Contacts of the strand formed by residues 95 - 106 (chain J) 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 LEU 95 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90J PRO* 3.2 34.5 - - + +
91J ILE* 3.9 3.4 - - + +
92J GLY* 2.8 31.4 + - - -
93J ASP 4.0 3.0 + - - +
94J THR* 1.3 84.1 + - - +
96J GLU* 1.3 64.4 + - - +
97J LYS 3.9 9.9 - - - +
98J ILE* 3.5 31.0 - - + -
120J TYR* 3.6 25.8 - - + -
121J HIS 3.0 40.8 - - - +
122J THR* 4.4 5.8 - - + -
132J GLN* 5.5 2.9 - - + -
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Residues in contact with GLU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J ILE 4.5 3.3 - - - +
91J ILE* 3.1 24.7 - - - +
94J THR 4.2 0.2 + - - -
95J LEU* 1.3 74.3 - - - +
97J LYS* 1.3 68.7 + - + +
121J HIS* 2.8 29.5 + - + +
122J THR 4.3 11.8 - - - +
123J LYS* 3.2 41.2 + - + -
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Residues in contact with LYS 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J ARG* 3.8 19.2 - - - +
84J SER* 3.8 14.2 + - - -
85J VAL 3.4 15.3 - - - +
86J ILE* 4.6 10.3 - - + +
91J ILE* 3.6 4.7 - - - +
95J LEU* 3.9 1.2 - - - +
96J GLU* 1.3 85.0 - - + +
98J ILE* 1.3 65.3 + - - +
99J SER* 3.6 19.4 + - - -
121J HIS* 3.0 48.7 + - + +
55L ASP* 3.8 30.4 + - + +
57L TYR* 5.9 0.4 - - - -
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Residues in contact with ILE 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J SER* 3.2 6.8 - - - -
85J VAL* 2.7 50.5 + - + -
90J PRO* 3.8 21.8 - - + -
91J ILE* 4.1 3.1 - - + -
95J LEU* 3.5 31.2 - - + -
97J LYS* 1.3 76.3 - - - +
99J SER* 1.3 64.4 + - - +
100J ASN* 3.1 25.2 + - - +
118J ASN* 4.3 2.5 - - - +
119J LYS 3.5 9.4 - - - +
120J TYR* 3.9 35.7 - - + -
132J GLN* 5.5 1.1 - - - +
136J SER* 5.8 1.3 - - - +
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Residues in contact with SER 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J TYR 3.7 5.6 - - - -
84J SER* 4.3 5.6 - - - -
97J LYS* 3.6 15.0 + - - -
98J ILE* 1.3 72.2 - - - +
100J ASN* 1.3 71.1 + - - +
118J ASN* 3.5 0.5 - - - -
119J LYS* 3.0 46.9 + - - -
121J HIS* 2.8 27.3 - - - -
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Residues in contact with ASN 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J ASN* 3.3 6.3 + - - +
83J TYR* 2.8 81.0 + - + +
85J VAL* 3.7 12.7 - - - +
98J ILE* 3.1 20.2 + - - +
99J SER* 1.3 88.1 - - - +
101J GLU* 1.3 63.8 + - - +
102J ILE* 5.5 1.6 - - + -
116J ILE* 5.9 1.6 - - + -
117J SER 3.9 6.7 - - - +
118J ASN* 2.9 22.7 - - - +
119J LYS* 3.3 6.1 + - - +
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Residues in contact with GLU 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J LYS* 2.9 42.5 + - + +
81J TYR 3.6 3.4 - - - -
82J ASN* 3.1 23.7 + - - +
100J ASN* 1.3 77.2 - - - +
102J ILE* 1.3 68.4 + - - +
103J LYS* 4.2 9.1 + - + +
115J LYS 3.7 0.9 - - - +
116J ILE* 3.3 6.6 - - - +
117J SER* 3.0 36.5 + - - +
119J LYS* 3.7 12.7 + - - +
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Residues in contact with ILE 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J PHE* 5.4 0.2 - - - -
22J PHE* 4.8 9.4 - - + -
23J ILE* 4.3 25.6 - - + -
79J PHE 3.5 4.0 - - - +
80J LYS* 3.5 0.2 - - - -
81J TYR* 2.9 43.8 + - + +
83J TYR* 4.2 25.1 - - + +
100J ASN* 5.5 0.9 - - + -
101J GLU* 1.3 79.9 - - - +
103J LYS* 1.3 67.7 + - - +
104J ILE* 4.5 14.4 - - + -
114J LEU* 4.9 8.7 - - + -
115J LYS 3.5 9.6 - - - +
116J ILE* 4.0 26.9 - - + -
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Residues in contact with LYS 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ASN* 3.2 31.7 + - - +
79J PHE 3.6 2.5 - - - -
80J LYS* 4.3 19.8 - - + +
101J GLU* 4.2 12.2 + - + +
102J ILE* 1.3 75.2 - - - +
104J ILE* 1.3 83.1 + - - +
105J VAL* 3.7 29.9 - - + +
113J ILE 3.6 0.9 - - - +
114J LEU* 3.5 5.0 - - - +
115J LYS* 3.0 47.7 + - + +
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Residues in contact with ILE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ALA* 3.3 33.9 - - + +
18J LEU* 4.0 23.8 - - + +
19J PHE* 4.0 28.7 - - + -
22J PHE* 5.0 2.2 - - + -
23J ILE* 4.6 10.3 - - + -
79J PHE* 3.3 39.0 + - + +
102J ILE* 4.5 8.3 - - + -
103J LYS* 1.3 89.0 - - - +
105J VAL* 1.3 59.5 + - - +
112J SER* 4.2 9.4 - - - +
113J ILE 3.3 7.4 - - - +
114J LEU* 4.0 18.2 - - + -
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Residues in contact with VAL 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ALA* 3.9 3.6 - - - -
103J LYS* 3.7 31.0 - - + +
104J ILE* 1.3 71.9 - - - +
106J ALA* 1.3 62.6 + - - +
107J THR* 3.4 1.1 + - + -
112J SER* 3.2 3.8 - - - -
113J ILE* 2.9 70.3 + - + +
115J LYS* 4.3 26.0 - - + +
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Residues in contact with ALA 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J PRO* 5.7 1.3 - - + -
15J ALA* 3.7 21.0 - - + +
16J ALA 5.5 0.4 - - - +
79J PHE* 5.8 2.4 - - + -
104J ILE 4.3 0.2 + - - -
105J VAL* 1.3 72.0 - - - +
107J THR* 1.3 66.8 + - - +
108J PRO* 3.9 1.9 - - - +
110J GLY 5.3 1.3 - - - +
111J GLY 3.8 10.1 - - - +
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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