Contacts of the helix formed by residues 321 - 329 (chain A) in PDB entry 2IVF
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 ASP 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU 3.9 0.6 + - - -
320A PHE* 1.3 69.1 - - - +
322A ARG* 1.3 62.3 + - - +
323A GLN* 3.6 9.0 + - - +
324A PHE* 3.2 32.8 + - + +
325A VAL* 3.0 24.8 + - - +
467A LEU 2.8 14.3 + - - +
468A SER* 4.1 6.1 - - - +
469A GLY* 3.9 17.2 - - - +
473A LYS* 4.2 10.0 + - - -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LYS* 6.2 3.8 - - - +
320A PHE* 3.1 37.1 + - + +
321A ASP* 1.3 72.0 + - - +
323A GLN* 1.3 57.7 + - - +
325A VAL* 3.3 3.0 + - - +
326A CYS* 2.9 38.5 + - - -
379A MET* 3.8 22.7 - - + -
380A PRO 5.4 2.7 + - - -
382A LEU* 3.7 26.4 - - + +
383A GLU* 2.9 41.6 + - - -
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASP* 3.3 8.3 + - - +
322A ARG* 1.3 79.0 - - - +
324A PHE* 1.3 57.7 + - - +
326A CYS* 3.3 2.6 + - - +
327A GLU* 3.0 39.9 + - - +
376A LEU* 4.4 5.0 - - + +
379A MET* 3.7 28.7 - - + +
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ASP* 3.2 25.5 + - + +
323A GLN* 1.3 77.0 - - - +
325A VAL* 1.3 58.5 + - - +
327A GLU* 4.6 4.9 - - - -
328A GLN* 2.8 53.7 + - + +
466A ALA* 3.2 28.9 - - + -
469A GLY* 3.5 24.9 - - - -
471A TRP* 3.3 71.8 - + - -
473A LYS* 4.2 3.6 - - - -
799A PHE* 3.9 26.7 - + - -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A PHE* 4.8 2.2 - - + -
321A ASP 3.0 18.6 + - - +
322A ARG* 3.7 3.4 - - - +
324A PHE* 1.3 77.6 - - - +
326A CYS* 1.3 63.7 + - - +
327A GLU 3.3 0.9 + - - -
329A THR* 2.7 33.3 + - - +
331A LEU* 3.6 33.7 - - + -
332A PRO* 3.7 2.8 - - - +
382A LEU* 3.9 24.2 - - + -
402A PHE* 4.8 1.3 - - + -
466A ALA* 3.4 26.5 - - + +
467A LEU* 3.7 25.8 - - + +
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Residues in contact with CYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 2.9 24.0 + - - +
323A GLN 3.7 4.7 - - - +
325A VAL* 1.3 77.9 - - - +
327A GLU* 1.3 60.5 + - - +
329A THR 4.4 1.4 - - - +
332A PRO* 3.6 20.9 - - - +
358A PHE* 4.1 4.9 - - - -
376A LEU* 3.7 25.2 - - + +
379A MET* 4.2 11.4 - - - -
380A PRO* 3.8 28.9 - - + -
382A LEU* 3.7 32.5 - - - -
811A ARG* 5.4 0.2 + - - -
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A GLN* 3.0 25.2 + - + +
324A PHE* 3.9 4.0 - - - +
326A CYS* 1.3 79.8 - - - +
328A GLN* 1.3 86.5 + - - +
329A THR 3.5 0.8 + - - -
358A PHE* 5.8 0.2 - - - -
374A LEU* 3.3 45.9 - - + +
375A LYS* 5.0 2.6 - - - -
376A LEU* 3.8 18.3 + - + +
799A PHE* 4.2 5.9 - - - -
802A LYS* 2.5 42.7 + - - +
811A ARG* 4.4 7.1 + - - +
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A PHE* 2.8 45.3 + - + +
327A GLU* 1.3 104.1 + - - +
329A THR* 1.3 59.0 + - + +
374A LEU* 3.8 11.4 - - - +
471A TRP* 3.0 35.4 + - + -
798A HIS* 3.0 32.3 + - - +
799A PHE* 3.7 6.5 - - - +
805A PHE* 3.7 19.1 - - - -
811A ARG* 3.6 5.2 - - - +
812A ALA* 2.9 24.8 + - - +
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A PHE* 4.6 0.7 - - + +
325A VAL* 2.7 25.7 + - - +
326A CYS 4.4 2.1 - - - +
328A GLN* 1.3 89.7 - - + +
330A ASP* 1.3 58.8 + - - +
331A LEU* 3.0 24.2 + - + +
332A PRO* 3.3 15.8 - - - +
466A ALA* 4.0 17.3 - - + -
471A TRP* 4.0 9.0 - - + -
811A ARG* 3.6 19.3 + - - -
812A ALA 3.1 12.1 - - - +
814A PHE* 3.9 23.3 - - + -
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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