Contacts of the helix formed by residues 366 - 384 (chain A) in PDB entry 4G1T
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 THR 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU* 1.3 68.8 - - - +
367A PRO* 1.3 65.0 - - + +
368A VAL* 4.1 13.1 - - - +
369A ALA* 2.7 45.6 + - - +
370A LYS 2.8 10.9 + - - -
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU 3.1 8.3 - - - +
366A THR* 1.3 82.0 - - + +
368A VAL* 1.3 62.6 + - + +
370A LYS* 3.7 7.7 - - + +
371A GLN* 3.0 23.9 + - - +
401A ILE* 3.8 19.4 - - + +
403A GLN* 3.4 33.2 - - + +
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 2.9 12.7 + - - +
367A PRO* 1.3 74.6 - - + +
369A ALA* 1.3 61.9 + - + +
371A GLN* 3.3 23.3 - - - +
372A LEU* 3.4 7.4 + - - +
403A GLN* 4.1 26.9 - - + +
405A SER* 5.6 5.2 - - - -
407A GLU* 5.2 9.8 - - - +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 4.3 18.4 - - + -
366A THR* 2.7 27.0 + - - +
368A VAL* 1.3 74.1 - - + +
370A LYS* 1.3 64.6 + - - +
371A GLN 3.0 2.0 - - - -
372A LEU* 2.9 17.0 + - + +
373A LEU* 2.8 23.0 + - - +
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Residues in contact with LYS 370 (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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361A PHE* 3.7 31.2 + - + +
365A LEU* 3.8 35.9 - - + +
366A THR 2.8 11.2 + - - +
367A PRO* 3.7 11.0 - - + +
369A ALA* 1.3 74.9 - - - +
371A GLN* 1.3 56.9 + - - +
373A LEU* 3.3 3.7 + - - +
374A HIS* 2.9 49.9 + - - +
397A GLU* 5.6 2.8 - - - +
401A ILE* 3.6 20.3 - - + +
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Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PRO 3.0 11.3 + - - +
368A VAL* 3.3 12.8 - - - +
370A LYS* 1.3 72.6 - - - +
372A LEU* 1.3 67.4 + - - +
373A LEU 2.9 2.0 + - - -
374A HIS* 3.0 10.2 + - - +
375A LEU* 2.9 22.5 + - - +
398A GLY 3.3 22.5 + - - +
401A ILE* 3.0 38.3 + - + +
403A GLN* 3.3 21.8 + - - +
405A SER* 2.4 30.6 + - - -
407A GLU* 4.4 2.5 - - + +
408A LYS* 3.5 12.6 + - - +
411A MET* 3.9 10.8 - - + +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER* 4.6 15.5 - - - +
368A VAL 3.4 7.6 + - - +
369A ALA* 2.9 20.7 + - + +
371A GLN* 1.3 76.8 - - - +
373A LEU* 1.3 66.5 + - + +
375A LEU* 3.6 9.3 - - + +
376A ARG* 2.9 37.5 + - + +
407A GLU* 4.4 22.2 - - + +
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Residues in contact with LEU 373 (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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338A SER* 4.6 11.9 - - - +
357A PHE* 4.0 29.6 - - + -
360A GLU* 3.6 33.7 - - + +
361A PHE* 3.5 36.8 - - + -
365A LEU* 3.9 16.8 - - + -
369A ALA 2.8 11.1 + - - +
370A LYS* 3.4 10.5 - - - +
371A GLN 3.0 0.2 - - - -
372A LEU* 1.3 83.1 - - + +
374A HIS* 1.3 59.1 + - - +
376A ARG* 3.1 3.3 + - + -
377A TYR* 2.8 30.4 + - - +
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Residues in contact with HIS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 3.8 20.2 - + - -
370A LYS* 2.9 45.8 + - + +
371A GLN 3.0 5.8 + - - +
373A LEU* 1.3 74.5 - - - +
375A LEU* 1.3 54.8 + - - +
377A TYR* 4.8 0.9 - - - -
378A GLY* 2.7 33.6 + - - -
394A HIS* 3.0 57.4 + + + +
395A PHE* 4.5 0.7 - - - -
397A GLU* 3.8 26.9 + - + +
398A GLY* 3.6 24.9 - - - -
401A ILE* 4.1 4.8 - - + +
411A MET* 4.4 2.2 - - - -
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Residues in contact with LEU 375 (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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371A GLN 2.9 11.0 + - - +
372A LEU* 3.6 10.1 - - + +
374A HIS* 1.3 74.8 - - - +
376A ARG* 1.3 72.3 + - - +
378A GLY* 3.7 0.2 - - - -
379A ASN* 2.9 50.5 + - - +
395A PHE* 4.1 4.9 - - + -
407A GLU* 4.2 24.7 - - + +
410A LYS* 4.4 22.7 - - + -
411A MET* 3.7 34.9 - - + -
414A LYS* 4.9 2.5 - - + -
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Residues in contact with ARG 376 (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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338A SER* 5.8 4.0 - - - +
