7 + - + +
245C ASN* 3.9 22.7 + - + +
64F GLN* 3.1 10.1 - - - +
82F PHE* 3.2 32.1 + - + +
83F ILE* 4.8 3.8 - - - +
84F SER* 3.8 15.3 - - - +
109F LYS* 5.3 3.6 - - - -
110F SER* 6.0 2.0 - - - -
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Residues in contact with SER 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 TYR* 3.7 31.3 - - - -
60C LYS 4.9 4.4 + - - -
62C GLY* 5.7 1.2 + - - -
63C ILE* 4.9 10.7 + - - +
85C ALA* 3.9 19.8 + - - +
86C SER 4.2 0.6 + - - -
87C LYS* 1.3 73.4 + - - +
89C ILE* 1.3 61.1 + - - +
90C VAL 3.6 3.0 + - - -
104C MET* 4.8 4.0 - - - -
105C LEU 3.6 5.2 - - - -
106C ILE* 4.4 11.5 - - - +
34F ASN* 5.2 0.3 - - - +
38F GLY* 5.7 0.3 - - - -
64F GLN* 2.7 32.1 + - - -
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Residues in contact with ILE 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* 3.7 20.6 - - + -
87C LYS* 3.7 17.2 - - + -
88C SER* 1.3 71.6 - - - +
90C VAL* 1.3 70.9 + - - +
92C PRO* 6.0 0.2 - - + -
104C MET* 3.4 2.5 - - - -
105C LEU* 2.7 40.4 + - + +
237C TRP* 3.7 11.1 - - + -
241C THR* 3.7 16.6 - - + -
245C ASN* 3.5 38.1 - - + +
64F GLN* 4.9 3.8 - - - +
82F PHE* 4.6 28.0 - - + -
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Residues in contact with VAL 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* 3.8 19.1 - - + +
59C TYR* 3.4 46.4 - - + -
88C SER 3.6 1.6 + - - -
89C ILE* 1.3 82.0 - - - +
91C HIS* 1.3 75.8 + - - +
92C PRO* 3.3 7.3 - - - +
94C TYR* 4.0 14.6 - - + -
104C MET* 3.8 14.6 - - + -
237C TRP* 4.4 0.4 - - - -
38F GLY* 4.1 23.5 - - - +
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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