Contacts of the strand formed by residues 137 - 146 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F MET* 4.7 2.9 - - - +
132F GLU 3.8 0.7 - - - +
133F ILE* 3.8 1.6 - - - -
134F TYR* 3.0 53.1 + - - +
135F ARG 3.6 0.4 + - - -
136F SER* 1.3 87.8 + - - +
138F TYR* 1.3 66.0 + - - +
139F LEU* 3.3 40.2 - - - +
153F GLU* 4.5 6.7 + - - +
154F ILE 3.2 12.8 - - - +
155F ASN* 3.7 18.2 - - + +
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Residues in contact with TYR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F MET* 3.9 29.6 - - + -
114F LYS* 3.5 45.2 + - + -
117F MET* 5.1 2.6 - - - +
118F LEU* 5.3 1.8 - - + -
131F VAL* 4.3 11.0 - - + -
132F GLU 3.6 2.5 - - - -
133F ILE* 3.4 49.4 - - + +
134F TYR 5.3 2.5 - - - -
137F ASN* 1.3 77.0 - - - +
139F LEU* 1.3 61.5 + - - +
152F PHE 4.0 0.3 - - - +
153F GLU* 3.2 7.1 - - - +
154F ILE* 2.9 40.1 + - + +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F VAL* 3.2 9.2 - - - +
132F GLU* 2.7 62.8 + - + +
134F TYR* 4.1 10.5 - - + -
137F ASN* 3.3 24.0 - - - +
138F TYR* 1.3 71.6 - - - +
140F ALA* 1.3 61.2 + - - +
141F ILE* 3.5 10.4 + - + +
151F ASN* 3.8 23.8 - - - +
152F PHE 4.2 0.2 - - - +
153F GLU* 3.3 39.7 - - + +
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F MET* 4.6 4.5 - - - -
118F LEU* 4.3 10.1 - - + -
121F LEU* 3.7 30.1 - - + -
128F LEU* 3.9 17.6 - - + +
130F LYS 4.2 3.6 - - - -
131F VAL* 4.7 2.5 - - + +
138F TYR 4.0 1.0 + - - -
139F LEU* 1.3 71.1 - - - +
141F ILE* 1.3 60.1 + - - +
142F LEU 3.6 0.5 + - - -
151F ASN* 3.1 5.4 - - - +
152F PHE* 2.8 39.3 + - + +
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F LEU* 3.2 7.8 - - - +
129F LYS* 2.8 46.2 + - + +
130F LYS* 3.2 25.6 + - + +
132F GLU* 3.4 41.5 - - + +
139F LEU* 4.2 14.8 - - + +
140F ALA* 1.3 71.3 - - - +
142F LEU* 1.3 70.6 + - - +
150F ARG* 4.3 5.4 - - + +
151F ASN* 3.9 11.9 - - + +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F PHE* 3.8 26.9 - - + -
127F VAL 3.6 6.1 - - - +
128F LEU* 3.7 21.5 - - + -
129F LYS* 4.0 6.0 + - - +
140F ALA 3.6 0.6 + - - +
141F ILE* 1.3 83.6 - - - +
143F GLU* 1.3 64.7 + - - +
144F LYS* 3.7 21.4 - - - +
145F ARG 5.1 0.2 + - - -
146F THR* 4.1 12.3 - - - +
149F ILE* 3.5 41.5 - - + +
150F ARG* 3.0 20.7 + - - +
151F ASN* 4.6 0.7 - - - -
152F PHE* 4.0 18.4 - - + -
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Residues in contact with GLU 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F VAL* 3.0 37.1 + - + +
128F LEU 4.2 0.7 - - - +
129F LYS* 3.5 44.5 + - - +
141F ILE 3.6 1.6 + - - -
142F LEU* 1.3 73.1 - - - +
144F LYS* 1.3 103.8 + - + +
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Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F VAL 4.7 0.6 + - - -
142F LEU* 3.7 13.0 - - - +
143F GLU* 1.3 125.6 + - + +
145F ARG* 1.3 71.1 + - - +
146F THR* 2.8 17.2 + - - +
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Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E GLU* 3.6 10.9 + - - -
142F LEU* 5.1 0.8 + - - -
144F LYS* 1.3 72.7 - - - +
146F THR* 1.3 59.1 + - - +
147F ASN 4.1 1.6 + - - -
148F GLY* 3.7 26.7 - - - +
149F ILE 3.3 17.9 - - - +
150F ARG* 2.8 46.4 - - + +
165F TYR* 3.3 33.5 - - - -
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Residues in contact with THR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PHE* 4.5 20.0 - - + -
142F LEU* 4.1 13.4 - - - +
144F LYS* 2.8 18.0 + - - +
145F ARG* 1.3 71.0 + - - +
147F ASN* 1.3 89.0 + - - +
148F GLY 3.0 0.2 - - - -
149F ILE* 2.8 29.5 + - + +
208F ALA 6.0 0.4 - - - +
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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