Contacts of the helix formed by residues 390 - 397 (chain B) in PDB entry 5J3V
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 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289B CYS 3.1 22.4 + - - -
290B LYS* 3.4 40.1 - - + +
293B LEU* 3.3 17.3 - - + +
294B VAL* 3.6 22.5 + - + -
297B LEU* 3.6 26.9 - - + -
386B LEU* 3.3 30.1 + - + -
389B VAL* 1.3 89.4 - - + +
391B ARG* 1.3 68.6 + - - +
392B ASP 3.1 1.2 + - - -
393B GLU* 3.0 31.4 + - + +
394B LEU* 3.9 31.0 - - + +
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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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386B LEU 4.2 0.8 + - - -
387B ALA 3.3 25.6 + - - +
388B ASN* 3.9 12.8 - - - +
389B VAL 3.3 12.1 - - - +
390B TYR* 1.3 79.6 - - - +
392B ASP* 1.3 69.0 + - - +
394B LEU* 3.0 16.9 + - - +
395B LEU 3.9 1.0 + - - -
427B GLY* 3.3 26.2 + - - +
428B CYS* 3.2 21.8 - - - -
429B MET* 6.3 0.6 - - - +
430B GLN* 4.6 18.8 - - - +
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Residues in contact with ASP 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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390B TYR 3.1 0.6 + - - -
391B ARG* 1.3 86.9 + - - +
393B GLU* 1.3 61.8 + - + +
394B LEU 3.2 1.7 + - - -
395B LEU* 3.6 14.8 + - + +
396B PRO* 3.5 14.6 - - - +
427B GLY 4.1 2.6 - - - +
428B CYS* 4.0 9.0 - - - -
430B GLN* 3.9 17.8 - - - +
431B GLY* 3.4 27.2 + - - -
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Residues in contact with GLU 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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290B LYS* 3.6 26.1 + - - -
297B LEU* 5.4 1.6 - - - +
390B TYR* 3.0 26.7 + - + +
392B ASP* 1.3 78.2 - - + +
394B LEU* 1.3 59.9 - - - +
395B LEU 3.5 0.4 - - - -
396B PRO* 3.6 16.9 - - - +
397B HIS* 3.8 11.1 + - - -
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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
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297B LEU* 4.4 10.5 - - + -
301B ILE* 3.6 23.6 - - + -
383B LEU* 4.7 6.3 - - + +
386B LEU* 3.6 28.9 - - + +
387B ALA* 3.7 18.2 - - + +
390B TYR* 3.9 29.5 - - + +
391B ARG 3.0 13.7 + - - +
393B GLU* 1.3 79.5 - - - +
395B LEU* 1.3 64.4 + - - +
396B PRO 3.5 0.4 - - - -
397B HIS* 3.2 15.3 + - - +
398B ILE* 3.5 31.9 - - + +
424B ILE* 4.8 0.9 - - + -
428B CYS* 4.2 6.5 - - - -
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Residues in contact with LEU 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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391B ARG 4.4 0.9 - - - +
392B ASP* 3.8 13.5 - - + +
394B LEU* 1.3 73.7 - - - +
396B PRO* 1.4 62.5 - - + +
397B HIS 3.0 5.4 - - - -
398B ILE* 2.9 7.3 + - + +
399B LEU* 2.9 56.4 + - + +
424B ILE* 4.2 12.1 - - + -
428B CYS* 3.7 33.7 - - + +
431B GLY* 3.6 41.1 - - - +
432B MET* 3.8 20.0 - - - +
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Residues in contact with PRO 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 ASP 3.5 12.8 - - - +
393B GLU* 3.6 15.0 - - - +
394B LEU 3.6 2.9 - - - -
395B LEU* 1.4 91.4 - - + +
397B HIS* 1.3 68.6 + - + +
398B ILE 3.4 0.2 - - - -
399B LEU* 5.1 4.3 - - + -
400B PRO* 3.7 18.5 - - + +
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Residues in contact with HIS 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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297B LEU* 3.4 25.6 - - + +
298B PRO* 3.9 31.2 - - + +
301B ILE* 3.6 31.8 - - + +
302B PRO* 5.6 0.7 - - - +
393B GLU 3.8 20.5 + - - -
394B LEU 3.2 3.3 + - - +
395B LEU 2.9 1.4 + - - -
396B PRO* 1.3 88.5 + - + +
398B ILE* 1.3 63.3 + - - +
400B PRO* 4.5 2.5 - - - -
401B LEU* 4.2 12.3 - - - +
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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