Contacts of the helix formed by residues 399 - 408 (chain A) in PDB entry 1TFZ
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 GLY 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ASP* 3.4 20.2 + - - -
356A LEU* 3.8 6.0 - - - +
358A GLN* 3.2 19.1 - - - -
396A GLY 4.9 0.2 + - - -
397A GLY* 3.8 0.6 - - - -
398A PHE* 1.3 81.9 - - - +
400A LYS* 1.3 65.8 + - - +
401A GLY 3.0 2.9 - - - -
402A ASN* 2.9 19.8 + - - +
403A PHE* 3.8 0.2 - - - -
551A 869 3.4 12.0 - - - -
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Residues in contact with LYS 400 (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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229A PHE 5.6 3.0 + - - -
230A ALA 6.1 2.6 - - - -
246A SER* 5.5 5.8 + - - -
247A ALA* 6.0 0.8 - - - +
248A VAL* 4.8 8.1 - - - +
349A ASP* 3.7 1.0 + - - -
398A PHE* 3.4 18.3 - - + +
399A GLY* 1.3 79.6 - - - +
401A GLY* 1.3 61.4 + - - +
402A ASN 3.2 0.7 + - - -
403A PHE* 3.2 33.5 + - + +
404A SER* 4.1 2.4 + - - -
551A 869 3.4 44.0 - - - +
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Residues in contact with GLY 401 (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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349A ASP* 2.9 22.7 + - - -
400A LYS* 1.3 79.1 - - - +
402A ASN* 1.3 56.0 + - - +
403A PHE 3.3 0.2 - - - -
404A SER* 3.5 8.3 + - - -
405A GLU* 3.0 36.2 + - - +
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Residues in contact with ASN 402 (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 TYR* 2.5 32.6 + - - -
328A ARG* 3.8 3.6 + - - -
347A LEU* 3.8 13.8 - - + +
348A VAL 2.9 23.6 + - - +
349A ASP* 3.4 12.6 + - - +
358A GLN* 2.7 27.1 + - - +
399A GLY 2.9 11.3 + - - +
401A GLY* 1.3 74.1 - - - +
403A PHE* 1.3 58.6 + - - +
404A SER 3.1 2.0 - - - -
405A GLU* 4.2 2.7 - - - -
406A LEU* 2.8 35.3 + - - +
551A 869 3.3 15.9 - - - +
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Residues in contact with PHE 403 (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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242A SER* 5.6 15.0 - - - +
244A LEU* 4.6 28.3 - - + -
399A GLY 3.8 1.8 - - - -
400A LYS* 3.2 32.9 + - + +
402A ASN* 1.3 78.9 - - - +
404A SER* 1.3 61.0 + - - +
406A LEU* 4.2 2.1 - - - +
407A PHE* 3.8 15.9 + - - +
551A 869 3.2 90.8 + + + +
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Residues in contact with SER 404 (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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400A LYS 4.9 2.5 - - - -
401A GLY* 3.5 9.6 + - - -
402A ASN 3.1 0.2 - - - -
403A PHE* 1.3 77.8 - - - +
405A GLU* 1.3 66.1 + - - +
406A LEU 3.1 1.8 - - - -
407A PHE* 3.0 7.0 + - - +
408A LYS* 2.8 30.4 + - - -
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Residues in contact with GLU 405 (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 TYR* 4.0 20.7 - - + -
324A ASN* 5.0 9.0 - - - +
328A ARG* 3.5 42.1 + - - +
401A GLY* 3.0 27.1 + - - +
402A ASN* 4.2 3.1 - - - -
404A SER* 1.3 79.8 + - - +
406A LEU* 1.3 51.5 + - - +
408A LYS* 2.7 40.5 - - - +
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Residues in contact with LEU 406 (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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317A PRO* 4.1 29.8 - - + -
318A PRO* 4.3 9.5 - - + +
321A TYR* 4.4 8.0 - - + -
347A LEU* 3.9 18.4 - - + -
402A ASN 2.8 18.0 + - - +
403A PHE* 4.2 4.3 - - - +
405A GLU* 1.3 77.6 - - - +
407A PHE* 1.3 61.3 + - - +
408A LYS* 3.3 12.4 + - - +
551A 869 3.8 33.2 - - + +
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Residues in contact with PHE 407 (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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403A PHE 3.8 11.3 + - - +
404A SER* 3.0 8.5 + - - +
406A LEU* 1.3 77.0 - - - +
408A LYS* 1.3 71.2 + - - +
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Residues in contact with LYS 408 (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 PRO* 3.1 27.3 - - + +
320A THR* 3.3 20.5 + - - +
321A TYR* 3.0 45.5 - - - +
324A ASN* 4.6 10.8 - - - +
404A SER* 2.8 13.7 + - - -
405A GLU* 2.7 26.5 - - - +
406A LEU* 3.3 7.6 + - - +
407A PHE* 1.3 88.7 - - - +
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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