Contacts of the strand formed by residues 355 - 360 (chain D) in PDB entry 3DC1
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 PHE 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLY 3.5 11.9 - - - -
39C GLY* 3.7 19.5 - - - -
426C GOL 4.8 0.4 - - - -
200D GLY 5.6 1.1 - - - -
201D ASN 5.2 2.9 - - - +
202D ASN* 3.6 30.1 - - + -
203D PRO 4.0 9.4 - - - +
204D THR 4.1 8.1 - - - +
205D GLY* 4.3 4.2 - - - +
233D TYR* 3.5 25.4 - + - -
350D PRO* 3.3 14.4 - - - +
352D ALA 4.8 0.8 + - - +
353D GLY 3.8 0.4 - - - -
354D MET* 1.3 97.5 - - + +
356D LEU* 1.3 58.5 + - - +
399D ARG* 3.2 54.5 - - + -
400D ALA 3.3 3.6 - - - -
401D SER* 3.6 20.2 - - - -
402D PHE* 3.1 15.0 - - - -
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Residues in contact with LEU 356 (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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203D PRO 4.7 1.1 - - - -
333D ILE* 3.8 47.3 - - + +
334D LEU* 3.8 15.3 - - + -
337D ALA* 4.4 7.9 - - + -
347D TRP* 3.6 29.4 - - + -
348D HIS 3.9 10.5 - - - +
350D PRO* 3.9 7.9 - - + -
355D PHE* 1.3 74.1 - - - +
357D TRP* 1.3 60.2 - - - +
358D ILE* 3.7 28.5 + - + +
398D LEU 3.8 0.7 - - - +
399D ARG* 3.6 1.9 - - - -
400D ALA* 2.8 39.2 + - + +
402D PHE* 3.8 1.7 - - + -
414D PHE* 4.1 3.8 - - + -
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Residues in contact with TRP 357 (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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140D PRO* 3.5 26.9 - - + +
203D PRO* 3.4 43.3 - - + +
204D THR* 3.5 37.7 + - + +
206D ASN* 5.4 1.8 - - - -
346D GLU 3.9 0.2 - - - +
347D TRP* 3.1 22.9 - - - +
348D HIS* 4.5 11.3 + + - +
356D LEU* 1.3 73.3 - - - +
358D ILE* 1.3 61.0 + - - +
359D LYS 4.1 0.2 + - - -
384D GLY* 3.8 27.8 - - - -
387D PHE* 4.3 4.0 - + - -
388D TYR* 3.7 9.6 - + - -
397D TYR* 3.2 59.2 + + + -
398D LEU 3.5 24.5 - - - -
399D ARG* 4.0 4.5 - - + -
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Residues in contact with ILE 358 (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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341D LEU* 3.9 13.0 - - + -
345D ALA* 3.8 23.8 - - + -
346D GLU 3.6 2.0 - - - -
347D TRP* 4.2 11.7 - - + -
356D LEU* 3.7 32.3 - - + -
357D TRP* 1.3 78.4 - - - +
359D LYS* 1.3 62.2 + - - +
360D VAL* 3.8 11.3 + - + +
381D MET* 4.9 7.4 - - - -
397D TYR* 3.1 9.2 - - - -
398D LEU* 2.8 50.1 + - + +
400D ALA* 4.5 11.2 - - + -
414D PHE* 3.7 24.0 - - + -
417D LEU* 6.0 0.2 - - + -
421D ILE* 6.3 0.7 - - + -
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Residues in contact with LYS 359 (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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345D ALA* 3.2 6.6 - - - -
346D GLU* 2.8 58.1 + - + +
358D ILE* 1.3 70.3 - - - +
360D VAL* 1.3 68.3 + - - +
361D LYS* 4.7 4.5 - - + +
396D PRO* 3.7 20.0 - - + +
397D TYR* 3.4 45.2 - - + +
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Residues in contact with VAL 360 (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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344D LEU 4.5 0.4 - - - +
345D ALA* 3.9 6.7 - - - -
358D ILE* 4.3 9.4 - - + +
359D LYS* 1.3 79.6 + - - +
361D LYS* 1.3 65.4 + - - +
362D GLY 3.9 1.0 + - - -
363D ILE* 3.8 36.9 - - + +
366D VAL* 4.0 20.6 - - + -
369D LEU* 4.7 2.7 - - + -
396D PRO* 2.9 33.6 + - + +
398D LEU* 4.3 18.8 - - + -
421D ILE* 3.9 28.0 - - + -
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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