Contacts of the helix formed by residues 389 - 401 (chain B) in PDB entry 3SRH
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 TYR 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ALA 4.4 1.1 - - - -
20B ALA 4.3 8.1 - - - -
22B ALA 2.5 30.2 + - - -
23B ASP* 3.2 4.3 - - - -
24B THR* 2.9 21.0 + - - -
25B PHE* 3.6 36.5 - + + -
28B HIS* 3.4 35.4 - + + +
387B ALA 3.6 1.8 + - - -
388B ILE* 1.3 74.9 - - - +
390B HIS* 1.3 65.2 + - - +
391B LEU* 3.3 23.6 - - + +
392B GLN* 3.2 43.9 + - + +
393B LEU* 3.1 21.3 + - - +
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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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20B ALA* 5.4 6.6 + - + +
385B GLU 3.5 23.2 + - - -
388B ILE* 3.1 39.5 + - + +
389B TYR* 1.3 70.4 - - - +
391B LEU* 1.3 59.9 + - - +
393B LEU* 4.2 8.5 - - + +
394B PHE* 2.8 35.3 + - - +
420B PHE* 3.9 24.4 - + + -
444B ARG* 4.0 17.4 + - + +
445B PRO 4.7 1.1 - - - -
446B ARG* 3.3 59.7 + - + +
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Residues in contact with LEU 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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395A GLU* 5.5 3.8 - - - +
398A ARG* 5.5 11.5 + - - +
399A ARG* 4.1 50.7 - - + +
20B ALA 4.0 17.9 + - - +
21B MET* 4.8 4.5 - - - -
22B ALA 4.6 5.2 - - - +
389B TYR* 3.3 21.1 - - + +
390B HIS* 1.3 78.6 - - - +
392B GLN* 1.3 61.8 + - - +
394B PHE* 4.7 1.9 - - - +
395B GLU* 3.6 23.1 + - + +
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Residues in contact with GLN 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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25B PHE* 4.1 15.4 - - - +
389B TYR* 3.2 43.9 + - + +
390B HIS 3.2 0.4 - - - -
391B LEU* 1.3 79.2 - - - +
393B LEU* 1.3 65.1 + - - +
395B GLU* 3.4 8.1 + - + +
396B GLU* 3.1 48.0 + - + +
25C PHE* 3.5 28.7 - - + +
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Residues in contact with LEU 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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317B ASN* 5.1 9.0 - - - +
353B ASP 6.1 0.2 - - - +
354B GLY* 6.5 0.7 - - - -
388B ILE* 3.8 26.5 - - + -
389B TYR 3.1 16.4 + - - +
390B HIS* 3.3 6.9 + - - +
392B GLN* 1.3 78.7 - - - +
394B PHE* 1.3 62.3 + - - +
396B GLU* 3.8 8.2 - - - +
397B LEU* 3.0 49.3 + - + +
444B ARG* 3.8 35.2 - - + +
26C LEU* 5.0 12.8 - - + -
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Residues in contact with PHE 394 (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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398A ARG* 3.6 18.6 - - - -
417A GLU* 4.7 1.1 - - - -
390B HIS* 2.8 22.1 + - + +
391B LEU* 4.7 2.0 - - - +
393B LEU* 1.3 73.4 - - - +
395B GLU* 1.3 60.1 + - - +
396B GLU 3.2 0.2 + - - -
397B LEU* 3.2 6.5 + - + -
398B ARG* 3.0 53.7 + - + +
413B VAL* 4.4 11.9 - - + -
416B VAL* 3.7 24.9 - - + -
417B GLU* 3.3 33.7 - - + -
420B PHE* 3.8 24.9 - + + -
443B TYR* 3.7 38.4 - + + +
444B ARG 5.6 0.7 - - - +
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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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391A LEU* 6.0 1.9 - - - +
