Contacts of the strand formed by residues 383 - 396 (chain D) in PDB entry 4OIN
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 GLY 383 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D VAL* 4.6 2.5 - - - -
214D GLU 3.1 15.3 - - - -
215D TYR* 4.0 4.9 - - - -
216D VAL* 4.0 7.5 - - - +
359D ALA 3.4 1.2 - - - +
360D ARG* 3.9 2.0 - - - -
361D VAL* 3.1 39.1 + - - +
381D ALA 3.3 5.0 + - - -
382D GLU* 1.3 74.1 - - - +
384D VAL* 1.3 64.8 + - - -
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Residues in contact with VAL 384 (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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213D VAL* 3.6 3.9 - - - -
214D GLU* 2.9 53.6 + - + +
216D VAL* 5.0 5.3 - - + +
340D THR* 5.6 4.5 - - + -
358D GLY* 5.1 8.5 - - - -
359D ALA 3.7 5.8 - - - +
360D ARG* 4.5 32.5 - - + +
383D GLY* 1.3 75.6 - - - +
385D VAL* 1.3 62.5 + - - +
386D HIS* 3.7 18.5 - - - +
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Residues in contact with VAL 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 3.7 25.8 - - + -
212D ARG 3.9 2.9 - - - +
213D VAL* 4.8 4.0 - - + +
355D VAL* 3.7 32.8 - - + -
356D PRO 4.1 3.4 - - - +
357D GLU* 3.8 0.3 - - - +
358D GLY* 2.7 32.9 + - - -
359D ALA 3.5 16.6 + - - +
361D VAL* 4.6 16.8 - - + -
367D ILE* 4.1 18.6 - - + -
384D VAL* 1.3 76.2 - - - +
386D HIS* 1.3 65.4 + - - +
387D LEU* 4.1 14.8 - - + -
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Residues in contact with HIS 386 (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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180D LYS* 3.8 10.2 + - - +
211D VAL* 3.7 3.6 - - - +
212D ARG* 2.9 45.7 + - + +
214D GLU* 3.8 26.3 - - + +
357D GLU* 3.4 20.9 + - - +
358D GLY* 5.5 4.0 - - - -
384D VAL* 3.7 25.1 - - + +
385D VAL* 1.3 79.0 - - - +
387D LEU* 1.3 64.4 + - - +
388D HIS* 3.4 23.9 + - - +
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Residues in contact with LEU 387 (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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180D LYS* 5.9 0.7 + - - +
181D ASP* 6.3 0.9 - - - -
205D TYR* 3.3 38.4 + - + -
208D PRO* 3.8 24.9 - - + -
210D ARG 4.5 0.2 - - - -
211D VAL* 3.6 31.9 - - + -
353D VAL* 3.8 14.4 - - + -
355D VAL 4.0 6.1 - - - +
356D PRO 3.9 7.4 - - - +
357D GLU* 2.9 50.8 + - + +
385D VAL* 4.1 6.3 - - + -
386D HIS* 1.3 71.1 - - - +
388D HIS* 1.3 67.3 + - - +
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Residues in contact with HIS 388 (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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176D ASP* 3.7 17.3 + - - +
180D LYS* 5.9 1.8 + - - -
205D TYR* 5.6 0.4 - - - -
208D PRO* 3.6 5.2 - - - +
209D ARG 3.5 2.4 + - - -
210D ARG* 2.9 65.7 + - - +
212D ARG* 4.0 17.2 - - + +
386D HIS* 3.4 34.6 + - + +
387D LEU* 1.3 83.5 - - - +
389D GLU* 1.3 73.1 + - - +
390D PRO* 3.6 3.1 - - - -
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Residues in contact with GLU 389 (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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174D GLY* 3.1 33.3 + - - +
175D VAL 4.4 10.8 - - - +
176D ASP* 3.1 35.7 + - + +
209D ARG* 2.6 44.2 + - + +
210D ARG* 4.0 21.6 + - + +
346D ARG* 4.1 18.8 + - - -
388D HIS* 1.3 73.9 - - - +
390D PRO* 1.3 67.8 - - - +
