Contacts of the strand formed by residues 192 - 198 (chain D) in PDB entry 5FL6
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 TYR 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D LEU* 3.4 34.5 - - + +
46D ARG 2.6 30.9 + - - -
48D LEU* 3.8 19.5 - - + +
82D LEU 4.3 4.7 + - - -
189D PHE 3.6 22.7 - - - -
190D SER 3.8 3.8 - - - -
191D ARG* 1.3 77.2 - - - +
193D PHE* 1.3 69.7 + - - +
194D GLN* 3.8 19.3 + - - -
211D THR* 3.6 24.0 - - + -
212D VAL 3.4 15.0 - - - +
213D PHE* 4.2 5.4 - + + -
214D ASN 4.1 2.9 - - - +
256D ALA* 3.4 2.8 - - - -
257D SER* 2.8 48.7 + - - -
258D PHE* 3.6 7.4 - - - -
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Residues in contact with PHE 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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34D ILE* 3.8 40.4 - - + -
36D PRO* 4.1 31.0 - - + -
39D ALA* 4.3 4.3 - - + -
109D VAL* 5.5 6.5 - - + -
146D PHE* 6.3 0.9 - + - -
192D TYR* 1.3 77.9 - - - +
194D GLN* 1.3 61.7 + - - +
195D TYR* 5.7 1.3 - - + -
211D THR* 3.3 5.0 - - - -
212D VAL* 2.8 51.6 + - + +
213D PHE 4.9 2.5 - - - -
214D ASN* 4.3 18.2 - - - -
254D ILE* 3.9 13.9 - - + -
255D GLU 3.2 13.9 - - - +
256D ALA* 4.1 12.8 - - + -
258D PHE* 3.7 27.6 - + - -
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Residues in contact with GLN 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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45D LEU* 3.5 31.4 - - + +
48D LEU* 5.0 0.2 - - - +
82D LEU* 4.1 11.3 - - - +
86D ARG* 2.8 31.8 + - - +
192D TYR* 3.8 17.0 + - + -
193D PHE* 1.3 75.2 - - - +
195D TYR* 1.3 64.2 - - - +
209D ILE* 3.8 14.4 - - + +
210D TRP 3.2 12.3 - - - +
211D THR* 2.8 21.8 + - - -
253D VAL 4.5 0.3 - - - +
254D ILE* 4.3 0.9 - - - -
255D GLU* 2.8 42.4 + - + +
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Residues in contact with TYR 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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30D SER* 2.9 32.3 + - - -
32D VAL* 3.6 29.5 + - + +
34D ILE* 5.6 1.8 - - + -
107D HIS* 2.6 34.4 + + - -
193D PHE* 5.7 0.7 - - + -
194D GLN* 1.3 79.8 - - - +
196D GLU* 1.3 73.8 + - - +
197D GLY* 4.1 0.9 - - - -
209D ILE* 3.8 4.5 - - - +
210D TRP* 2.9 52.3 + + + +
212D VAL* 4.6 6.7 - - + -
249D LEU* 4.9 4.0 - - + -
252D ARG* 3.8 19.7 - - + -
253D VAL 4.4 6.5 - - - +
254D ILE* 4.1 28.5 - - + -
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Residues in contact with GLU 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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28D PHE* 4.7 1.4 - - - +
137D PRO* 4.8 8.2 - - - +
138D GLY 5.2 3.1 + - - -
195D TYR* 1.3 78.0 - - - +
197D GLY* 1.3 61.6 + - - +
207D GLY* 3.4 30.2 + - - +
208D VAL 3.4 11.2 - - - +
209D ILE* 3.9 20.3 - - + +
252D ARG* 2.8 31.6 + - - +
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Residues in contact with GLY 197 (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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28D PHE* 3.5 7.2 - - - -
30D SER* 3.4 13.7 - - - -
195D TYR* 3.9 3.2 + - - -
196D GLU* 1.3 74.6 - - - +
198D SER* 1.3 61.0 + - - -
206D GLN* 3.3 2.3 - - - +
207D GLY 3.1 12.1 + - - -
208D VAL 2.8 32.2 + - - -
210D TRP* 4.1 1.4 - - - -
252D ARG* 3.4 12.3 - - - -
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Residues in contact with SER 198 (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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29D GLN* 3.4 34.3 + - - -
30D SER* 2.9 32.1 + - - -
197D GLY* 1.3 74.6 - - - -
199D LEU* 1.3 81.3 + - - +
204D CYS 3.5 1.8 - - - -
205D ALA 3.1 13.7 - - - -
206D GLN* 3.9 3.6 - - - -
208D VAL* 3.7 7.6 - - - -
210D TRP* 2.9 21.8 + - - +
244D ARG* 3.8 0.3 + - - -
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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