Contacts of the strand formed by residues 159 - 165 (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 ASN 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C ASN* 2.9 31.2 + - - +
157C ASN* 2.8 29.7 + - - +
158C GLY* 1.3 80.8 - - - +
160C MET* 1.3 61.0 - - - +
161C ARG 4.1 0.2 - - - -
193C ASP* 4.1 27.7 + - + +
194C ILE 3.4 12.5 + - - +
195C LYS* 3.2 33.8 + - - +
196C ARG* 3.3 7.9 - - - -
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Residues in contact with MET 160 (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* 4.1 26.2 - - + -
152C PHE* 4.5 10.3 - - + -
153C GLU 3.2 11.0 - - - +
154C ILE* 4.4 4.9 - - + -
159C ASN* 1.3 73.7 - - - +
161C ARG* 1.3 65.7 + - - +
162C ILE* 4.5 3.1 - - + -
180C MET* 4.3 1.1 - - - +
193C ASP* 3.4 4.7 - - - +
194C ILE* 2.8 40.4 + - + +
196C ARG* 3.5 17.2 - - + +
200C ASN 4.6 0.4 - - - +
201C ILE* 3.8 44.2 - - + -
204C VAL* 3.9 25.8 - - + -
205C ILE* 4.2 15.0 - - + -
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Residues in contact with ARG 161 (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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151C ASN 4.0 0.3 - - - +
152C PHE* 3.5 3.1 - - - -
153C GLU* 2.7 60.6 + - + +
155C ASN* 3.7 19.1 - - - +
159C ASN 4.1 0.4 + - - -
160C MET* 1.3 74.0 - - - +
162C ILE* 1.3 79.7 + - - +
183C LYS* 5.5 5.5 - - - +
191C TYR* 3.4 44.4 - - - +
192C LEU 3.1 8.1 - - - +
193C ASP* 2.9 40.5 + - - +
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Residues in contact with ILE 162 (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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149C ILE* 4.0 31.0 - - + -
151C ASN 3.5 2.5 - - - -
152C PHE* 3.9 26.0 - - + -
160C MET* 4.5 6.3 - - + -
161C ARG* 1.3 82.6 - - - +
163C PHE* 1.3 66.8 + - - +
167C MET* 4.4 4.5 - - + -
175C PHE* 5.0 6.5 - - + -
180C MET* 3.4 17.7 - - + -
190C VAL 3.5 3.8 - - - +
191C TYR* 3.5 2.1 - - - -
192C LEU* 2.8 54.2 + - + +
204C VAL* 3.3 30.7 - - + -
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Residues in contact with PHE 163 (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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149C ILE* 3.8 0.9 - - - +
150C ARG* 2.8 50.6 + - + +
151C ASN* 2.9 46.2 + - - +
153C GLU* 3.6 20.6 - - - +
161C ARG 4.0 0.6 - - - -
162C ILE* 1.3 74.3 - - - +
164C GLY* 1.3 72.6 + - - +
189C ASN* 3.4 38.6 - - + -
190C VAL 3.4 3.6 - - - -
191C TYR* 3.5 26.7 - + + -
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Residues in contact with GLY 164 (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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148C GLY 3.0 15.5 - - - -
149C ILE* 4.1 0.4 - - - -
150C ARG* 4.0 3.4 - - - -
162C ILE* 4.0 2.2 - - - +
163C PHE* 1.3 83.6 - - - +
165C TYR* 1.3 61.3 + - - +
167C MET* 4.1 11.2 - - - -
189C ASN* 3.5 5.0 - - - -
190C VAL* 2.8 40.8 + - - +
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Residues in contact with TYR 165 (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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109B ASP* 3.3 42.0 + - + +
113B ASP* 6.1 0.2 - - - -
196B ARG* 4.5 0.5 + - - -
145C ARG* 3.0 30.9 + - - -
148C GLY 2.8 13.3 + - - +
150C ARG* 3.5 35.9 - - - +
164C GLY* 1.3 74.6 - - - +
166C LYS* 1.3 113.8 + - + +
167C MET* 3.3 2.6 + - - +
187C ASN 4.1 16.4 - - - -
188C GLY* 3.8 23.1 - - - -
189C ASN* 4.2 9.6 - - - +
190C VAL* 4.3 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