Contacts of the strand formed by residues 189 - 195 (chain D) 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 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D ARG* 4.5 7.1 - - - +
163D PHE* 4.1 17.2 - - + -
164D GLY 3.7 6.5 + - - -
165D TYR* 3.4 21.6 - - - -
183D LYS 3.7 1.0 - - - +
184D ILE* 3.6 2.9 - - - -
185D ALA* 2.9 27.9 + - + +
187D ASN* 2.9 29.0 - - - +
188D GLY* 1.3 77.5 - - - +
190D VAL* 1.3 58.8 + - - +
191D TYR* 3.4 33.5 + - + +
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Residues in contact with VAL 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ILE 3.6 0.7 - - - +
163D PHE* 3.6 7.3 - - - -
164D GLY 2.9 40.4 + - - +
166D LYS* 4.1 2.0 - - - +
167D MET* 4.1 30.7 - - - +
172D ILE* 4.2 19.1 - - + -
182D CYS* 4.2 4.7 - - - -
183D LYS 3.4 5.8 - - - +
184D ILE* 4.4 14.8 - - + -
188D GLY 3.4 16.2 - - - +
189D ASN* 1.3 75.9 - - - +
191D TYR* 1.3 66.9 + - - +
192D LEU* 4.1 26.7 - - + -
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Residues in contact with TYR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ARG* 3.3 45.8 - - - +
162D ILE 3.6 4.0 - - - -
163D PHE* 3.7 29.0 - + - -
181D SER 3.7 0.7 - - - +
182D CYS* 3.5 2.9 - - - -
183D LYS* 2.9 70.3 + - + +
185D ALA* 4.7 7.7 - - + +
189D ASN* 3.4 38.3 + - + +
190D VAL* 1.3 75.5 - - - +
192D LEU* 1.3 62.0 + - - +
193D ASP* 4.1 4.4 + - - +
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Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ARG* 3.2 5.5 - - - -
162D ILE* 2.9 45.5 + - + +
167D MET* 4.2 18.2 - - + -
172D ILE* 4.1 13.0 - - + -
175D PHE* 3.5 42.2 - - + -
176D THR* 4.9 2.2 - - + -
180D MET* 3.5 18.1 - - + +
181D SER 3.3 4.9 - - - +
182D CYS* 3.5 39.0 - - + -
190D VAL* 4.1 9.4 - - + -
191D TYR* 1.3 74.1 - - - +
193D ASP* 1.3 60.0 + - - +
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Residues in contact with ASP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASN* 4.7 18.4 - - + +
160D MET 3.4 5.2 - - - +
161D ARG* 2.7 56.0 + - - +
179D GLY 4.4 0.3 - - - +
180D MET* 3.1 8.0 - - - -
181D SER* 2.8 49.9 + - - +
183D LYS* 5.7 2.1 - - - +
191D TYR* 4.2 8.0 - - - +
192D LEU* 1.3 74.7 - - - +
194D ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASN* 3.4 7.4 + - - -
160D MET* 2.8 33.8 + - + +
178D ILE* 4.1 14.6 - - + +
179D GLY* 4.0 27.4 - - - +
180D MET* 3.9 26.0 - - + +
193D ASP* 1.3 79.2 - - - +
195D LYS* 1.3 76.3 + - + +
200D ASN* 3.7 30.5 - - + +
204D VAL* 4.0 16.2 - - + -
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Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLY* 4.2 6.2 + - - +
159D ASN* 3.7 13.1 + - - +
194D ILE* 1.3 78.2 - - + +
196D ARG* 1.3 74.4 + - - +
197D SER* 3.4 5.1 + - - -
200D ASN* 2.8 36.5 + - - +
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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