Contacts of the strand formed by residues 84 - 90 (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 SER 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 4.9 1.2 - - - +
75A ASP* 4.2 0.2 - - - -
76A SER* 2.9 29.2 + - - -
77A LEU* 3.2 4.4 + - - -
82A GLU* 3.2 28.9 + - - -
83A PHE* 1.3 78.5 - - - +
85A MET* 1.3 60.9 + - - +
86A ASP* 5.4 0.6 - - - -
101A THR* 4.3 9.0 - - - -
102A VAL 3.0 5.4 - - - -
103A THR* 3.4 20.6 - - - -
124A ASN* 3.8 13.1 + - - -
128A TYR* 4.7 5.9 - - - -
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Residues in contact with MET 85 (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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50A LEU* 4.2 26.5 - - + +
55A ARG* 3.3 13.9 - - - +
58A PHE* 4.9 3.6 - - + -
63A LEU* 4.2 16.2 - - - -
72A VAL* 4.7 8.3 - - + -
74A ARG 3.4 14.4 - - - +
75A ASP* 3.0 28.3 - - + +
77A LEU* 3.3 23.3 - - + -
84A SER* 1.3 75.5 - - - +
86A ASP* 1.3 65.1 + - - +
87A LEU* 3.7 19.6 - - + +
100A VAL 3.8 0.5 - - - +
101A THR* 3.2 4.5 - - - +
102A VAL* 2.6 45.4 + - + +
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Residues in contact with ASP 86 (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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72A VAL* 3.8 0.9 - - - -
73A ILE* 2.9 30.6 + - + -
74A ARG* 3.0 54.3 + - + +
84A SER* 5.4 0.7 - - - -
85A MET* 1.3 71.4 - - - +
87A LEU* 1.3 62.8 + - - +
100A VAL 3.4 4.5 - - - +
101A THR* 2.8 30.1 + - - +
120A GLY* 6.2 1.8 - - - -
124A ASN* 2.8 30.6 + - - +
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Residues in contact with LEU 87 (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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50A LEU* 5.5 0.2 - - + -
63A LEU* 3.7 33.2 - - + -
65A LEU* 4.6 3.6 - - + -
70A CYS* 3.6 29.8 - - + -
71A SER 3.0 13.7 - - - +
72A VAL* 4.3 4.5 - - + -
73A ILE* 4.3 2.0 - - - +
85A MET* 3.7 27.8 - - + +
86A ASP* 1.3 78.5 - - - +
88A ARG* 1.3 71.3 + - - +
99A ASN* 3.7 4.7 - - - +
100A VAL* 2.8 44.1 + - + +
102A VAL* 3.9 24.7 - - + -
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Residues in contact with ARG 88 (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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70A CYS* 3.7 0.8 - - - -
71A SER* 3.1 31.2 + - - -
73A ILE* 3.5 30.1 - - + -
87A LEU* 1.3 84.1 - - - +
89A THR* 1.3 69.1 + - - +
97A THR* 2.5 47.9 + - - +
98A PHE 3.1 6.3 - - - -
99A ASN* 2.9 29.8 + - - +
100A VAL* 5.2 0.2 - - - -
140A PO4 4.4 14.7 + - - -
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Residues in contact with THR 89 (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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68A GLN* 4.2 24.5 - - + -
69A LYS 4.0 4.5 - - - -
70A CYS* 4.3 5.2 - - - -
71A SER* 5.2 0.7 - - - -
88A ARG* 1.3 79.7 + - - +
90A LYS* 1.3 60.7 + - - +
91A SER* 4.0 4.0 + - - -
97A THR* 3.5 23.6 - - - +
98A PHE* 2.6 55.2 + - + +
100A VAL* 4.1 10.5 - - + +
113A MET* 4.0 25.8 - - + -
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Residues in contact with LYS 90 (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 4.5 8.5 + - - -
62A GLY* 4.7 1.2 - - - -
68A GLN* 3.5 16.1 + - - -
69A LYS* 3.2 48.7 + - + +
70A CYS 3.5 17.6 + - - -
71A SER* 3.8 29.1 + - - +
88A ARG 3.5 0.6 + - - -
89A THR* 1.3 73.8 - - - +
91A SER* 1.3 65.4 + - - +
92A THR* 5.7 2.2 - - + -
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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