Contacts of the strand formed by residues 149 - 154 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C PHE* 4.9 4.7 - - + -
142C LEU* 3.4 13.1 - - + +
145C ARG* 3.3 6.3 - - - -
146C THR 2.9 37.0 + - - +
147C ASN 4.1 5.2 - - - +
148C GLY* 1.3 79.5 - - - +
150C ARG* 1.3 62.5 + - - +
151C ASN 3.9 15.7 - - - +
152C PHE* 3.7 41.7 - - + -
162C ILE* 4.0 17.5 - - + -
163C PHE 4.0 2.5 - - - -
164C GLY* 4.1 1.3 - - - -
167C MET* 4.3 7.6 - - + -
175C PHE* 4.3 13.5 - - + -
208C ALA* 4.1 17.0 - - + -
211C LEU* 4.4 9.4 - - + -
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Residues in contact with ARG 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER* 4.4 15.7 - - - -
109B ASP* 4.1 23.2 + - - +
112B GLU* 4.6 4.2 + - - -
141C ILE* 4.5 0.3 - - - +
142C LEU* 2.9 31.8 + - - +
144C LYS 6.0 0.2 - - - -
145C ARG* 3.8 30.9 - - + +
148C GLY 4.4 6.5 - - - +
149C ILE* 1.3 78.5 - - - +
151C ASN* 1.3 68.8 + - - +
163C PHE* 2.8 47.2 + - + +
164C GLY* 4.5 4.0 - - - -
165C TYR* 3.5 37.7 - - - +
189C ASN* 5.7 0.4 + - - -
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Residues in contact with ASN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU* 4.9 9.1 - - - +
140C ALA 3.2 11.0 - - - +
141C ILE* 3.5 33.5 - - - +
149C ILE* 3.9 5.5 - - - +
150C ARG* 1.3 95.5 - - - +
152C PHE* 1.3 66.7 + - - +
153C GLU* 3.2 26.5 + - + +
162C ILE* 3.5 3.6 - - - -
163C PHE* 2.9 57.0 + - + +
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Residues in contact with PHE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C MET* 3.7 20.6 - - - +
121C LEU* 3.7 35.4 - - + -
126C PHE* 4.0 22.2 - + - -
140C ALA* 2.8 37.7 + - + +
142C LEU* 4.1 14.1 - - + -
149C ILE* 3.7 32.3 - - + -
151C ASN* 1.3 75.4 - - - +
153C GLU* 1.3 61.0 + - - +
160C MET* 4.5 11.0 - - + -
161C ARG 3.5 3.6 - - - -
162C ILE* 3.9 28.9 - - + -
204C VAL* 4.7 3.4 - - + -
205C ILE* 4.6 7.4 - - + -
208C ALA* 4.1 15.3 - - + -
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C MET* 4.2 2.3 - - - -
138C TYR 3.3 7.0 - - - +
139C LEU* 3.4 24.3 - - + +
151C ASN* 3.2 33.1 + - + +
152C PHE* 1.3 81.6 - - - +
154C ILE* 1.3 63.5 + - - +
155C ASN* 3.8 15.9 + - - +
160C MET* 3.2 10.0 - - - +
161C ARG* 2.7 66.5 + - + +
163C PHE* 3.6 16.0 - - - +
191C TYR* 5.6 1.1 - - - -
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Residues in contact with ILE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C MET* 3.7 26.4 - - + +
113C ASP* 3.9 20.0 - - + +
114C LYS* 4.0 13.0 - - - +
117C MET* 4.0 26.9 - - + -
137C ASN* 3.6 0.9 - - - -
138C TYR* 2.8 46.0 + - + -
153C GLU* 1.3 76.3 - - - +
155C ASN* 1.3 62.6 + - - +
159C ASN 4.0 0.9 - - - -
160C MET* 4.4 8.1 - - + -
196C ARG* 3.7 39.7 - - + +
201C ILE* 4.3 9.4 - - + -
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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