Contacts of the helix formed by residues 324 - 335 (chain A) in PDB entry 5TF6
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 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PRO 3.6 15.4 + - - -
152A LEU* 3.5 15.3 - - - -
156A THR 4.6 3.8 - - - -
158A ARG 5.9 1.8 - - - -
322A LYS 3.5 4.2 + - - -
323A VAL* 1.3 75.8 - - - +
325A PRO* 1.3 75.3 - - - +
326A SER* 3.5 4.4 + - - -
327A LEU* 2.9 30.8 + - - +
328A ILE* 3.1 15.3 + - - +
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Residues in contact with PRO 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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156A THR* 3.5 35.4 - - + +
324A SER* 1.3 89.1 - - - +
326A SER* 1.3 55.8 + - - +
328A ILE* 3.1 7.8 + - + +
329A CYS* 2.9 28.1 + - - +
346A ILE* 3.6 42.6 - - + +
348A LEU* 4.0 18.5 - - + +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PRO* 3.3 43.5 - - - +
127A SER* 3.8 7.2 - - - -
324A SER* 3.2 4.3 + - - -
325A PRO* 1.3 75.4 - - - +
327A LEU* 1.3 65.8 + - - +
329A CYS* 3.4 8.8 + - - +
330A GLN* 3.0 23.7 + - - +
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Residues in contact with LEU 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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127A SER* 3.5 29.8 - - - +
128A TYR 4.8 4.0 - - - +
129A THR* 3.5 24.0 - - + -
322A LYS 5.5 0.7 - - - +
323A VAL* 4.4 19.5 - - + -
324A SER* 2.9 21.5 + - - +
326A SER* 1.3 76.9 - - - +
328A ILE* 1.3 63.1 + - - +
330A GLN* 3.4 11.8 + - - +
331A PHE* 3.0 21.7 + - - +
377A PHE* 4.2 12.4 - - + -
378A GLN* 3.8 27.1 - - + +
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Residues in contact with ILE 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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316A LEU* 4.3 22.9 - - + -
319A LEU* 4.0 9.9 - - + -
323A VAL* 3.8 22.0 - - + -
324A SER 3.1 13.2 + - - +
325A PRO* 3.1 9.6 + - + +
327A LEU* 1.3 77.7 - - - +
329A CYS* 1.3 61.6 + - - +
331A PHE* 3.1 11.3 + - + +
332A LEU* 2.9 29.2 + - + +
346A ILE* 4.1 19.3 - - + -
348A LEU* 4.2 11.4 - - + -
355A ALA* 3.9 26.5 - - + -
357A ILE* 4.5 3.4 - - + -
377A PHE* 4.1 10.3 - - + -
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Residues in contact with CYS 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 PRO 2.9 17.8 + - - +
326A SER* 3.6 12.6 - - - +
328A ILE* 1.3 71.3 - - - +
330A GLN* 1.3 63.1 + - - +
332A LEU* 3.0 8.0 + - - +
333A GLN* 3.0 48.1 + - - +
340A GLU* 5.4 7.2 - - - -
343A ILE* 4.7 13.7 - - - -
346A ILE* 3.7 17.2 - - + +
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Residues in contact with GLN 330 (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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127A SER* 3.6 17.1 + - - -
129A THR* 4.7 2.2 - - - +
326A SER 3.0 17.8 + - - +
327A LEU* 3.7 14.6 + - - +
329A CYS* 1.3 74.7 - - - +
331A PHE* 1.3 60.1 + - - +
333A GLN* 3.3 6.9 + - - -
334A GLU* 2.7 59.5 + - + +
505A GOL 2.6 56.3 + - - -
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Residues in contact with PHE 331 (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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316A LEU* 4.6 7.9 - - + -
327A LEU 3.0 6.7 + - - +
328A ILE* 3.2 12.3 - - + +
330A GLN* 1.3 80.7 - - - +
332A LEU* 1.3 64.7 + - + +
334A GLU* 5.2 0.2 - - - -
335A GLU* 2.9 52.5 + - + +
336A ILE* 3.2 21.4 + - + +
372A LEU* 4.0 20.2 - - + -
375A SER* 3.8 16.6 - - - -
376A GLN 3.1 28.0 - - - -
377A PHE* 3.5 42.2 - + + -
382A ILE* 4.5 9.6 - - + -
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Residues in contact with LEU 332 (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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316A LEU* 5.0 1.1 - - + -
328A ILE* 2.9 19.3 + - + +
329A CYS* 3.0 6.7 + - - +
331A PHE* 1.3 85.0 - - + +
333A GLN* 1.3 57.1 + - - +
336A ILE* 3.3 8.4 - - + +
337A HIS 3.1 10.0 + - - -
338A ILE* 3.0 40.9 + - + +
343A ILE* 3.8 28.3 - - + -
346A ILE* 4.1 12.6 - - + -
357A ILE* 3.8 39.0 - - + -
359A PHE* 4.9 0.9 - - + -
372A LEU* 3.9 26.2 - - + -
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Residues in contact with GLN 333 (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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329A CYS* 3.0 38.9 + - - +
330A GLN* 3.9 5.5 + - - +
332A LEU* 1.3 76.8 - - - +
334A GLU* 1.3 68.7 + - + +
337A HIS* 3.3 19.2 + - - -
338A ILE 3.4 19.2 + - - +
339A ASN* 5.4 0.4 - - - +
340A GLU* 3.9 41.5 + - - +
343A ILE* 4.7 4.9 - - + -
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Residues in contact with GLU 334 (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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330A GLN* 2.7 53.8 + - + +
331A PHE* 5.2 0.2 - - - -
333A GLN* 1.3 78.4 - - + +
335A GLU* 1.3 75.9 + - + +
337A HIS* 3.3 21.7 + - - -
505A GOL 4.3 10.9 + - - -
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Residues in contact with GLU 335 (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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331A PHE* 2.9 39.8 + - + +
334A GLU* 1.3 93.7 - - + +
336A ILE* 1.3 67.4 + - + +
337A HIS* 3.3 16.3 + - - -
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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