Contacts of the helix formed by residues 378 - 395 (chain A) in PDB entry 3TG4
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 4.3 2.9 - - - -
374A TYR* 3.5 30.9 - - - -
375A PRO* 3.5 20.4 + - - -
376A LEU 3.9 1.8 + - - -
377A TYR* 1.3 75.8 - - - +
379A LEU* 1.3 62.4 + - - +
380A ASN* 3.2 16.3 + - - +
381A VAL* 3.4 14.7 + - - +
382A ALA* 3.1 22.2 + - - +
411A ILE* 3.8 8.0 - - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 3.8 25.6 - - + +
214A ILE* 3.5 27.6 - - + +
215A VAL 3.8 12.3 - - - +
216A THR* 4.0 5.6 - - + -
378A SER* 1.3 73.1 + - - +
380A ASN* 1.3 61.7 + - - +
382A ALA* 3.8 9.1 - - + +
383A SER* 2.9 33.4 + - - -
411A ILE* 5.7 1.1 - - + -
415A ALA* 3.8 23.3 - - + -
416A HIS* 3.5 29.8 - - + +
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Residues in contact with ASN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 3.5 18.3 - - - +
242A ASP* 4.3 13.3 + - - +
243A LEU 5.2 2.4 - - - +
370A TYR* 3.9 10.8 - - + -
374A TYR* 3.4 48.4 + - + +
378A SER* 3.2 8.4 + - - +
379A LEU* 1.3 79.7 - - - +
381A VAL* 1.3 60.9 + - - +
383A SER* 3.3 8.3 + - - -
384A MET* 3.3 22.5 + - - +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 4.5 3.6 - - + -
370A TYR* 3.7 22.0 - - + +
371A SER* 3.7 22.0 - - - +
374A TYR* 3.6 34.8 - - + -
375A PRO 5.0 2.7 - - - +
376A LEU 5.9 2.0 - - - +
378A SER* 3.3 13.7 + - - +
380A ASN* 1.3 73.4 - - - +
382A ALA* 1.3 65.7 + - - +
384A MET* 3.2 5.2 + - - +
385A TRP* 3.0 40.8 + - + +
411A ILE* 3.8 11.4 - - + -
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A SER 3.1 16.8 + - - +
379A LEU* 3.8 10.8 - - + +
380A ASN 3.4 0.2 - - - -
381A VAL* 1.3 77.8 - - - +
383A SER* 1.3 56.5 + - - +
385A TRP* 3.2 4.9 + - - +
386A LEU* 3.0 26.6 + - - +
408A ALA* 3.6 8.6 - - - +
411A ILE* 3.7 32.3 - - + +
412A MET* 4.0 21.5 - - + -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU 3.6 24.5 - - - -
190A GLU* 3.7 20.1 + - - +
191A LEU* 3.6 17.7 - - - +
344A TYR* 5.7 1.4 + - - -
379A LEU 2.9 20.8 + - - -
380A ASN* 3.3 9.0 + - - -
382A ALA* 1.3 73.4 - - - +
384A MET* 1.3 59.6 + - - +
386A LEU* 3.3 4.4 + - - +
387A LYS* 2.9 37.4 + - - +
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Residues in contact with MET 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TYR* 3.5 39.7 - - + -
347A MET* 3.7 33.0 - - - +
363A GLY* 4.2 10.8 - - - -
366A ILE* 3.9 24.0 - - + -
367A ILE* 3.7 24.7 - - + -
370A TYR* 4.1 8.7 - - + -
380A ASN 3.3 16.0 + - - +
381A VAL 3.2 6.1 + - - +
383A SER* 1.3 75.9 + - - +
385A TRP* 1.3 65.2 + - - +
387A LYS* 3.4 6.9 + - + -
388A LEU* 2.9 30.5 + - + +
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Residues in contact with TRP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.5 35.1 - - + +
368A LYS* 4.9 10.5 - - + -
371A SER* 4.2 8.4 + - - -
381A VAL* 3.0 39.3 + - + +
382A ALA 3.2 7.4 + - - +
384A MET* 1.3 74.5 - - - +
386A LEU* 1.3 57.6 + - - +
388A LEU* 3.4 16.2 + - + +
389A GLY* 2.8 25.3 + - - -
392A TYR* 6.2 1.1 - + - -
403A LYS* 6.3 1.1 - - + -
404A ALA* 3.5 47.1 - - + +
407A LYS* 3.5 46.4 - - + +
408A ALA 3.8 5.8 - - - +
411A ILE* 4.1 12.6 - - + +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 3.4 47.6 - - + +
190A GLU* 4.4 3.6 - - + -
382A ALA 3.0 13.3 + - - +
383A SER 3.5 8.5 - - - +
385A TRP* 1.3 74.2 - - - +
387A LYS* 1.3 60.1 - - - +
389A GLY* 3.3 0.9 + - - -
390A ARG* 2.9 58.1 + - - +
405A LEU* 3.6 21.5 - - + -
408A ALA* 3.8 8.9 - - + +
412A MET* 4.4 6.3 - - - -
426A ILE* 3.7 31.6 - - + -
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLU* 3.6 54.1 + - - +
192A SER* 5.6 1.8 - - - -
344A TYR* 3.2 36.4 + - - -
347A MET* 4.1 26.1 - - + -
351A LEU* 4.4 15.3 - - + +