395A GLU* 3.4 34.8 - - - +
398A ARG* 5.1 1.3 - - - +
391B LEU* 3.6 18.5 + - + +
392B GLN* 3.4 14.7 + - + +
394B PHE* 1.3 79.2 - - - +
396B GLU* 1.3 81.5 + - - +
398B ARG* 3.7 14.3 + - - +
399B ARG* 3.0 44.2 + - - +
24C THR* 4.6 1.2 + - - -
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Residues in contact with GLU 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 GLN* 3.1 42.5 + - + +
393B LEU* 3.8 7.8 - - + +
395B GLU* 1.3 89.0 - - - +
397B LEU* 1.3 65.3 + - - +
399B ARG* 3.6 4.2 - - - +
400B LEU* 3.2 32.6 + - - +
24C THR* 2.9 28.7 + - + +
25C PHE* 2.9 23.2 + - - +
26C LEU* 3.3 33.1 + - + +
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Residues in contact with LEU 397 (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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317B ASN* 3.9 29.6 - - + +
318B ARG* 5.0 1.6 - - - -
393B LEU* 3.0 43.3 + - + +
394B PHE* 3.8 3.8 - - - +
396B GLU* 1.3 77.8 - - - +
398B ARG* 1.3 61.7 + - - +
400B LEU* 4.2 1.9 - - - +
401B ALA* 3.3 25.6 + - - +
442B ARG* 3.6 24.3 + - - +
443B TYR* 4.0 32.2 - - + +
444B ARG* 4.3 6.5 - - + -
26C LEU* 3.7 26.2 - - + -
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Residues in contact with ARG 398 (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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391A LEU* 5.2 10.9 - - - +
394A PHE* 3.8 14.7 - - - -
395A GLU* 2.8 33.7 + - - +
398A ARG* 5.6 1.1 - - - +
417A GLU* 2.9 38.4 + - - +
420A PHE* 4.8 11.7 - - - +
421A LYS* 5.0 7.0 + - + +
394B PHE* 3.0 57.9 + - + +
395B GLU* 3.7 13.6 + - - +
396B GLU 3.4 0.2 - - - -
397B LEU* 1.3 77.9 - - - +
399B ARG* 1.3 58.7 + - - +
401B ALA* 3.6 14.4 - - - +
413B VAL* 4.6 5.2 - - + -
417B GLU* 5.1 0.2 - - - -
443B TYR* 4.2 18.2 - - + -
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Residues in contact with ARG 399 (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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21A MET 4.0 8.9 + - - -
22A ALA 4.0 2.6 + - - -
23A ASP* 3.2 49.2 + - - +
391A LEU* 4.0 36.8 - - + +
395B GLU* 3.0 41.4 + - - +
396B GLU* 3.6 9.2 - - - +
398B ARG* 1.3 81.8 - - + +
400B LEU* 1.3 73.4 + - + +
401B ALA 3.3 7.5 - - - +
402B PRO* 5.6 0.2 - - - +
23C ASP* 5.0 11.4 + - - -
24C THR* 5.1 5.6 + - - -
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ARG* 3.8 30.0 - - + +
396B GLU* 3.2 26.7 + - + +
397B LEU* 4.3 3.8 - - - +
399B ARG* 1.3 87.7 - - + +
401B ALA* 1.3 60.7 + - - +
402B PRO* 3.7 8.3 - - - +
23C ASP* 5.7 2.7 - - - +
24C THR* 3.9 31.0 - - + +
26C LEU* 3.8 24.7 - - + -
27C GLU* 4.1 15.5 - - + +
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Residues in contact with ALA 401 (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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421A LYS* 3.4 20.7 + - - +
397B LEU 3.3 18.1 + - - +
398B ARG 3.6 16.2 - - - +
399B ARG* 3.3 6.4 - - - +
400B LEU* 1.3 76.8 - - - +
402B PRO* 1.3 71.9 - - + +
442B ARG* 4.1 22.4 - - - +
443B TYR* 4.2 8.3 - - + +
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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