Contacts of the strand formed by residues 183 - 189 (chain D) in PDB entry 1KLG
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 THR 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D PRO* 5.3 2.2 - - + +
11D LEU* 4.1 28.2 - - + +
12D HIS 3.5 18.6 - - - +
13D LYS* 4.1 14.8 - - + -
181D TYR* 4.1 3.6 - - - +
182D GLU* 1.3 94.3 - - + +
184D GLY* 1.3 58.8 + - - +
201D MET* 4.1 7.2 - - - -
233D HIS 5.4 0.2 + - - -
234D LEU* 3.4 3.7 - - - +
235D THR* 2.5 54.2 + - - +
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Residues in contact with GLY 184 (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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11D LEU* 4.9 3.3 - - - +
12D HIS 4.9 0.4 + - - -
183D THR* 1.3 78.8 - - - +
185D TYR* 1.3 59.3 + - - +
199D ASP* 3.5 8.0 + - - +
200D MET* 2.7 39.0 + - - +
201D MET* 4.0 7.3 + - - +
233D HIS 3.2 12.1 - - - -
234D LEU* 3.7 13.0 - - - -
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Residues in contact with TYR 185 (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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5D ASP* 4.5 10.5 + - - +
6D PRO* 3.7 30.9 + - + +
11D LEU* 3.6 28.5 - - + -
184D GLY* 1.3 75.0 - - - +
186D ILE* 1.3 59.3 + - - +
187D LYS* 4.1 19.5 - - + +
197D TRP* 4.0 28.5 - - + -
198D TYR 3.1 14.4 - - - +
199D ASP* 4.4 0.2 - - - -
200D MET* 3.3 10.2 - - - +
232D VAL* 3.6 0.3 - - - -
233D HIS* 3.0 78.0 + + + -
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Residues in contact with ILE 186 (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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160D ASP* 3.5 45.8 - - - +
163D ALA* 4.0 13.2 - - + -
164D ARG* 5.5 1.6 - - + -
185D TYR* 1.3 74.5 - - - +
187D LYS* 1.3 59.4 + - - +
188D PHE* 3.8 16.5 + - + -
197D TRP* 3.1 4.9 - - - -
198D TYR* 3.0 46.5 + - + +
200D MET* 4.0 16.4 - - + -
230D ILE* 3.7 30.1 - - + -
231D GLU 3.6 2.7 - - - -
232D VAL* 4.2 8.3 - - + +
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Residues in contact with LYS 187 (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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5D ASP* 2.6 43.7 + - - +
185D TYR* 4.0 19.2 - - + -
186D ILE* 1.3 74.0 - - - +
188D PHE* 1.3 69.9 + - - +
189D ILE* 4.2 12.0 - - + +
195D THR* 3.6 28.7 + - - +
196D PHE 3.5 9.6 - - - +
197D TRP* 3.9 5.6 - - + -
229D LYS 3.8 0.2 - - - +
230D ILE* 3.4 5.7 - - - +
231D GLU* 2.8 63.7 + - + +
233D HIS* 5.1 1.1 - - + -
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Residues in contact with PHE 188 (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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156D ALA* 3.6 28.7 - - + -
159D LEU* 3.9 16.6 - - + -
160D ASP* 4.0 11.2 - - + -
186D ILE* 3.8 27.8 - - + -
187D LYS* 1.3 76.7 - - - +
189D ILE* 1.3 63.3 + - - +
190D GLU 4.1 0.4 - - - -
194D ASN 4.6 0.2 - - - -
195D THR* 3.1 30.0 - - - -
196D PHE* 2.8 50.5 + + + +
198D TYR* 4.1 19.3 - + - -
223D VAL* 4.8 2.7 - - + -
228D VAL* 4.1 12.3 - - + -
229D LYS 3.6 1.6 - - - -
230D ILE* 3.6 32.3 - - + -
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Residues in contact with ILE 189 (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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187D LYS* 4.2 15.7 - - + +
188D PHE* 1.3 79.5 - - - +
190D GLU* 1.3 73.1 + - - +
193D GLY* 5.3 3.8 - - - -
194D ASN 3.8 1.8 - - - -
195D THR* 4.1 18.8 - - + -
227D SER 4.2 0.9 - - - +
228D VAL* 3.3 5.4 - - - +
229D LYS* 2.7 60.6 + - + +
231D GLU* 2.7 40.2 - - + +
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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