Contacts of the helix formed by residues 344 - 355 (chain 3) in PDB entry 5U8T
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 344 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3433 THR* 1.3 90.4 - - - +
3453 PHE* 1.3 65.0 + - - +
3463 ASP 3.0 2.7 + - - -
3473 ILE* 3.2 13.5 + - - +
3483 ARG* 2.9 27.8 + - - +
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Residues in contact with PHE 345 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3433 THR* 4.4 2.9 - - - +
3443 ASP* 1.3 78.4 - - - +
3463 ASP* 1.3 63.5 + - - +
3483 ARG* 3.3 38.9 + - - +
3493 ASN* 2.7 44.4 + - - -
43C LYS* 6.3 0.7 - - - -
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Residues in contact with ASP 346 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3413 MET 3.8 7.1 - - - +
3423 LEU* 3.0 21.5 - - + +
3433 THR* 2.9 23.5 + - - +
3443 ASP 3.0 0.4 - - - -
3453 PHE* 1.3 85.7 - - - +
3473 ILE* 1.3 55.7 + - - +
3483 ARG 3.0 4.0 - - - -
3493 ASN* 2.6 33.7 + - - +
3503 ILE* 2.9 19.6 + - + +
6553 PHE* 4.5 4.8 - - + -
6583 LYS* 5.4 9.3 - - + +
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Residues in contact with ILE 347 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3423 LEU* 3.6 20.7 + - + -
3433 THR 4.4 4.3 - - - +
3443 ASP* 3.2 21.3 + - - +
3463 ASP* 1.3 80.0 - - - +
3483 ARG* 1.3 56.0 + - - +
3503 ILE* 3.5 15.9 - - + +
3513 ASN* 2.3 51.4 + - - +
6623 TYR* 3.4 48.7 - - + +
6663 ARG* 5.2 6.1 - - - +
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Residues in contact with ARG 348 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3443 ASP* 2.9 17.6 + - - +
3453 PHE* 3.3 47.8 + - - +
3463 ASP 3.0 0.2 - - - -
3473 ILE* 1.3 80.3 - - + +
3493 ASN* 1.3 59.4 + - - +
3513 ASN* 3.9 6.7 - - - +
3523 LYS* 2.9 37.1 + - + +
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Residues in contact with ASN 349 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3453 PHE* 2.7 42.1 + - - -
3463 ASP* 2.6 19.6 + - - +
3483 ARG* 1.3 74.0 + - - +
3503 ILE* 1.3 64.6 + - - +
3523 LYS* 3.4 26.2 + - - +
3533 LEU* 2.9 26.5 + - - +
6553 PHE* 4.3 14.1 - - + -
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Residues in contact with ILE 350 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3423 LEU* 4.6 10.1 - - + -
3463 ASP* 2.9 32.2 + - + +
3473 ILE* 3.1 20.8 + - + +
3493 ASN* 1.3 76.8 - - - +
3513 ASN* 1.3 65.6 + - - +
3533 LEU* 3.6 3.6 + - - +
3543 SER* 2.9 23.4 + - - -
6553 PHE* 3.4 33.4 - - + -
6583 LYS* 4.5 12.1 - - + +
6593 TYR* 3.5 39.5 - - + -
6623 TYR* 3.8 27.1 - - + -
7173 LEU* 4.4 1.6 - - + -
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Residues in contact with ASN 351 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3473 ILE* 2.3 50.4 + - - +
3483 ARG* 4.0 6.2 - - - +
3503 ILE* 1.3 73.4 - - - +
3523 LYS* 1.3 65.9 + - - +
3533 LEU 3.2 1.8 - - - -
3543 SER* 2.5 27.2 + - - +
3553 LYS* 3.1 27.5 + - - +
6623 TYR* 4.0 10.6 + - - -
7173 LEU* 3.8 20.1 - - - +
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Residues in contact with LYS 352 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3483 ARG* 2.9 29.5 + - - +
3493 ASN* 3.4 28.8 + - - +
3513 ASN* 1.3 77.2 - - - +
3533 LEU* 1.3 61.9 + - - +
3553 LYS* 3.7 16.6 + - - +
3563 LYS* 3.9 8.0 - - - +
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Residues in contact with LEU 353 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3493 ASN 2.9 15.5 + - - +
3503 ILE* 3.8 6.1 - - - +
3523 LYS* 1.3 74.2 - - - +
3543 SER* 1.3 68.7 + - - +
3553 LYS 3.0 2.2 - - - -
3563 LYS* 3.0 28.4 + - + +
3593 ILE* 3.2 49.0 - - + +
3623 ILE* 5.7 6.7 - - + -
3633 LEU* 4.5 19.7 - - + -
6513 VAL 5.7 6.7 - - - +
6553 PHE* 4.5 19.5 - - + -
6593 TYR* 4.6 12.6 - - + -
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Residues in contact with SER 354 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3503 ILE 2.9 17.7 + - - -
3513 ASN* 2.5 28.8 + - - +
3533 LEU* 1.3 78.8 - - - +
3553 LYS* 1.3 70.7 + - - +
3563 LYS 3.4 6.8 + - - +
3573 LYS* 5.2 2.3 + - - +
3593 ILE* 3.7 14.5 - - - +
6593 TYR* 4.7 4.5 - - - -
7163 ARG* 4.1 14.2 + - - +
7173 LEU* 4.0 27.9 - - - +
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Residues in contact with LYS 355 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513 ASN* 3.1 34.9 + - - +
3523 LYS* 3.7 12.6 - - - +
3533 LEU 3.0 0.6 - - - -
3543 SER* 1.3 90.0 + - - +
3563 LYS* 1.3 62.1 + - + +
3573 LYS* 3.0 32.4 + - - +
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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