Contacts of the strand formed by residues 137 - 146 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B MET* 4.0 1.8 - - - -
132B GLU 3.4 1.0 - - - +
133B ILE* 3.2 7.9 - - - -
134B TYR* 2.9 36.7 + - + +
135B ARG* 3.4 20.1 + - - +
136B SER* 1.3 78.6 - - - +
138B TYR* 1.3 62.6 + - - +
139B LEU* 4.6 3.0 - - + +
153B GLU* 3.5 19.2 + - + +
154B ILE 3.6 7.2 - - - +
155B ASN* 3.2 22.1 - - - +
156B ASN* 2.9 40.5 + - - +
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Residues in contact with TYR 138 (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 ILE* 3.6 26.8 - - + +
110B MET* 3.8 32.1 - - + -
111B GLU* 3.4 21.9 + - + +
114B LYS* 3.7 45.9 + - + +
117B MET* 5.5 2.2 - - - +
131B VAL* 4.2 11.0 - - + -
132B GLU 3.4 4.9 - - - -
133B ILE* 3.5 34.2 - - + +
137B ASN* 1.3 72.6 - - - +
139B LEU* 1.3 59.4 + - - +
152B PHE 4.0 0.2 - - - +
153B GLU* 3.2 8.7 - - - +
154B ILE* 2.9 46.6 + - + +
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Residues in contact with LEU 139 (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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130B LYS 3.9 0.2 - - - +
131B VAL* 3.2 7.8 - - - +
132B GLU* 2.8 53.3 + - + +
134B TYR* 4.0 34.8 - - + +
137B ASN* 4.6 4.9 - - + +
138B TYR* 1.3 73.2 - - - +
140B ALA* 1.3 61.1 + - - +
141B ILE* 3.6 18.7 + - + +
151B ASN* 4.2 19.1 - - - +
152B PHE 3.7 1.6 - - - +
153B GLU* 3.4 44.9 - - + +
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Residues in contact with ALA 140 (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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117B MET* 4.2 11.0 - - + -
118B LEU* 4.9 3.4 - - + -
121B LEU* 3.8 29.4 - - + -
128B LEU* 4.2 13.5 - - + +
130B LYS 4.1 3.8 - - - -
131B VAL* 4.5 8.7 - - + -
138B TYR 4.3 0.4 - - - -
139B LEU* 1.3 70.1 - - - +
141B ILE* 1.3 62.5 + - - +
142B LEU 3.7 0.9 + - - -
151B ASN* 3.1 5.8 - - - +
152B PHE* 2.8 38.3 + - + +
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Residues in contact with ILE 141 (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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128B LEU* 3.4 7.8 - - - +
129B LYS* 2.8 52.4 + - + +
130B LYS* 3.1 21.5 + - + +
132B GLU* 3.4 37.7 - - + +
139B LEU* 4.3 16.8 - - + +
140B ALA* 1.3 74.4 - - - +
142B LEU* 1.3 64.5 + - - +
150B ARG 4.3 5.4 - - - +
151B ASN* 4.0 15.9 - - + +
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Residues in contact with LEU 142 (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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126B PHE* 3.9 24.5 - - + -
127B VAL 3.6 9.2 - - - +
128B LEU* 3.5 23.8 - - + -
129B LYS* 3.1 16.0 + - - +
140B ALA 4.9 0.2 - - - +
141B ILE* 1.3 77.1 - - - +
143B GLU* 1.3 64.3 + - - +
144B LYS* 3.4 13.0 + - - +
146B THR* 3.7 25.1 - - - +
149B ILE* 3.5 35.2 - - + +
150B ARG* 3.1 20.7 + - - +
151B ASN* 4.8 0.2 - - - -
152B PHE* 4.2 17.0 - - + -
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Residues in contact with GLU 143 (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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112A GLU* 4.1 3.5 - - - +
127B VAL* 2.9 46.1 + - + +
128B LEU 4.5 0.4 - - - +
129B LYS* 2.9 39.6 + - + +
141B ILE 3.7 0.6 + - - -
142B LEU* 1.3 72.1 - - - +
144B LYS* 1.3 92.6 + - + +
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Residues in contact with LYS 144 (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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112A GLU* 3.2 21.3 - - + +
115A ASP* 5.9 2.5 - - - -
127B VAL 4.8 0.2 + - - -
142B LEU* 3.4 15.0 - - - +
143B GLU* 1.3 114.2 + - + +
145B ARG* 1.3 68.1 + - - +
146B THR* 2.9 17.6 + - - +
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Residues in contact with ARG 145 (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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109A ASP* 2.9 33.6 + - - +
112A GLU* 2.9 25.1 + - - +
113A ASP* 5.0 10.1 + - - -
197A SER* 5.9 5.5 - - - +
144B LYS* 1.3 73.5 - - - +
146B THR* 1.3 58.8 + - - +
147B ASN 4.1 1.4 + - - -
148B GLY* 3.6 36.6 - - - +
149B ILE 3.3 9.0 - - - +
150B ARG* 3.5 29.4 - - + +
165B TYR* 3.1 35.8 + - - -
166B LYS* 4.6 10.1 + - - +
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Residues in contact with THR 146 (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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126B PHE* 4.5 19.8 - - + -
142B LEU* 3.7 17.3 - - - +
144B LYS* 2.9 17.0 + - - +
145B ARG* 1.3 71.1 + - - +
147B ASN* 1.3 87.0 + - - +
149B ILE* 2.8 31.1 + - - +
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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