Contacts of the strand formed by residues 81 - 90 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65F VAL 2.9 14.0 - - - +
66F ARG* 3.1 2.1 - - - -
67F LEU* 3.0 41.6 + - + +
70F GLU* 4.7 1.2 + - - -
79F ASN* 5.4 7.2 + - - +
80F GLU* 1.3 81.1 - - - +
82F PHE* 1.3 65.2 + - - +
83F ILE* 3.8 8.5 - - + +
112F ALA* 4.3 10.7 - - - +
113F SER* 2.8 39.0 + - - -
115F ASN* 5.7 0.8 + - - +
118F VAL* 3.3 27.0 - - - +
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Residues in contact with PHE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LYS* 3.2 30.1 + - + +
89C ILE* 4.6 29.8 - - + -
245C ASN* 3.7 27.5 + - - +
34F ASN* 5.6 5.6 - - - -
64F GLN* 5.6 13.7 - - + +
65F VAL 3.4 5.8 - - - -
66F ARG* 3.3 44.9 - - + -
70F GLU* 4.2 1.8 - - - -
80F GLU* 3.4 34.1 - - + -
81F GLN* 1.3 78.2 - - - +
83F ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LYS* 4.8 5.8 - - - +
64F GLN* 3.5 3.8 - - - -
65F VAL* 2.8 43.2 + - - +
67F LEU* 3.9 22.7 - - + -
81F GLN* 4.4 11.2 - - + +
82F PHE* 1.3 77.3 - - - +
84F SER* 1.3 76.8 + - - +
108F LEU* 3.8 16.4 - - + -
109F LYS* 4.4 1.6 - - + -
110F SER* 3.7 42.2 - - - +
111F ALA 4.6 2.2 - - - +
112F ALA* 4.1 19.5 - - + -
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Residues in contact with SER 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C SER* 2.7 40.8 + - - -
87C LYS* 3.8 12.3 - - - +
63F ILE 4.1 6.3 - - - -
64F GLN* 4.6 5.2 - - - +
82F PHE 4.4 0.4 + - - -
83F ILE* 1.3 79.8 - - - +
85F ALA* 1.3 55.7 + - - +
108F LEU* 3.7 0.6 - - - -
109F LYS* 2.7 55.0 + - - +
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Residues in contact with ALA 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLY* 5.7 2.9 - - - -
63F ILE* 3.3 26.8 + - + +
65F VAL* 4.8 4.7 - - + -
83F ILE 3.8 0.2 + - - -
84F SER* 1.3 73.9 - - - +
86F SER* 1.3 65.3 + - - +
87F LYS 4.8 0.2 - - - +
88F SER* 4.0 15.1 + - - +
106F ILE* 3.4 31.9 - - + -
107F LYS 3.3 5.2 - - - +
108F LEU* 4.3 1.6 - - - +
109F LYS* 4.9 1.4 - - - -
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Residues in contact with SER 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ALA* 1.3 75.0 - - - +
87F LYS* 1.3 81.3 + - - +
88F SER 4.3 0.3 + - - -
107F LYS* 2.6 21.3 + - - -
108F LEU 4.4 0.4 - - - -
109F LYS* 3.6 27.3 - - - +
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Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 5.2 5.9 - - - +
51F TRP* 4.7 0.7 - - + -
86F SER* 1.3 99.3 - - - +
88F SER* 1.3 61.9 + - - +
89F ILE* 3.7 23.8 - - + -
105F LEU 3.9 1.2 - - - +
106F ILE* 3.6 1.7 - - - +
107F LYS* 2.8 54.8 + - + +
245F ASN* 3.8 27.2 + - + +
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Residues in contact with SER 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F TYR* 3.5 38.5 - - - -
60F LYS 4.8 4.7 + - - -
62F GLY 5.6 1.4 + - - -
63F ILE* 4.7 11.4 + - - +
85F ALA* 4.0 19.6 + - - +
86F SER 4.2 1.0 + - - -
87F LYS* 1.3 72.6 + - - +
89F ILE* 1.3 60.6 + - - +
90F VAL* 3.6 1.9 + - - +
104F MET* 4.7 3.6 - - - -
105F LEU 3.6 4.7 - - - -
106F ILE* 4.5 12.3 - - - +
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F TRP* 3.8 15.7 - - + -
87F LYS* 4.2 15.7 - - + -
88F SER* 1.3 71.6 - - - +
90F VAL* 1.3 69.8 + - - +
92F PRO* 6.1 0.2 - - + -
104F MET* 3.5 2.8 - - - -
105F LEU* 2.8 40.6 + - + +
237F TRP* 3.8 19.3 - - + -
241F THR* 3.7 14.8 - - + -
245F ASN* 3.5 37.7 - - + +
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Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ALA* 3.6 21.8 - - + +
59F TYR* 3.4 44.9 - - + -
88F SER 3.6 1.8 + - - -
89F ILE* 1.3 81.6 - - - +
91F HIS* 1.3 79.0 + - - +
92F PRO* 3.3 5.5 - - - +
94F TYR* 4.1 13.5 - - + -
104F MET* 3.9 11.9 - - - -
237F TRP* 4.4 0.9 - - - -
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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