Contacts of the strand formed by residues 87 - 93 (chain F) in PDB entry 1CKL
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 TYR 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62F ARG* 3.7 20.0 + - - -
80F ASN* 3.2 37.2 - - + +
82F THR* 3.3 31.2 - - + +
84F GLU* 3.1 39.1 + - + +
85F PHE 3.4 13.4 - - - -
86F GLY* 1.3 85.8 - - - +
88F GLN* 1.3 65.8 + - - +
106F TYR* 3.8 4.0 - - - +
107F CYS* 3.0 29.0 + - - +
116F TRP* 5.0 0.7 - - - -
1R NAG 3.8 26.0 - - + +
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Residues in contact with GLN 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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78F PRO* 3.8 3.6 - - - +
79F ALA* 3.3 26.1 + - + +
80F ASN* 3.1 6.5 + - - +
82F THR 5.1 0.8 - - - +
86F GLY 5.8 0.4 + - - -
87F TYR* 1.3 79.9 - - - +
89F MET* 1.3 60.2 + - - +
90F HIS* 3.2 23.4 + - + +
104F ILE* 3.7 17.0 - - + +
105F LEU 3.0 14.8 - - - +
106F TYR* 3.3 25.9 - - + -
116F TRP* 4.1 6.5 - - - -
1R NAG 3.5 22.1 + - - +
2R NAG 3.0 30.7 + - - +
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Residues in contact with MET 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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68F ILE* 3.5 23.3 - - + +
76F ALA* 4.1 4.5 - - - -
77F VAL 3.4 33.7 - - - -
78F PRO* 3.5 5.8 - - + -
83F TYR* 3.2 42.2 - - + +
88F GLN* 1.3 73.3 - - - +
90F HIS* 1.3 61.9 + - - +
91F PHE* 3.6 29.5 - - + -
103F GLU 4.0 0.3 - - - +
104F ILE* 3.4 6.9 - - - +
105F LEU* 2.9 30.1 + - + +
116F TRP* 3.3 32.7 - - + -
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Residues in contact with HIS 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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77F VAL* 2.9 45.4 + - + +
79F ALA* 3.7 26.9 - - + +
88F GLN* 3.2 27.1 + - + -
89F MET* 1.3 79.3 - - - +
91F PHE* 1.3 73.6 + - - +
92F ILE* 5.6 3.1 - - + -
103F GLU* 3.6 17.5 + - - +
104F ILE* 3.9 23.1 - - + +
1R NAG 4.2 9.5 - - - -
2R NAG 5.3 2.9 - - - -
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Residues in contact with PHE 91 (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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68F ILE* 3.9 24.0 - - + -
71F PRO* 4.4 13.5 - - + -
75F GLN 3.7 6.3 - - - +
76F ALA* 4.0 17.0 - - + -
89F MET* 3.6 29.6 - - + -
90F HIS* 1.3 77.4 - - - +
92F ILE* 1.3 66.4 + - - +
99F LEU* 3.5 21.9 - - + +
102F GLU 3.9 1.3 - - - -
103F GLU* 3.0 35.9 + - - +
105F LEU* 4.2 20.9 - - + -
120F PRO* 4.0 14.1 - - + -
121F PRO* 3.5 44.4 - - + -
123F CYS* 6.1 2.5 - - - -
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Residues in contact with ILE 92 (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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74F GLY* 3.5 2.6 - - - -
75F GLN* 3.4 30.3 + - + +
77F VAL* 4.7 16.6 - - + -
90F HIS* 5.6 3.1 - - + -
91F PHE* 1.3 79.4 - - - +
93F CYS* 1.3 76.7 + - - +
94F ASN* 4.5 1.2 - - - +
99F LEU* 4.7 2.0 - - - -
123F CYS* 4.4 1.4 - - - -
2M NAG 6.3 2.0 - - + -
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Residues in contact with CYS 93 (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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92F ILE* 1.3 87.5 - - - +
94F ASN* 1.3 65.6 + - - +
95F GLU* 3.8 1.2 + - - -
97F TYR* 3.4 26.9 - - + +
98F TYR 3.7 0.7 - - - -
99F LEU* 3.5 37.9 - - + +
123F CYS* 2.0 53.8 - - - -
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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