Contacts of the strand formed by residues 149 - 154 (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 ILE 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B PHE* 5.1 5.4 - - + -
142B LEU* 3.5 12.0 - - + +
145B ARG* 3.3 6.9 - - - -
146B THR* 2.8 37.0 + - + +
147B ASN* 4.1 5.4 - - + +
148B GLY* 1.3 80.0 - - - +
150B ARG* 1.3 61.7 + - - +
151B ASN 3.9 15.7 - - - +
152B PHE* 3.7 41.1 - - + -
162B ILE* 4.0 15.9 - - + -
163B PHE 4.0 2.7 - - - -
164B GLY* 4.2 1.3 - - - -
167B MET* 4.4 8.7 - - + -
175B PHE* 4.1 14.6 - - + -
208B ALA* 4.3 4.3 - - + +
211B LEU* 4.1 22.0 - - + -
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Residues in contact with ARG 150 (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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108A SER* 5.5 4.9 - - - -
109A ASP* 2.7 43.9 + - - +
141B ILE* 4.0 4.7 - - - +
142B LEU* 3.1 29.6 + - - +
145B ARG* 3.5 17.5 - - + +
149B ILE* 1.3 78.3 - - - +
151B ASN* 1.3 62.8 + - - +
163B PHE* 2.8 51.7 + - + +
164B GLY* 4.4 5.4 - - - -
165B TYR* 3.3 32.5 - - - +
189B ASN* 5.3 2.2 - - - +
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Residues in contact with ASN 151 (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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139B LEU* 4.2 23.9 - - - +
140B ALA 3.1 21.3 - - - +
141B ILE* 4.0 14.4 - - + +
142B LEU 4.6 0.2 - - - +
149B ILE* 3.8 5.3 - - - +
150B ARG* 1.3 81.9 - - - +
152B PHE* 1.3 73.7 + - - +
153B GLU* 4.3 4.7 - - - +
162B ILE* 3.5 4.9 - - - -
163B PHE* 3.2 52.3 + - - +
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Residues in contact with PHE 152 (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* 3.7 23.6 - - + +
121B LEU* 3.8 26.7 - - + -
126B PHE* 4.4 4.9 - + - -
139B LEU* 3.7 0.9 - - - -
140B ALA* 2.8 38.2 + - + +
142B LEU* 4.2 18.4 - - + -
149B ILE* 3.7 26.2 - - + -
151B ASN* 1.3 79.9 - - - +
153B GLU* 1.3 61.9 + - - +
160B MET* 4.0 5.2 - - + -
161B ARG 3.4 3.4 - - - +
162B ILE* 3.9 31.0 - - + -
204B VAL* 4.6 1.1 - - + -
205B ILE* 3.5 27.1 - - + -
208B ALA* 3.9 24.7 - - + -
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Residues in contact with GLU 153 (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* 4.0 2.5 - - - +
137B ASN* 3.5 18.2 + - + +
138B TYR 3.2 10.3 - - - +
139B LEU* 3.4 25.0 - - + +
151B ASN* 4.3 4.5 - - - +
152B PHE* 1.3 76.4 - - - +
154B ILE* 1.3 74.1 + - - +
155B ASN* 3.4 25.4 + - + +
160B MET* 3.1 11.6 - - - +
161B ARG* 2.7 65.8 + - + +
163B PHE* 6.0 1.7 - - - +
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Residues in contact with ILE 154 (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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110B MET* 3.7 27.2 - - + +
113B ASP* 4.1 18.6 - - + +
114B LYS* 4.2 16.4 - - - -
117B MET* 3.6 33.0 - - + -
137B ASN* 3.6 2.3 - - - -
138B TYR* 2.9 43.1 + - + -
153B GLU* 1.3 75.3 - - - +
155B ASN* 1.3 58.5 + - - +
159B ASN 4.1 1.3 - - - -
160B MET* 4.4 4.0 - - + -
196B ARG* 3.6 36.3 - - + +
201B ILE* 4.4 11.0 - - + -
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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