Contacts of the strand formed by residues 104 - 111 (chain B) in PDB entry 2KFK
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 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B PRO* 4.6 5.2 - - - +
102B LEU* 2.5 26.6 + - - +
103B GLY* 1.3 72.7 - - - -
105B ILE* 1.3 63.4 + - - +
106B LEU 4.1 0.2 + - - -
119B LEU* 3.0 26.7 - - - +
121B GLU* 2.5 40.5 + - - +
179B LYS* 2.9 24.9 - - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B SER* 1.3 74.9 - - - +
106B LEU* 1.3 58.8 + - - +
107B PHE* 3.7 11.9 - - + -
119B LEU* 3.2 4.0 - - - -
120B VAL* 2.6 60.4 + - + +
122B LYS* 3.3 47.6 - - + +
170B LYS* 5.7 4.5 - - + -
173B LEU* 3.6 23.3 - - + -
179B LYS 3.3 3.4 - - - -
180B PHE 3.3 28.7 - - - +
181B LEU* 3.5 18.8 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 1.3 73.2 - - - +
107B PHE* 1.3 58.6 + - - +
108B ARG* 3.1 25.0 + - + +
117B THR* 3.2 57.7 - - + +
118B LEU 3.6 7.9 - - - +
119B LEU* 3.5 17.1 - - + +
179B LYS 3.3 7.2 + - - +
180B PHE* 3.4 28.9 - - + -
181B LEU 2.7 29.5 + - - -
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.6 18.4 - - + -
106B LEU* 1.3 76.0 - - - +
108B ARG* 1.3 63.9 + - - +
109B ILE* 2.8 26.4 + - + +
116B PHE 3.2 0.3 - - - +
118B LEU* 2.6 26.9 + - + +
120B VAL* 2.9 39.5 - - + -
129B LEU* 3.5 44.0 - - + -
133B ILE* 3.6 22.9 - - + -
148B ILE* 4.6 3.1 - - + -
160B LEU* 5.6 2.0 - - + -
181B LEU* 3.8 18.8 - - + -
183B ILE* 3.9 22.2 - - + -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.1 20.7 + - + +
107B PHE* 1.3 67.6 - - - +
109B ILE* 1.3 52.0 + - - +
115B ILE* 4.1 17.7 - - + +
116B PHE 3.8 2.0 - - - -
117B THR* 3.1 30.7 - - - +
180B PHE* 4.6 16.2 - - + -
181B LEU 2.6 21.1 + - - +
182B ASN* 4.1 6.3 - - + -
183B ILE* 2.4 42.6 + - - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PHE* 2.9 31.6 - - + +
108B ARG* 1.3 73.0 - - - +
110B SER* 1.3 60.0 + - - +
111B TYR* 3.7 7.4 + - + +
115B ILE* 3.3 2.6 - - - -
116B PHE* 2.5 54.9 + - + +
118B LEU* 3.8 17.5 - - + -
133B ILE* 4.4 11.0 - - + -
136B LYS* 5.4 0.2 - - + -
137B ILE* 3.8 20.9 - - + -
183B ILE* 3.3 25.4 - - + -
185B LEU* 3.6 39.7 - - + +
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG 4.1 0.2 - - - -
109B ILE* 1.3 73.1 - - - +
111B TYR* 1.3 59.0 + - - +
112B ASN 3.7 9.9 + - - +
113B SER 5.0 0.5 - - - -
114B GLU 2.9 10.8 + - - -
115B ILE* 2.7 28.6 - - - +
183B ILE 3.2 13.9 + - - -
184B ARG* 3.8 10.8 + - - +
185B LEU 3.2 18.9 + - - +
186B TYR 4.4 2.1 - - - +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ILE* 3.7 6.0 + - + -
110B SER* 1.3 69.8 - - - +
112B ASN* 1.3 88.7 + - + +
113B SER 3.2 2.3 + - - -
114B GLU* 3.2 19.4 + - - +
116B PHE* 3.9 10.1 - + + -
140B THR* 3.4 38.8 - - + -
142B ILE* 2.8 60.8 - - + +
145B ILE* 4.4 1.3 - - + -
185B LEU* 3.2 37.2 - - + +
186B TYR* 3.2 34.4 - + + -
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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