Contacts of the strand formed by residues 137 - 146 (chain E) in PDB entry 1KAF
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 ASN 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E LYS* 5.9 0.7 - - - -
134E TYR* 2.9 48.7 + - + +
135E ARG 3.6 1.0 - - - -
136E SER* 1.3 85.2 + - - +
138E TYR* 1.3 66.6 + - - +
139E LEU* 3.0 30.1 - - + +
153E GLU* 3.2 19.4 + - - +
154E ILE 3.3 13.7 - - - +
155E ASN* 3.5 23.6 + - - +
156E ASN* 4.1 0.6 + - - -
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Residues in contact with TYR 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E LYS* 3.6 54.5 + - + +
117E MET* 3.9 26.5 - - + -
118E LEU* 2.8 41.6 - - + +
131E VAL* 3.5 22.8 - - + +
132E GLU 3.7 2.2 - - - -
133E ILE* 3.9 31.2 - - + +
137E ASN* 1.3 76.2 + - - +
139E LEU* 1.3 61.9 + - - +
140E ALA* 5.2 0.9 - - + -
153E GLU* 3.2 8.3 - - - +
154E ILE* 3.1 35.9 + - + +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E LYS 3.8 0.2 - - - +
131E VAL* 3.1 8.8 - - - -
132E GLU* 2.8 55.0 + - + +
134E TYR* 3.9 23.8 - - + -
137E ASN* 3.0 34.5 - - - +
138E TYR* 1.3 72.3 - - - +
140E ALA* 1.3 61.0 + - - +
141E ILE* 3.5 15.6 + - + +
151E ASN* 4.7 11.0 - - + +
152E PHE 4.1 1.8 - - - -
153E GLU* 3.1 30.3 - - + +
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E MET* 4.0 10.0 - - + +
118E LEU* 4.7 2.7 - - + -
121E LEU* 3.7 29.6 - - + -
128E LEU* 4.0 12.3 - - + +
130E LYS 4.0 3.6 - - - -
131E VAL* 4.4 11.2 - - + -
138E TYR* 4.0 1.5 + - + -
139E LEU* 1.3 70.7 - - - +
141E ILE* 1.3 62.1 + - - +
142E LEU 3.7 1.0 + - - -
151E ASN* 3.3 5.2 - - - +
152E PHE* 2.9 39.5 + - + +
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Residues in contact with ILE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E LEU* 3.3 6.2 - - - +
129E LYS* 2.7 47.5 + - + +
130E LYS* 3.0 27.6 + - + +
132E GLU* 3.5 39.3 - - + +
139E LEU* 4.0 15.9 - - + +
140E ALA* 1.3 73.0 - - - +
142E LEU* 1.3 65.0 + - - +
150E ARG* 4.3 1.3 - - + +
151E ASN* 3.6 25.4 - - - +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 3.9 26.7 - - + -
127E VAL 3.7 7.0 - - - +
128E LEU* 3.7 19.5 - - + -
129E LYS* 4.0 5.1 + - - +
140E ALA 3.7 0.9 + - - +
141E ILE* 1.3 82.3 - - - +
143E GLU* 1.3 64.8 + - - +
144E LYS* 3.4 14.7 - - - +
145E ARG 4.9 0.2 + - - -
146E THR* 3.8 22.7 - - - +
149E ILE* 3.5 39.7 - - + +
150E ARG* 3.0 19.8 + - - +
152E PHE* 4.0 19.7 - - + -
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Residues in contact with GLU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E VAL* 2.9 40.0 + - + +
128E LEU 4.3 1.9 - - - +
129E LYS* 3.5 45.1 + - - +
141E ILE 3.6 2.0 + - - -
142E LEU* 1.3 73.6 - - - +
144E LYS* 1.3 84.2 + - + +
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Residues in contact with LYS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E VAL 4.7 0.4 + - - -
142E LEU* 3.4 13.8 - - - +
143E GLU* 1.3 106.2 + - + +
145E ARG* 1.3 70.4 + - - +
146E THR* 2.8 17.8 + - - +
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Residues in contact with ARG 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLU* 5.0 3.6 + - - -
142E LEU* 4.9 1.9 + - - -
144E LYS* 1.3 74.3 - - - +
146E THR* 1.3 60.8 + - - +
147E ASN 4.1 1.1 + - - -
148E GLY* 3.7 28.5 - - - +
149E ILE 3.4 19.5 - - - +
150E ARG* 3.5 38.0 - - - +
165E TYR* 3.4 33.5 - - - +
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Residues in contact with THR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 4.4 21.3 - - + -
142E LEU* 3.8 15.4 - - - +
144E LYS* 2.8 18.8 + - - +
145E ARG* 1.3 71.3 + - - +
147E ASN* 1.3 81.6 + - - +
148E GLY 3.0 0.2 - - - -
149E ILE* 2.8 36.7 + - + +
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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