342A SER* 4.8 16.9 - - - -
357A PHE* 4.3 19.3 - - + -
372A LEU* 2.9 27.2 + - + +
373A LEU* 3.1 8.0 + - + +
375A LEU* 1.3 85.3 - - - +
377A TYR* 1.3 57.8 + - - +
379A ASN* 3.3 41.5 + - - +
380A PHE* 3.0 25.2 + - - +
383A TYR* 5.3 2.8 - - - -
384A GLN* 5.2 7.5 - - - +
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Residues in contact with TYR 377 (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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354A GLU* 2.5 31.9 + - - -
357A PHE* 3.4 43.3 - + + -
358A GLN* 4.5 8.4 + - + +
361A PHE* 3.6 25.8 - + + -
373A LEU 2.8 20.1 + - - +
374A HIS 4.1 1.6 - - - +
376A ARG* 1.3 70.6 - - - +
378A GLY* 1.3 67.2 + - - +
380A PHE* 2.8 27.9 + + - +
381A GLN* 2.8 35.6 + - + +
394A HIS* 3.1 31.6 - + + -
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Residues in contact with GLY 378 (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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374A HIS 2.7 23.2 + - - -
375A LEU 3.7 0.7 - - - -
377A TYR* 1.3 71.9 - - - +
379A ASN* 1.3 50.8 + - - +
381A GLN* 2.8 6.9 + - - +
382A LEU* 2.7 33.6 + - - +
391A ALA* 3.7 13.9 - - - +
394A HIS* 4.2 9.3 - - - -
395A PHE* 3.7 19.5 - - - -
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Residues in contact with ASN 379 (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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375A LEU* 2.9 45.0 + - - +
376A ARG* 3.3 41.3 - - - +
378A GLY* 1.3 72.3 - - - +
380A PHE* 1.3 62.3 + - - +
382A LEU* 4.1 4.0 - - - -
383A TYR* 2.9 47.4 + - + +
384A GLN* 4.2 1.3 - - - +
395A PHE* 3.7 7.0 - - - -
410A LYS* 5.9 1.4 - - - +
414A LYS* 3.4 23.8 + - - +
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Residues in contact with PHE 380 (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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345A ALA* 4.3 9.4 - - + -
350A TYR* 3.6 33.7 - + - -
353A ALA* 3.9 13.5 - - + -
354A GLU* 3.7 26.0 - - + -
357A PHE* 3.8 23.6 - + + -
376A ARG* 3.0 12.9 + - - +
377A TYR* 2.8 29.8 + + - +
379A ASN* 1.3 77.1 - - - +
381A GLN* 1.3 65.2 + - - +
384A GLN* 2.8 60.9 - - + +
385A MET* 3.1 31.1 + - + -
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Residues in contact with GLN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLU* 3.4 13.7 + - - -
377A TYR* 2.8 55.0 + - + +
378A GLY* 3.2 7.0 - - - +
380A PHE* 1.3 79.2 - - - +
382A LEU* 1.3 56.4 + - - +
383A TYR 3.1 0.7 + - - -
385A MET* 2.5 57.1 - - - +
387A CYS* 3.4 20.6 + - - +
390A LYS* 3.5 41.7 + - + +
391A ALA* 3.8 7.9 - - - +
394A HIS* 4.9 1.3 - - + -
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Residues in contact with LEU 382 (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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378A GLY 2.7 18.6 + - - +
379A ASN* 3.3 8.0 + - - +
381A GLN* 1.3 74.1 - - - +
383A TYR* 1.3 87.9 + - + +
385A MET 3.8 4.0 - - - +
386A LYS 5.2 2.8 - - - +
387A CYS 4.4 2.9 - - - -
388A GLU* 4.3 26.2 - - + +
391A ALA* 3.8 15.0 - - + +
395A PHE* 4.1 20.6 - - + -
414A LYS* 4.7 6.7 - - + +
418A ILE* 4.9 11.4 - - + -
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Residues in contact with TYR 383 (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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376A ARG* 5.3 3.4 - - - -
379A ASN* 2.9 47.8 + - + +
382A LEU* 1.3 98.4 - - + +
384A GLN* 1.3 80.2 + - - +
385A MET 3.8 2.9 - - - +
414A LYS* 2.6 27.3 + - - -
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Residues in contact with GLN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 4.2 15.9 - - - +
350A TYR* 3.4 48.3 + - + -
376A ARG* 5.2 6.7 - - - +
379A ASN 4.2 4.4 + - - -
380A PHE* 2.8 43.6 + - + +
383A TYR* 1.3 93.1 - - - +
385A MET* 1.3 66.3 + - - +
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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
------------------------------------------------------------
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