Contacts of the strand formed by residues 325 - 331 (chain D) in PDB entry 3CB4
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 325 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D PRO* 4.1 15.9 - - + -
296D TYR* 3.5 21.1 - + - -
323D SER 3.2 2.4 + - - +
324D LEU* 1.3 76.9 - - - +
326D TYR* 1.3 74.7 + - - +
327D GLU* 3.6 28.0 - - + -
339D ARG* 3.4 37.2 - - - -
340D CYS* 3.2 7.6 - - - +
341D GLY* 2.7 47.7 + - - +
385D ASP* 5.9 0.2 - - - -
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Residues in contact with TYR 326 (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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311D ARG* 4.7 7.8 + - + -
314D LEU* 3.7 42.2 - - + -
315D GLY* 3.4 20.3 - - - -
318D SER* 3.9 18.7 + - - -
324D LEU* 4.1 14.3 + - + -
325D PHE* 1.3 90.2 - - - +
327D GLU* 1.3 67.1 + - - +
328D PRO* 5.8 0.9 - - + -
338D PHE* 4.0 24.0 - + + -
339D ARG 3.5 5.8 - - - -
340D CYS* 3.8 18.6 - - - -
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Residues in contact with GLU 327 (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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325D PHE* 3.6 21.5 - - + -
326D TYR* 1.3 81.3 - - - +
328D PRO* 1.3 81.3 - - + +
338D PHE* 3.4 5.4 - - - -
339D ARG* 2.8 68.8 + - + +
389D LYS* 4.9 9.5 + - - -
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Residues in contact with PRO 328 (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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307D TYR* 4.5 8.5 - - - +
326D TYR* 5.8 0.9 - - + -
327D GLU* 1.3 99.1 - - + +
329D GLU* 1.3 60.3 + - - +
337D GLY 3.8 1.3 - - - +
338D PHE* 3.7 24.2 - - + -
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Residues in contact with GLU 329 (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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298D GLY* 4.4 2.4 - - - -
300D PHE* 3.5 16.2 - - + -
327D GLU 3.6 0.2 + - - -
328D PRO* 1.3 76.7 - - - +
330D SER* 1.3 66.4 + - - +
336D PHE* 3.9 2.0 - - - -
337D GLY* 2.8 39.9 + - - +
338D PHE 4.5 0.9 - - - -
339D ARG* 3.5 43.5 - - + +
493D ASP* 4.6 5.0 - - - +
494D ALA* 3.3 40.5 + - + +
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Residues in contact with SER 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D PHE* 4.9 0.2 - - - -
329D GLU* 1.3 82.1 - - - +
331D SER* 1.3 67.3 + - - +
335D GLY 3.5 5.8 - - - -
336D PHE* 3.7 34.9 - - - -
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Residues in contact with SER 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D PHE* 4.0 10.0 - - - -
329D GLU* 5.1 0.2 - - - +
330D SER* 1.3 79.0 + - - +
332D SER* 1.3 64.9 + - - +
333D ALA 3.9 1.3 - - - -
334D LEU* 3.5 35.7 - - - +
335D GLY* 2.9 22.4 + - - -
492D VAL* 3.9 24.9 - - - +
493D ASP 5.6 0.2 + - - -
494D ALA* 4.1 6.1 + - - +
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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
------------------------------------------------------------
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