Contacts of the helix formed by residues 373 - 386 (chain f) in PDB entry 5T0J
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 373 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371f CYS* 3.2 8.7 - - - -
372f ASN 1.3 75.4 + - - -
374f ASP* 1.3 63.4 + - - +
375f VAL 3.4 0.5 + - - -
376f THR* 3.5 17.4 + - - -
377f SER* 3.8 8.5 + - - -
410f LYS* 5.6 5.4 + - - -
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Residues in contact with ASP 374 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371f CYS 3.2 2.6 + - - -
372f ASN* 3.5 2.1 - - + -
373f GLY* 1.3 79.4 - - - +
375f VAL* 1.3 57.7 + - + +
377f SER* 3.5 7.4 + - - +
378f THR* 2.5 48.5 + - - -
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Residues in contact with VAL 375 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338f VAL* 4.7 23.1 - - + -
363f CYS* 3.8 20.9 - - - +
370f SER* 3.5 35.2 - - - +
371f CYS 2.9 19.5 + - - +
372f ASN* 5.3 1.3 - - + -
374f ASP* 1.3 77.4 - - + +
376f THR* 1.3 59.5 + - - +
378f THR* 3.6 6.2 - - - -
379f ILE* 2.8 48.5 + - + +
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Residues in contact with THR 376 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371f CYS* 3.2 27.1 + - - +
373f GLY 3.5 10.0 + - - -
374f ASP 3.3 0.6 - - - -
375f VAL* 1.3 79.3 - - - +
377f SER* 1.3 65.3 + - - +
379f ILE* 3.1 3.8 + - - +
380f LEU* 3.0 37.3 + - + +
403f LEU* 4.6 14.4 - - + +
407f HIS* 5.0 0.7 - - - -
410f LYS* 3.7 30.1 - - - +
412f GLU* 3.8 22.0 - - + -
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Residues in contact with SER 377 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373f GLY 3.8 7.8 + - - -
374f ASP* 3.5 10.3 + - - -
376f THR* 1.3 82.2 - - - +
378f THR* 1.3 56.8 + - - +
380f LEU* 4.0 7.5 - - - +
381f GLN* 3.1 32.2 + - - +
412f GLU* 5.0 9.8 + - - +
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Residues in contact with THR 378 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342f LEU* 3.7 29.6 - - + -
363f CYS* 5.7 1.1 - - - -
374f ASP* 2.5 39.9 + - - -
375f VAL* 3.6 8.3 - - - -
376f THR 3.1 0.2 - - - -
377f SER* 1.3 75.9 - - - +
379f ILE* 1.3 56.4 + - - +
381f GLN* 3.3 6.1 + - - +
382f THR* 2.4 40.8 + - - +
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Residues in contact with ILE 379 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342f LEU* 5.0 3.1 - - + -
363f CYS* 3.9 14.4 - - + +
364f GLY* 3.7 30.1 - - - +
370f SER 5.3 0.4 - - - +
375f VAL* 2.8 39.1 + - + +
376f THR* 3.8 4.7 - - - +
378f THR* 1.3 75.5 - - - +
380f LEU* 1.3 70.1 + - + +
382f THR* 3.2 6.9 + - - -
383f ILE* 3.1 24.1 + - - +
399f LEU* 3.8 29.4 - - + +
402f GLY* 4.5 15.5 - - - +
414f ILE* 4.9 2.9 - - + -
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Residues in contact with LEU 380 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376f THR* 3.0 31.8 + - + +
377f SER* 4.2 6.5 - - - +
379f ILE* 1.3 82.4 - - + +
381f GLN* 1.3 59.2 + - - +
383f ILE* 3.2 14.8 - - - +
384f MET* 3.2 22.6 - - - +
403f LEU* 5.0 11.0 - - + -
412f GLU* 3.9 34.1 - - + +
413f ALA 4.5 15.0 - - - +
414f ILE* 3.8 34.3 - - + -
417f ILE* 4.4 7.4 - - + +
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Residues in contact with GLN 381 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377f SER* 3.1 21.8 + - - +
378f THR* 3.8 5.9 - - + +
380f LEU* 1.3 75.4 - - - +
382f THR* 1.3 65.2 + - - +
384f MET* 3.3 19.3 + - + +
385f GLU* 3.6 7.1 + - - +
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Residues in contact with THR 382 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342f LEU* 3.5 32.8 - - + +
345f VAL* 3.7 18.2 - - + -
346f MET* 5.0 9.3 - - + +
378f THR* 2.4 29.0 + - - +
379f ILE* 3.2 8.0 + - - -
381f GLN* 1.3 78.1 - - - +
383f ILE* 1.3 60.9 + - - +
385f GLU* 3.3 20.7 + - + +
386f LYS* 3.1 31.4 + - - +
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Residues in contact with ILE 383 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379f ILE 3.1 14.6 + - - +
380f LEU* 3.2 21.8 - - - +
382f THR* 1.3 74.6 - - - +
384f MET* 1.3 61.7 + - - +
386f LYS* 2.7 42.4 - - - +
387f SER* 4.5 3.1 - - - -
390f GLU* 3.3 27.8 - - + +
395f TYR* 3.7 28.0 - - + -
399f LEU* 3.6 21.8 - - + -
414f ILE* 4.5 2.5 - - + -
417f ILE* 4.2 17.5 - - + -
418f LEU* 4.3 12.3 - - + -
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Residues in contact with MET 384 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380f LEU 3.2 16.6 - - - +
381f GLN* 3.3 13.9 + - + +
382f THR 3.3 1.2 - - - -
383f ILE* 1.3 80.6 - - - +
385f GLU* 1.3 59.9 + - - +
386f LYS 4.8 1.3 - - - -
387f SER* 4.9 7.4 - - - -
417f ILE* 3.9 40.6 - - + +
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Residues in contact with GLU 385 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346f MET* 4.8 21.5 - - + +
349f SER 4.7 10.8 + - - -
381f GLN 3.6 6.9 + - - +
382f THR* 3.3 12.5 + - + +
383f ILE 3.2 0.8 - - - -
384f MET* 1.3 80.9 - - - +
386f LYS* 1.3 74.4 + - - +
387f SER* 4.0 2.0 + - - -
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Residues in contact with LYS 386 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345f VAL* 3.4 23.7 - - + +
346f MET* 6.3 0.4 - - - -
349f SER 4.6 9.2 - - - +
350f LYS* 3.3 44.2 - - + +
356f ALA* 5.3 0.7 - - + +
360f ALA* 3.9 6.5 - - - +
382f THR* 3.1 42.3 + - - +
383f ILE* 2.7 41.1 + - + +
385f GLU* 1.3 88.3 + - - +
387f SER* 1.3 58.7 + - - +
389f THR* 4.1 16.8 - - - +
390f GLU* 4.0 6.4 - - + +
395f TYR* 4.7 1.4 + - - -
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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