Contacts of the strand formed by residues 102 - 107 (chain H) in PDB entry 1FSK
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 THR 102 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6H GLN* 3.4 24.2 - - + +
7H SER 5.0 2.0 - - - +
8H PRO* 2.7 30.7 + - - +
9H LYS 3.5 6.9 + - - -
10H SER* 4.1 4.9 + - - -
21H LEU* 3.3 40.4 - - + +
22H SER 5.4 1.1 - - - +
85H ASP* 3.2 3.9 + - - -
86H TYR* 3.1 28.4 + - + +
101H GLY* 1.3 72.5 - - - -
103H LYS* 1.3 63.3 + - - +
104H LEU 3.5 1.6 + - - -
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Residues in contact with LYS 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LYS 3.2 8.7 + - - +
10H SER* 3.3 12.0 - - - -
11H MET* 2.9 27.1 + - - +
21H LEU* 6.1 0.2 - - - -
83H LEU* 5.6 4.0 - - + -
84H ALA 3.7 13.2 - - - +
85H ASP* 3.6 14.4 + - + +
101H GLY 4.2 0.2 - - - -
102H THR* 1.3 70.5 - - - +
104H LEU* 1.3 63.5 + - - +
105H GLU* 3.6 40.0 + - + +
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Residues in contact with LEU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H MET* 3.7 21.3 - - + +
13H VAL* 4.5 8.5 - - + -
19H VAL* 4.3 24.2 - - + -
21H LEU* 5.4 7.0 - - + -
75H ILE* 4.0 15.7 - - + -
78H VAL* 4.0 24.0 - - + -
82H ASP 3.2 23.1 - - - +
83H LEU* 2.8 32.6 - - - +
84H ALA 2.8 19.7 + - - +
86H TYR* 3.7 19.1 - - + -
102H THR 3.5 2.3 + - - +
103H LYS* 1.3 73.2 - - - +
105H GLU* 1.3 58.1 + - - +
106H ILE* 5.5 0.9 - - + +
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Residues in contact with GLU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H SER* 3.7 23.2 + - - -
11H MET 2.6 15.9 + - - +
12H SER* 2.9 42.4 + - - +
13H VAL* 3.1 6.2 + - - +
83H LEU* 4.0 1.1 - - + -
103H LYS* 3.6 38.5 + - + +
104H LEU* 1.3 80.5 - - - +
106H ILE* 1.3 63.7 + - - +
166H GLN* 3.7 11.4 - - - +
173H TYR* 4.0 14.3 + - - +
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H SER* 5.5 0.7 - - - -
13H VAL* 3.2 10.3 - - + +
15H VAL* 3.9 20.4 - - + +
78H VAL* 4.6 11.2 - - + -
79H GLN 3.1 12.1 - - - +
80H ALA* 3.1 44.6 - - - +
83H LEU* 4.0 17.9 - - + +
104H LEU* 5.6 1.1 - - + -
105H GLU* 1.3 74.8 - - - +
107H LYS* 1.3 73.4 + - - +
108H ARG* 5.2 0.2 - - + -
140H TYR* 3.7 1.9 + - - -
166H GLN* 2.3 39.7 + - - +
171H SER* 3.4 25.7 - - - +
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Residues in contact with LYS 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H SER* 5.0 8.5 - - - +
13H VAL* 2.8 19.6 + - - +
14H SER* 3.5 35.2 + - - +
15H VAL* 4.2 3.6 + - - +
105H GLU 3.9 0.2 + - - -
106H ILE* 1.3 79.0 - - - +
108H ARG* 1.3 72.5 + - - +
140H TYR* 3.0 16.8 - - + +
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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