Contacts of the helix formed by residues 395 - 406 (chain K) in PDB entry 3E20
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 SER 395 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277K TYR* 4.7 8.7 - - - -
280K GLU* 2.8 30.0 + - - +
281K LYS* 3.3 33.5 - - - +
394K ARG* 1.3 83.9 - - - +
396K GLN* 1.3 65.6 + - - +
398K GLY* 3.1 18.0 + - - -
399K MET* 3.1 21.7 + - - +
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Residues in contact with GLN 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577J TYR* 3.2 26.0 - - - -
578J SER* 3.1 37.5 - - - +
647J ASP* 3.2 23.3 + - - +
281K LYS* 5.0 3.8 - - - +
394K ARG 3.9 0.4 + - - -
395K SER* 1.3 69.7 - - - +
397K GLU* 1.3 78.6 + - - +
399K MET* 3.2 9.0 + - + +
400K GLN* 2.9 52.2 + - + +
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Residues in contact with GLU 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K LYS* 3.1 57.5 - - - +
284K ILE* 3.8 21.6 - - + +
285K GLN* 3.7 33.0 - - + +
288K PHE* 4.0 15.0 - - + -
395K SER* 4.3 1.1 - - - +
396K GLN* 1.3 85.2 + - - +
398K GLY* 1.3 63.1 + - - +
400K GLN* 3.0 10.3 + - - +
401K PHE* 2.8 21.5 + - - +
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Residues in contact with GLY 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284K ILE* 3.8 14.5 - - - +
391K VAL* 5.7 0.9 - - - -
392K SER 3.6 22.2 - - - -
393K ASP* 4.1 6.1 - - - -
395K SER* 3.1 12.4 + - - -
396K GLN 3.2 0.2 - - - -
397K GLU* 1.3 78.7 - - - +
399K MET* 1.3 63.9 + - - +
401K PHE* 2.8 5.5 + - - +
402K VAL* 2.8 26.1 + - - +
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Residues in contact with MET 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576J GLY* 3.7 20.0 - - - +
578J SER* 5.2 8.3 - - - -
393K ASP* 3.5 41.6 - - - +
395K SER 3.1 11.5 + - - +
396K GLN* 3.2 13.4 + - + +
398K GLY* 1.3 73.5 - - - +
400K GLN* 1.3 58.4 + - - +
402K VAL* 3.3 3.3 + - - -
403K LYS* 2.8 51.5 + - + +
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Residues in contact with GLN 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572J ILE 3.9 13.0 + - - +
573J LEU* 4.1 0.4 - - - +
574J THR* 3.0 42.1 + - - +
576J GLY* 3.6 10.1 - - - -
577J TYR* 3.5 29.6 - - - +
288K PHE* 3.7 26.0 - - + -
396K GLN* 2.9 35.2 + - - +
397K GLU* 3.0 8.2 + - - +
399K MET* 1.3 73.1 - - - +
401K PHE* 1.3 60.4 + - - +
402K VAL 3.0 1.6 - - - -
404K GLY* 2.7 34.7 + - - -
405K PHE* 3.7 3.5 + - - -
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Residues in contact with PHE 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284K ILE* 3.6 24.0 - - + -
287K PHE* 4.1 31.6 - + - -
288K PHE* 4.5 1.5 - - - -
318K LEU* 3.1 57.0 - - + -
320K PHE 4.4 0.9 - - - -
391K VAL* 3.9 22.0 - - + -
397K GLU 2.8 10.4 + - - +
398K GLY* 2.8 7.5 + - - +
400K GLN* 1.3 71.9 - - - +
402K VAL* 1.3 62.5 + - + +
405K PHE* 3.4 20.8 + + + +
407K GLY* 3.1 39.5 + - - -
408K ILE 3.7 5.2 - - - -
409K GLY* 3.4 16.8 - - - -
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Residues in contact with VAL 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320K PHE* 3.6 52.0 - - + -
391K VAL* 6.1 0.4 - - + -
392K SER 5.3 0.2 - - - -
393K ASP* 3.8 17.0 - - + +
398K GLY* 2.8 20.7 + - - +
399K MET* 3.7 6.1 - - - +
400K GLN 2.9 0.4 + - - -
401K PHE* 1.3 80.1 - - + +
403K LYS* 1.3 65.0 + - + +
404K GLY 3.1 5.0 + - - -
406K GLY* 3.3 22.2 + - - -
407K GLY* 3.4 10.4 + - - -
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Residues in contact with LYS 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575J THR* 3.4 22.6 - - + +
576J GLY* 4.0 15.0 - - - +
591J SER* 4.7 13.7 + - - +
592J PHE 5.7 2.5 - - - +
624J GLU* 5.3 7.1 + - - -
399K MET* 2.8 37.8 + - + +
402K VAL* 1.3 76.1 - - + +
404K GLY* 1.3 56.8 + - - +
406K GLY 4.9 0.7 - - - -
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Residues in contact with GLY 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574J THR* 4.9 2.7 - - - -
575J THR* 4.2 18.2 - - - -
576J GLY 4.5 2.2 - - - -
611J MET* 5.1 4.5 - - - +
300K PHE* 4.6 4.2 - - - -
400K GLN* 2.7 16.4 + - - +
403K LYS* 1.3 79.8 - - - +
405K PHE* 1.3 79.9 + - - +
406K GLY 3.8 1.1 - - - -
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Residues in contact with PHE 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574J THR* 3.8 30.3 - - + -
611J MET* 4.1 26.9 - - + -
287K PHE* 4.0 12.3 - + - -
288K PHE* 3.4 25.8 - + - -
291K ILE* 3.7 21.5 - - + -
300K PHE* 3.5 52.2 - + + -
301K GLY* 4.2 3.7 - - - -
400K GLN 4.0 2.0 - - - -
401K PHE* 3.4 30.1 + + + +
404K GLY* 1.3 91.4 - - - +
406K GLY* 1.3 53.3 + - - +
407K GLY 2.7 15.7 + - - -
408K ILE 3.4 15.2 + - - +
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Residues in contact with GLY 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K GLY* 5.9 0.4 - - - -
302K VAL* 5.5 2.0 - - - +
323K LEU* 4.3 11.4 - - - +
402K VAL* 3.3 13.6 + - - +
403K LYS 4.9 0.4 - - - -
404K GLY 3.8 1.4 - - - -
405K PHE* 1.3 74.8 - - - +
407K GLY* 1.3 59.5 + - - +
408K ILE* 3.4 10.0 + - - +
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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