383A SER* 2.9 23.7 + - - +
384A MET* 3.8 10.5 - - + +
386A LEU* 1.3 74.4 - - - +
388A LEU* 1.3 59.0 + - - +
390A ARG* 3.3 2.0 + - - +
391A LEU* 2.9 36.4 + - + +
441A GOL 4.0 11.2 - - - -
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 5.0 2.5 - - + -
360A LEU* 3.8 22.5 - - + +
363A GLY* 3.6 32.5 - - - +
364A GLN* 3.7 9.6 - - + +
367A ILE* 3.7 40.6 - - + -
384A MET* 2.9 23.0 + - + +
385A TRP* 3.5 16.8 - - + +
387A LYS* 1.3 75.6 - - - +
389A GLY* 1.3 57.1 + - - +
391A LEU* 3.1 6.7 + - - +
392A TYR* 2.9 41.8 + - + +
404A ALA* 4.3 6.3 - - + -
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Residues in contact with GLY 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A TRP 2.8 19.8 + - - -
386A LEU 3.3 0.2 + - - -
388A LEU* 1.3 72.6 - - - +
390A ARG* 1.3 56.0 + - - +
392A TYR* 3.4 1.9 + - - +
393A MET* 2.9 34.7 + - - +
401A GLY* 3.7 13.9 - - - -
404A ALA* 3.7 16.1 - - - +
405A LEU* 3.8 14.4 - - - -
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Residues in contact with ARG 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 4.5 11.0 - - - +
189A GLU* 2.8 35.4 + - - +
190A GLU* 3.0 35.8 + - - +
386A LEU* 2.9 31.0 + - + +
387A LYS 3.7 3.4 - - - +
389A GLY* 1.3 74.1 - - - +
391A LEU* 1.3 63.8 + - - +
393A MET* 3.5 6.8 + - + +
394A GLY* 3.1 19.9 + - - -
405A LEU* 3.9 2.2 - - + +
425A GLU* 5.3 5.7 + - - +
426A ILE* 4.2 10.5 - - - +
429A GLU* 2.9 42.8 + - - +
441A GOL 3.5 25.9 + - - +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 3.8 24.5 - - + -
351A LEU* 3.9 9.0 - - + -
356A TRP* 3.8 40.6 - - + +
359A ALA* 3.9 4.3 - - + -
360A LEU* 3.8 36.6 - - + +
387A LYS* 2.9 22.6 + - + +
388A LEU* 3.5 7.6 - - + +
390A ARG* 1.3 73.7 - - - +
392A TYR* 1.3 64.5 + - - +
394A GLY* 3.4 3.0 + - - -
395A LEU* 3.2 30.4 + - + +
441A GOL 3.7 20.4 - - - +
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Residues in contact with TYR 392 (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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360A LEU* 3.8 21.8 - - + -
364A GLN* 2.7 39.7 + - - +
385A TRP* 6.2 1.1 - + - -
388A LEU* 2.9 40.2 + - + +
389A GLY* 4.3 1.3 - - - -
391A LEU* 1.3 74.2 - - - +
393A MET* 1.3 58.1 + - - +
395A LEU* 3.2 5.5 + - - -
396A GLU 3.1 4.3 + - - -
397A HIS* 2.8 51.4 + + + +
400A ALA* 3.7 37.9 - - + -
401A GLY* 3.4 21.5 - - - +
404A ALA* 4.4 4.7 - - + -
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Residues in contact with MET 393 (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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389A GLY 2.9 24.3 + - - +
390A ARG* 3.8 7.0 - - - +
391A LEU 3.3 0.4 - - - -
392A TYR* 1.3 75.1 - - - +
394A GLY* 1.3 58.9 + - - +
396A GLU* 3.0 29.1 + - - +
397A HIS 4.8 1.3 - - - +
398A LYS* 4.0 32.7 - - + +
401A GLY* 4.0 11.7 - - - -
402A GLU* 4.0 16.4 - - + +
405A LEU* 3.9 25.4 - - + -
429A GLU* 3.6 25.8 - - + +
430A ILE* 4.1 13.0 - - - +
432A SER 5.6 2.0 - - - -
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Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG 3.1 14.3 + - - -
391A LEU 3.4 3.6 + - - -
392A TYR 3.3 0.4 - - - -
393A MET* 1.3 76.6 - - - +
395A LEU* 1.3 59.9 + - - +
396A GLU* 3.2 9.3 + - - +
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TRP* 4.8 15.5 - - + +
357A GLU* 3.7 39.9 - - + +
360A LEU* 3.6 33.9 - - + -
391A LEU 3.2 19.3 + - - +
392A TYR* 3.2 6.2 + - - +
394A GLY* 1.3 74.8 - - - +
396A GLU* 1.3 70.8 + - - +
397A HIS* 3.3 26.4 + - + +
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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
------------------------------------------------------------
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