Contacts of the strand formed by residues 191 - 196 (chain D) in PDB entry 3K75
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 MET 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D ILE* 4.5 1.6 - - - +
155D MET* 3.7 24.5 - - + +
158D MET* 3.3 55.2 - - + -
159D GLN* 3.6 15.7 - - + +
162D VAL* 4.3 10.8 - - - -
177D VAL* 4.1 12.3 - - + -
190D ASP* 1.3 74.3 - - - +
192D ASP* 1.3 59.8 + - - +
193D VAL* 3.6 25.8 - - + -
223D PHE* 4.8 0.7 - - - -
239D CYS* 5.6 0.4 - - - -
254D ARG 3.2 10.5 + - - +
255D ILE* 3.6 19.4 - - + -
256D ASP* 3.0 26.7 + - - +
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Residues in contact with ASP 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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177D VAL* 3.5 5.5 - - - +
178D CYS* 2.7 48.5 + - - +
179D GLY* 4.6 4.4 + - - +
190D ASP* 3.6 13.3 + - - +
191D MET* 1.3 70.4 - - - +
193D VAL* 1.3 61.7 + - - +
194D LEU* 4.1 14.9 - - - +
256D ASP* 3.5 23.4 - - - +
258D ARG* 4.1 11.7 + - - +
272D PHE* 4.2 26.3 - - - +
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Residues in contact with VAL 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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162D VAL* 4.4 18.6 - - + -
163D LEU* 6.0 0.4 - - + -
175D ALA* 4.3 16.2 - - + -
176D THR 4.1 6.7 - - - +
177D VAL* 4.1 12.8 - - + +
191D MET* 3.6 31.2 - - + -
192D ASP* 1.3 74.0 - - - +
194D LEU* 1.3 79.6 + - - +
195D LEU* 5.2 2.0 - - + -
255D ILE* 4.7 6.7 - - + -
256D ASP 2.9 16.2 + - - +
257D ILE* 3.4 19.4 - - + -
258D ARG* 2.9 24.1 + - - +
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Residues in contact with LEU 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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175D ALA* 3.2 4.5 - - - +
176D THR 3.0 32.6 + - - +
178D CYS* 3.7 16.2 - - - -
192D ASP* 4.1 12.8 - - - +
193D VAL* 1.3 88.8 - - - +
195D LEU* 1.3 60.5 + - - +
258D ARG* 3.5 28.3 - - + -
260D ILE* 3.7 16.6 - - + -
265D TYR* 3.2 18.7 + - + +
268D GLY 3.6 33.9 - - - +
269D VAL* 3.6 14.1 - - + +
272D PHE* 3.8 12.3 - - + -
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Residues in contact with LEU 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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166D VAL* 3.9 21.5 - - + -
173D TYR* 3.9 21.3 - - + -
174D ILE 3.5 3.6 - - - +
175D ALA* 3.9 15.0 - - + -
193D VAL* 5.2 2.0 - - + -
194D LEU* 1.3 75.0 - - - +
196D THR* 1.3 67.3 + - - +
210D LEU 3.9 7.6 - - - +
211D LEU* 4.2 12.8 - - + -
214D VAL* 3.6 32.1 - - + -
257D ILE* 4.4 8.7 - - + -
258D ARG 2.6 17.3 + - - +
259D LEU* 3.8 21.1 - - + -
260D ILE* 2.8 29.3 + - - +
265D TYR* 4.0 1.3 - - - -
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Residues in contact with THR 196 (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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173D TYR* 3.5 8.9 - - - -
174D ILE* 3.0 52.0 + - + -
195D LEU* 1.3 75.8 - - - +
197D HIS* 1.3 69.1 + - - +
259D LEU* 4.4 5.6 - - - -
260D ILE 2.5 24.6 + - - -
261D PRO 3.4 0.2 - - - -
262D LYS* 3.1 32.0 + - + -
265D TYR* 3.4 29.8 - - + -
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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