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Residues in contact with PRO 390 (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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171D LEU* 3.3 35.1 - - + +
175D VAL 5.3 0.5 - - - +
176D ASP* 4.3 6.1 - - - +
177D ALA* 4.3 3.6 - - + +
205D TYR* 3.5 43.7 - - + -
206D ARG 3.7 8.7 - - - +
208D PRO* 3.6 12.6 - - + -
209D ARG* 4.7 0.8 - - - +
388D HIS 3.6 2.2 - - - -
389D GLU* 1.3 91.7 - - - +
391D ALA* 1.3 65.1 + - - +
392D SER 3.6 14.4 - - - +
393D ILE* 4.1 5.4 - - + -
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Residues in contact with ALA 391 (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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170D PRO* 4.4 0.9 - - - +
171D LEU* 3.4 25.2 + - - +
206D ARG 2.8 5.4 + - - +
207D PHE* 2.7 23.9 + - + +
209D ARG* 3.4 34.6 + - - +
389D GLU 3.8 0.4 + - - -
390D PRO* 1.3 72.3 - - - +
392D SER* 1.3 64.3 + - - +
97F GLU* 3.5 18.8 - - - +
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Residues in contact with SER 392 (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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168D THR* 3.8 17.2 - - - +
169D TYR 3.2 18.2 - - - -
170D PRO* 4.5 2.7 - - - -
171D LEU* 4.5 1.6 - - - -
206D ARG* 2.9 45.4 + - - +
207D PHE* 4.5 6.4 - - - -
390D PRO* 3.2 6.5 - - - +
391D ALA* 1.3 80.3 - - - +
393D ILE* 1.3 65.5 + - - +
98F GLU* 4.8 5.7 + - - -
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Residues in contact with ILE 393 (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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168D THR* 3.5 3.3 - - - -
169D TYR* 2.9 43.1 + - + +
171D LEU* 3.7 36.1 - - + -
177D ALA* 4.4 13.0 - - + -
179D VAL* 4.5 5.6 - - + -
191D LEU* 3.6 51.4 - - + +
195D VAL* 5.5 0.7 - - + -
203D ALA* 4.3 15.3 - - + -
204D LEU 3.5 12.6 - - - +
205D TYR* 4.7 6.5 - - + -
390D PRO* 4.1 7.0 - - + -
392D SER* 1.3 78.6 - - - +
394D LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 394 (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 GLN* 4.1 19.5 - - - +
167D GLU 3.2 13.9 - - - +
168D THR* 3.2 23.3 - - - +
202D VAL 3.5 2.8 - - - +
203D ALA* 3.5 1.8 - - - -
204D LEU* 2.9 52.0 + - + +
206D ARG* 3.8 36.3 - - + +
393D ILE* 1.3 70.7 - - - +
395D VAL* 1.3 60.8 + - - +
396D VAL* 3.6 26.2 - - + -
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Residues in contact with VAL 395 (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 GLN* 3.4 3.3 - - - +
167D GLU 2.9 36.7 + - - +
169D TYR* 3.6 15.9 - - + -
185D VAL* 5.2 4.3 - - + -
191D LEU* 3.6 30.7 - - + -
197D SER* 3.4 28.3 - - - +
199D LEU* 3.8 25.8 - - + +
201D GLY 4.5 14.1 - - - +
202D VAL 4.0 3.6 - - - +
203D ALA* 4.7 7.4 - - + +
393D ILE 3.8 0.4 + - - -
394D LEU* 1.3 73.0 - - - +
396D VAL* 1.3 67.0 + - - +
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Residues in contact with VAL 396 (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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165D LYS 4.0 7.0 - - - +
166D GLN* 3.9 14.4 - - + +
199D LEU* 4.7 0.9 - - - -
200D ASP 4.5 0.9 - - - -
201D GLY* 3.2 3.8 - - - -
202D VAL* 2.7 42.7 + - + +
204D LEU* 5.0 8.5 - - + -
394D LEU* 3.6 34.8 - - + +
395D VAL* 1.3 78.6 - - - +
397D LYS* 1.3 76.3 + - - +
398D ALA* 3.5 11.5 + - + -
445D ARG* 5.7 2.7 - - - +
447D VAL* 3.7 26.9 - - + -
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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