Contacts of the helix formed by residues 318 - 329 (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 PRO 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A SER 4.4 2.5 - - - +
317A PRO* 1.3 91.4 - - + +
319A PRO* 1.3 76.7 - - + +
320A THR* 3.0 17.0 - - + +
321A TYR* 3.0 14.9 + - - +
322A TYR* 3.5 5.8 - - - -
406A LEU* 4.3 10.5 - - + +
408A LYS* 3.1 24.9 - - + +
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Residues in contact with PRO 319 (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 4.6 0.2 - - - +
318A PRO* 1.3 88.4 - - + +
320A THR* 1.3 59.9 + - + +
322A TYR* 2.9 20.0 + - + +
323A GLN* 3.1 26.0 + - + +
342A GLU* 3.7 22.3 - - - +
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Residues in contact with THR 320 (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* 3.4 11.6 - - + +
319A PRO* 1.3 80.8 - - + +
321A TYR* 1.3 63.2 + - - +
323A GLN* 3.1 26.3 + - - +
324A ASN* 3.0 32.5 + - - -
408A LYS* 3.3 25.9 + - - +
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Residues in contact with TYR 321 (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* 3.5 23.6 - - + -
318A PRO 3.0 11.8 + - - +
320A THR* 1.3 75.2 - - - +
322A TYR* 1.3 75.4 + + - +
324A ASN* 3.7 5.4 + - + +
325A LEU* 3.1 37.5 + - + +
328A ARG* 3.4 16.0 + - - -
347A LEU* 3.6 14.7 - - + -
348A VAL 2.8 25.0 + - - -
402A ASN* 2.5 31.0 + - - -
405A GLU* 4.0 23.3 - - + -
406A LEU* 4.4 9.9 - - + -
408A LYS* 3.0 30.2 - - - +
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Residues in contact with TYR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER* 5.6 0.7 - - - -
317A PRO* 3.3 37.8 - - + +
318A PRO 3.5 10.8 - - - -
319A PRO 2.9 7.0 + - - +
321A TYR* 1.3 83.6 - + - +
323A GLN* 1.3 62.7 + - - +
325A LEU* 3.3 34.4 + - + +
326A LYS* 3.4 11.6 + - - +
338A ILE* 3.9 18.4 - - + +
341A CYS 3.8 1.6 - - - -
342A GLU* 3.5 66.2 - - + +
345A GLY* 3.2 19.3 - - - -
346A ILE 2.8 29.4 + - - -
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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
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319A PRO* 3.1 22.9 + - + +
320A THR* 3.1 34.3 + - - +
322A TYR* 1.3 76.7 - - - +
324A ASN* 1.3 69.4 + - - +
326A LYS* 3.3 30.8 + - - +
327A LYS* 3.9 9.4 + - - +
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Residues in contact with ASN 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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320A THR* 3.0 22.2 + - - +
321A TYR* 4.0 6.3 - - + +
323A GLN* 1.3 84.4 + - - +
325A LEU* 1.3 62.3 + - - +
326A LYS 3.2 0.9 - - - -
327A LYS* 3.2 27.6 + - - +
328A ARG* 3.0 34.5 + - - +
405A GLU* 5.0 8.5 - - - +
408A LYS* 4.6 13.9 - - - +
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Residues in contact with LEU 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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321A TYR* 3.1 21.3 + - + +
322A TYR* 3.4 39.3 - - + +
323A GLN 3.2 0.4 - - - -
324A ASN* 1.3 75.9 - - - +
326A LYS* 1.3 64.4 + - - +
328A ARG* 3.4 31.6 - - + +
329A VAL* 3.0 50.0 + - + +
330A GLY 3.8 0.3 + - - -
338A ILE* 4.3 13.9 - - + -
341A CYS* 4.9 2.9 - - + -
348A VAL* 3.5 39.3 - - + +
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Residues in contact with LYS 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 TYR 3.4 7.6 + - - +
323A GLN* 3.3 25.1 + - - +
324A ASN 3.2 0.2 - - - -
325A LEU* 1.3 79.9 - - - +
327A LYS* 1.3 60.8 + - + +
330A GLY* 3.4 20.8 - - - -
335A ASP* 3.5 36.8 - - - +
338A ILE* 3.7 20.4 - - + +
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Residues in contact with LYS 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 4.1 8.5 - - - +
324A ASN* 3.2 31.0 + - - +
325A LEU 3.1 0.6 - - - -
326A LYS* 1.3 84.3 - - + +
328A ARG* 1.3 59.1 + - + +
329A VAL 3.7 0.2 - - - -
330A GLY* 4.5 1.4 + - - -
331A ASP* 5.6 0.3 - - - +
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Residues in contact with ARG 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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321A TYR* 3.4 21.2 + - - -
324A ASN* 3.0 23.5 + - - +
325A LEU* 3.3 28.5 + - + +
327A LYS* 1.3 78.9 - - - +
329A VAL* 1.3 61.1 + - + +
330A GLY 3.7 0.4 - - - -
331A ASP* 4.7 1.3 - - - -
348A VAL 2.9 25.7 + - - -
349A ASP* 2.9 33.5 + - - +
350A ARG* 2.9 31.3 + - + +
402A ASN* 3.8 2.2 + - - -
405A GLU* 3.5 40.1 + - - +
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Residues in contact with VAL 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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325A LEU* 3.0 40.6 + - + +
328A ARG* 1.3 83.0 - - + +
330A GLY* 1.3 52.8 + - - +
331A ASP* 2.7 7.1 + - - -
332A VAL* 2.7 33.6 + - + +
333A LEU* 3.2 20.7 + - + +
338A ILE* 4.5 6.3 - - + -
348A VAL* 3.8 26.5 - - + -
349A ASP* 5.0 3.4 - - - +
350A ARG* 3.5 30.7 - - + +
355A THR* 4.5 4.0 - - + -
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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