Contacts of the strand formed by residues 68 - 76 (chain A) in PDB entry 1FIK
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR* 4.0 15.5 + - - +
64A THR* 3.3 1.5 - - - -
65A LEU* 3.1 33.6 + - + +
66A GLY 3.2 2.0 + - - +
67A GLY* 1.3 75.8 - - - +
69A LYS* 1.3 86.6 + - - +
70A CYS* 3.6 6.0 + - - -
89A THR* 4.2 25.1 - - + -
90A LYS 3.5 18.2 + - - -
113A MET* 5.1 6.2 - - + +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASN 3.4 25.6 + - - -
62A GLY 4.5 0.2 - - - -
63A LEU* 3.7 21.6 + - - +
64A THR* 3.9 16.7 - - + +
67A GLY 3.7 4.6 + - - -
68A GLN* 1.3 86.9 + - - +
70A CYS* 1.3 65.7 + - - +
90A LYS* 3.2 51.3 + - + +
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Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY* 3.4 5.2 - - - -
63A LEU* 2.8 34.0 + - + +
65A LEU* 4.3 19.1 - - - -
68A GLN* 3.7 16.2 - - - -
69A LYS* 1.3 82.3 - - - +
71A SER* 1.3 59.2 + - - +
87A LEU* 3.6 31.4 - - + -
88A ARG 3.7 8.1 - - - +
89A THR* 4.3 17.0 - - - -
90A LYS* 3.5 13.7 + - - +
100A VAL* 5.0 4.0 - - - -
113A MET* 6.4 0.2 - - - -
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR 5.7 1.4 + - - -
62A GLY* 4.4 4.0 - - - -
70A CYS* 1.3 75.4 - - - +
72A VAL* 1.3 64.2 + - - +
73A ILE* 4.8 5.8 - - - +
87A LEU* 3.0 27.5 - - - +
88A ARG* 3.1 23.5 + - - -
89A THR 5.2 0.4 - - - -
90A LYS* 3.8 26.7 + - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.9 38.6 + - + +
59A TYR* 3.5 27.6 + - + +
62A GLY* 4.6 5.3 - - - -
63A LEU* 4.0 26.2 - - + -
71A SER* 1.3 79.1 + - - +
73A ILE* 1.3 65.3 + - - +
74A ARG 3.8 25.8 - - - +
75A ASP* 4.2 12.1 - - + -
85A MET* 4.7 5.6 - - + -
86A ASP 3.9 3.6 - - - +
87A LEU* 4.3 7.2 - - + -
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.1 20.0 + - - -
71A SER* 4.9 6.7 - - - +
72A VAL* 1.3 76.7 - - - +
74A ARG* 1.3 89.0 + - + +
86A ASP* 2.9 21.3 + - + +
87A LEU 4.3 1.6 - - - +
88A ARG* 3.5 42.2 - - + +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.1 8.1 - - - +
72A VAL* 3.6 4.4 - - - +
73A ILE* 1.3 103.1 - - + +
75A ASP* 1.3 61.5 + - - +
76A SER* 4.1 6.7 - - - +
82A GLU* 5.6 6.3 - - - -
84A SER 5.7 0.9 - - - +
85A MET* 3.4 8.2 - - - +
86A ASP* 3.0 57.7 + - + +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 2.7 52.2 + - - +
58A PHE* 4.2 8.3 - - + -
59A TYR* 4.4 11.0 + - + +
72A VAL* 4.2 13.7 - - + +
74A ARG* 1.3 77.9 - - - +
76A SER* 1.3 58.6 + - - +
77A LEU* 3.1 5.5 - - - +
79A GLN* 3.3 17.3 + - - +
84A SER 4.2 1.1 - - - -
85A MET* 3.0 23.8 - - + +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 5.2 5.4 - - - +
75A ASP* 1.3 76.4 + - - +
77A LEU* 1.3 62.2 + - - +
78A LEU 3.3 2.7 - - - -
79A GLN* 3.0 30.1 + - - +
82A GLU* 3.4 36.6 + - - +
83A PHE 2.9 20.6 + - - -
84A SER 2.9 14.6 + - - -
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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