Contacts of the helix formed by residues 323 - 331 (chain D) in PDB entry 3RIK
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 THR 323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319C PRO* 6.2 5.6 - - + -
285D ARG* 3.5 41.9 + - + +
286D LEU* 4.1 11.4 - - + -
288D LEU* 3.6 20.0 - - - +
289D PRO* 4.7 0.2 - - - +
319D PRO 4.4 10.8 - - - +
320D ALA* 3.1 19.2 + - - -
321D LYS 3.1 0.6 - - - -
322D ALA* 1.3 85.1 - - + +
324D LEU* 1.3 72.8 + - - +
325D GLY 3.3 0.4 + - - -
326D GLU* 3.5 1.6 + - - +
327D THR* 2.8 30.0 + - - -
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Residues in contact with LEU 324 (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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285D ARG* 4.0 22.4 - - - -
288D LEU* 4.2 4.7 - - + -
310D VAL* 4.1 22.9 - - + -
320D ALA* 3.0 14.2 + - + +
323D THR* 1.3 82.3 + - - +
325D GLY* 1.3 57.3 + - - +
327D THR* 3.4 2.6 + - - -
328D HIS* 3.0 30.5 + - - +
336D LEU* 3.7 28.8 - - + +
369D THR* 5.2 0.7 - - + +
370D ASN* 4.0 17.7 - - - +
373D TYR* 3.9 28.2 - - + +
375D VAL* 3.8 26.5 - - + -
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Residues in contact with GLY 325 (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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320D ALA 3.3 3.6 + - - -
321D LYS* 3.1 17.8 + - - -
324D LEU* 1.3 79.5 - - - +
326D GLU* 1.3 64.4 + - - +
328D HIS* 3.2 5.0 + - - +
329D ARG* 3.0 23.2 + - - +
373D TYR* 4.0 16.9 - - - -
374D HIS* 4.9 5.1 + - - -
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Residues in contact with GLU 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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289D PRO* 4.1 16.2 - - + -
321D LYS* 3.0 24.5 + - - +
322D ALA* 3.9 27.6 - - + +
323D THR 3.5 1.5 + - - +
325D GLY* 1.3 73.6 - - - +
327D THR* 1.3 63.4 + - - +
329D ARG* 2.7 45.2 + - - +
330D LEU* 3.0 32.4 + - + +
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Residues in contact with THR 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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288D LEU* 3.5 9.7 - - + +
289D PRO* 3.4 25.3 - - - +
292D ALA* 4.2 11.2 - - + -
308D ILE* 3.7 29.8 - - + -
323D THR 2.8 22.0 + - - -
324D LEU* 3.7 6.3 - - - -
326D GLU* 1.3 76.0 - - - +
328D HIS* 1.3 53.5 + - - +
330D LEU* 3.2 4.3 + - - -
331D PHE* 2.8 37.9 + - + +
334D THR 5.9 0.4 - - - +
336D LEU* 3.9 15.0 - - + -
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Residues in contact with HIS 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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75D PHE* 6.2 0.2 - + - -
76D GLN* 6.1 1.6 - - - +
324D LEU 3.0 17.2 + - - +
325D GLY 3.6 4.0 - - - +
327D THR* 1.3 74.6 - - - +
329D ARG* 1.3 68.7 + - - +
331D PHE 4.4 4.3 - - - +
332D PRO* 3.0 58.4 + - + +
334D THR 5.4 4.5 - - - -
335D MET* 6.6 0.2 - - - -
336D LEU* 4.5 7.8 - - + +
374D HIS* 3.2 59.0 + + + +
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Residues in contact with ARG 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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321D LYS* 5.7 6.3 - - - +
325D GLY 3.0 14.2 + - - +
326D GLU* 2.7 47.3 + - - +
328D HIS* 1.3 81.8 + - - +
330D LEU* 1.3 64.1 + - + +
332D PRO* 3.4 9.7 - - - +
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Residues in contact with LEU 330 (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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289D PRO* 4.1 17.3 - - + -
293D LYS* 4.1 34.8 - - + +
326D GLU* 3.0 23.7 + - + +
327D THR* 4.7 0.2 - - - -
329D ARG* 1.3 81.4 - - + +
331D PHE* 1.3 87.2 + - + +
332D PRO* 3.4 3.8 - - - +
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Residues in contact with PHE 331 (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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289D PRO 5.2 0.2 - - - -
292D ALA* 3.7 36.8 - - + -
293D LYS* 3.9 17.9 - - + -
296D LEU* 3.7 32.8 - - + -
297D THR* 4.1 15.5 - - + -
308D ILE* 5.4 1.3 - - + -
327D THR* 2.8 25.0 + - + +
328D HIS* 3.6 3.1 - - - -
330D LEU* 1.3 109.0 - - + +
332D PRO* 1.3 60.9 - - - +
333D ASN 3.0 3.1 - - - -
334D THR* 2.8 48.7 + - - +
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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