Contacts of the strand formed by residues 197 - 205 (chain D) in PDB entry 3O9Z
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 ALA 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D GLY 3.8 1.2 + - - -
196D ARG* 1.3 73.7 + - - +
198D LEU* 1.3 62.7 + - - +
199D HIS 3.5 1.1 + - - +
200D VAL* 4.0 19.8 - - + +
214D LEU* 4.9 2.5 - - + -
215D GLU 4.4 0.9 - - - +
216D LEU* 3.6 25.8 - - + -
284D GLU* 2.9 18.1 + - - +
287D ARG* 2.9 25.3 + - - +
288D VAL* 3.8 19.5 - - + -
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Residues in contact with LEU 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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196D ARG* 3.8 35.0 - - + +
197D ALA* 1.3 74.5 - - - +
199D HIS* 1.3 61.4 + - + +
215D GLU* 2.8 13.1 + - + +
216D LEU 4.7 2.0 - - - +
217D GLU* 4.2 28.3 - - + +
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Residues in contact with HIS 199 (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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197D ALA* 3.5 0.9 - - - +
198D LEU* 1.3 77.5 + - - +
200D VAL* 1.3 72.8 + - - +
201D GLU* 2.7 42.9 + - + +
213D TYR* 4.3 12.1 - + - -
214D LEU* 3.4 4.3 - - - +
215D GLU* 2.9 57.8 + - + +
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Residues in contact with VAL 200 (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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197D ALA* 4.0 20.0 - - + +
198D LEU 5.4 0.2 - - - -
199D HIS* 1.3 88.2 + - - +
201D GLU* 1.3 67.3 + - - +
202D VAL* 5.1 0.2 - - + -
213D TYR 3.7 3.4 - - - -
214D LEU* 3.9 14.6 - - + -
288D VAL* 4.8 4.9 - - + -
291D LEU* 4.2 24.2 - - + -
292D LEU* 3.6 31.9 - - + -
295D LEU* 3.6 31.1 - - + +
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Residues in contact with GLU 201 (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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199D HIS* 2.7 35.5 + - + +
200D VAL* 1.3 77.9 - - - +
202D VAL* 1.3 64.6 + - - +
203D HIS* 2.8 36.9 + - - +
212D GLY* 3.3 2.4 - - - -
213D TYR* 2.8 47.2 + - - +
223D TRP* 4.2 4.7 - - - -
295D LEU* 5.1 0.9 - - - -
298D SER* 3.8 14.7 + - - +
299D GLN 5.3 0.9 - - - +
300D PRO* 4.6 4.7 - - - +
301D SER 5.3 0.5 + - - -
304D ASN* 4.1 13.7 + - - +
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Residues in contact with VAL 202 (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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201D GLU* 1.3 77.6 - - - +
203D HIS* 1.3 63.6 + - - +
204D ALA 3.6 20.2 - - - +
205D ARG* 4.0 23.3 - - + +
210D ASN* 5.8 0.9 - - - -
211D ALA 3.8 6.1 - - - +
212D GLY* 4.2 0.2 - - - -
223D TRP* 5.0 5.8 - - + -
291D LEU 4.7 0.2 - - - +
292D LEU* 4.0 39.0 - - + +
295D LEU* 4.4 14.9 - - + +
296D PRO 4.7 8.1 + - - +
297D LEU* 3.4 17.4 - - + -
298D SER* 3.0 27.5 + - - +
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Residues in contact with HIS 203 (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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201D GLU* 2.8 30.1 + - + +
202D VAL* 1.3 77.9 - - - +
204D ALA* 1.3 62.2 + - - +
211D ALA 2.8 9.4 + - - +
212D GLY* 3.6 12.8 + - - -
213D TYR* 3.6 15.7 - - + -
297D LEU* 3.7 9.2 - - - +
298D SER* 3.6 27.1 - - - +
300D PRO* 3.5 34.4 - - + +
304D ASN 3.3 26.7 + - - -
305D ARG* 4.4 2.2 - - - -
306D HIS 5.0 0.4 + - - -
309D LEU* 3.7 23.8 - - + +
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Residues in contact with ALA 204 (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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202D VAL* 3.6 4.3 - - - +
203D HIS* 1.3 79.9 - - - +
205D ARG* 1.3 63.3 + - - +
206D THR* 5.3 6.1 - - + -
209D VAL* 4.0 13.2 - - + +
210D ASN* 3.1 4.3 - - - -
211D ALA* 3.0 34.2 + - + +
297D LEU* 3.6 5.7 - - - +
309D LEU* 4.1 24.5 - - + -
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Residues in contact with ARG 205 (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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172D GLU* 6.1 1.1 - - - -
202D VAL* 4.0 16.2 - - + +
204D ALA* 1.3 75.7 - - - +
206D THR* 1.3 64.0 + - - +
209D VAL 3.5 4.0 - - - -
210D ASN* 3.5 21.3 - - - +
292D LEU 3.0 28.9 + - - -
293D ARG* 3.9 20.5 + - - +
294D THR 4.8 1.2 + - - -
295D LEU 2.8 33.5 + - - +
296D PRO* 4.3 1.8 - - - +
297D LEU* 3.9 32.6 - - + +
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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