Contacts of the helix formed by residues 382 - 396 (chain B) in PDB entry 3GSB
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 ASP 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367B PHE* 3.2 21.6 + - + +
380B LYS 3.9 0.8 + - - -
381B SER* 1.3 69.4 - - - +
383B LEU* 1.3 62.2 + - - +
384B GLN* 3.4 10.4 + - - +
385B LYS* 3.1 44.8 + - + +
386B PHE* 3.1 19.3 + - - +
388B ARG* 5.5 0.9 + - - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER 4.9 3.9 - - - +
167B THR 5.8 2.2 - - - +
379B LYS* 5.3 5.2 - - - +
381B SER* 3.0 39.0 + - - +
382B ASP* 1.3 71.8 - - - +
384B GLN* 1.3 57.6 + - - +
386B PHE* 3.8 6.4 - - + +
387B SER* 3.0 26.7 + - - -
404B GLN* 3.9 24.2 - - + +
405B PHE* 4.2 21.3 - - + -
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ASP* 3.1 8.8 + - - +
383B LEU* 1.3 75.7 - - - +
385B LYS* 1.3 65.8 + - - +
387B SER* 3.5 8.8 + - - -
388B ARG* 3.0 67.9 + - - +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLY 5.3 0.6 + - - -
352B HIS* 3.3 42.1 - - + +
353B ALA 4.9 3.2 + - - +
367B PHE* 3.7 33.7 - - + -
382B ASP* 3.1 37.5 + - - +
384B GLN* 1.3 78.5 - - - +
386B PHE* 1.3 52.0 + - - +
388B ARG* 3.2 27.1 + - - +
389B PHE* 2.6 36.9 + - - +
433B LEU* 3.7 13.8 - - + +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.7 25.8 - - + -
365B PHE* 4.6 7.2 - + - -
367B PHE* 3.6 20.1 - + + -
382B ASP 3.1 10.4 + - - +
383B LEU* 3.8 12.3 - - + +
384B GLN 3.3 0.2 - - - -
385B LYS* 1.3 76.1 - - - +
387B SER* 1.3 58.7 + - - +
389B PHE* 3.6 13.4 - + - +
390B HIS* 2.7 46.3 + + + +
400B LEU* 5.9 2.5 - - + -
401B ALA 3.9 7.9 - - - -
403B SER 3.6 9.9 - - - -
404B GLN* 3.5 62.1 - - + +
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER 4.1 11.8 + - - -
37B VAL* 3.8 34.7 - - - +
38B GLY* 3.8 4.7 + - - -
383B LEU 3.0 19.8 + - - -
384B GLN* 3.6 13.2 + - - -
386B PHE* 1.3 75.6 - - - +
388B ARG* 1.3 64.4 + - - +
390B HIS* 3.5 2.1 - - - +
391B ARG* 3.1 23.0 + - - +
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ASP* 5.5 0.8 + - - -
384B GLN* 3.0 60.4 + - - +
385B LYS* 3.6 29.6 - - - +
387B SER* 1.3 79.6 - - - +
389B PHE* 1.3 63.8 + - - +
391B ARG* 3.3 8.0 + - - +
392B GLY* 3.0 19.8 + - - -
429B VAL* 5.4 0.2 - - - +
433B LEU* 3.8 38.3 - - + +
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Residues in contact with PHE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 5.7 4.3 - - + -
365B PHE* 4.9 20.6 - + - -
367B PHE* 3.5 29.4 - + + -
385B LYS 2.6 21.6 + - - +
386B PHE* 3.6 16.6 - + - +
388B ARG* 1.3 71.8 - - - +
390B HIS* 1.3 67.7 + - + +
392B GLY* 3.1 2.9 + - - -
393B MET* 3.1 53.7 + - + +
400B LEU* 4.0 19.5 - - + -
426B ALA* 5.0 3.4 - - + -
429B VAL* 3.8 15.6 - - + +
430B MET* 4.2 27.1 - - + -
433B LEU* 3.4 15.2 - - + +
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Residues in contact with HIS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 4.2 20.4 - + - -
37B VAL* 3.1 26.0 - - + +
386B PHE* 2.7 35.0 + + + +
387B SER 3.5 4.5 - - - +
389B PHE* 1.3 79.6 - - - +
391B ARG* 1.3 65.0 + - - +
392B GLY 3.0 0.7 + - - -
393B MET* 3.1 7.9 + - - +
394B LEU* 3.0 35.5 + - + +
400B LEU* 2.7 38.4 + - + +
401B ALA 3.4 17.9 - - - -
402B PRO* 3.4 14.5 - - + +
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.8 27.8 - - - -
9B THR* 4.7 11.9 + - - +
34B PHE* 5.5 1.6 - - - -
37B VAL* 5.3 9.6 - - + +
40B GLN* 4.0 26.0 + - - +
42B ILE* 5.3 2.6 - - - +
387B SER 3.1 11.0 + - - +
388B ARG* 3.7 10.3 - - - +
390B HIS* 1.3 84.2 + - - +
392B GLY* 1.3 64.3 + - - +
394B LEU* 3.4 24.0 + - - +
395B GLU* 3.4 37.7 + - - +
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Residues in contact with GLY 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ARG 3.0 13.2 + - - -
389B PHE 3.1 3.8 + - - -
390B HIS 3.0 0.4 - - - -
391B ARG* 1.3 75.4 - - - +
393B MET* 1.3 65.4 + - - +
395B GLU* 2.8 23.5 + - - +
396B GLN* 3.3 8.3 + - - -
429B VAL* 3.7 22.8 - - - +
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Residues in contact with MET 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LEU* 5.0 3.8 - - + -
389B PHE* 3.1 41.9 + - + +
390B HIS 3.1 7.4 + - - +
392B GLY* 1.3 72.4 - - - +
394B LEU* 1.3 64.5 + - - +
396B GLN* 2.9 14.9 + - - +
397B GLY 3.2 0.2 + - - -
398B ILE* 3.1 34.2 + - + +
400B LEU* 3.9 23.8 - - + -
422B THR* 3.8 35.0 - - + +
425B ALA* 3.8 12.1 - - - +
426B ALA* 3.7 30.3 - - + +
429B VAL* 3.8 6.8 - - + +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.6 12.5 - - + -
34B PHE* 4.3 14.6 - - + -
42B ILE* 3.9 24.5 - - + -
60B TYR* 3.5 26.0 - - + -
390B HIS* 3.0 25.9 + - + +
391B ARG* 3.4 34.1 - - - +
393B MET* 1.3 77.9 - - - +
395B GLU* 1.3 57.8 + - + +
397B GLY* 3.2 12.5 + - - -
398B ILE 3.5 11.6 + - - +
399B TYR* 3.4 35.2 - - + -
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.8 45.6 - - + +
391B ARG* 3.6 37.7 + - - +
392B GLY* 2.8 12.2 + - - +
394B LEU* 1.3 72.9 - - - +
396B GLN* 1.3 64.7 + - - +
397B GLY 3.0 6.3 + - - -
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Residues in contact with GLN 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B GLY 3.3 7.7 + - - +
393B MET* 2.9 10.6 + - - +
395B GLU* 1.3 83.5 + - - +
397B GLY* 1.3 60.4 + - - +
398B ILE* 3.6 5.5 - - + +
425B ALA* 3.3 40.9 - - + +
428B THR* 4.2 23.0 + - - +
429B VAL* 4.0 15.7 - - + +
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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