Contacts of the helix formed by residues 386 - 395 (chain B) in PDB entry 5FW2
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 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B LEU* 3.9 17.7 - - + -
380B LEU* 2.8 51.9 + - + +
383B MET* 3.6 23.7 + - + -
384B ASP 3.8 8.3 - - - +
385B GLY* 1.3 78.0 - - - +
387B GLU* 1.3 69.3 + - - +
388B GLU 3.2 2.9 - - - -
389B LEU* 2.9 20.7 + - - +
390B LEU* 3.3 15.9 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 6.1 0.5 - - - -
383B MET 4.3 8.0 - - - +
384B ASP* 4.5 6.4 - - - +
385B GLY* 3.3 24.5 + - - -
386B THR* 1.3 87.7 + - - +
388B GLU* 1.3 61.8 + - - +
390B LEU* 3.5 16.0 + - + +
391B VAL* 3.4 22.1 + - - +
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Residues in contact with GLU 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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331B ASP* 5.3 2.9 - - - +
385B GLY 5.4 0.2 + - - -
386B THR 3.2 0.4 - - - -
387B GLU* 1.3 78.0 - - - +
389B LEU* 1.3 62.8 + - + +
391B VAL* 3.1 15.7 + - + +
392B LYS* 2.9 51.9 + - + +
395B ARG* 6.3 0.7 - - - +
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Residues in contact with LEU 389 (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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331B ASP* 2.9 46.7 - - + +
334B LEU* 4.1 26.0 - - + -
335B LEU* 4.6 13.7 - - + -
338B LEU* 4.3 9.0 - - + -
380B LEU* 3.6 37.0 - - + +
386B THR* 2.9 13.4 + - - +
388B GLU* 1.3 81.3 - - + +
390B LEU* 1.3 57.4 + - - +
392B LYS* 3.2 6.9 + - - +
393B LEU* 2.8 27.7 + - - +
398B LEU* 3.9 14.1 - - + +
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Residues in contact with LEU 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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377B LYS* 4.5 16.4 - - + +
380B LEU* 4.2 13.0 - - + -
381B GLU* 3.8 40.6 - - + +
386B THR* 3.3 28.5 + - - +
387B GLU* 3.7 16.8 - - - +
388B GLU 3.2 0.2 - - - -
389B LEU* 1.3 75.1 - - - +
391B VAL* 1.3 64.4 + - + +
393B LEU* 3.0 17.7 + - + +
394B ASN* 2.8 31.1 + - - +
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Residues in contact with VAL 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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387B GLU 3.4 15.3 - - - +
388B GLU* 3.1 17.9 + - + +
390B LEU* 1.3 77.9 - - + +
392B LYS* 1.3 62.2 + - - +
393B LEU 3.3 0.7 + - - -
394B ASN* 3.5 7.1 + - - +
395B ARG* 3.3 52.4 + - - +
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Residues in contact with LYS 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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327B GLU* 3.7 27.1 + - + +
331B ASP* 2.9 34.1 + - - +
388B GLU* 2.9 43.2 + - + +
389B LEU* 3.2 8.5 + - - +
391B VAL* 1.3 75.5 - - - +
393B LEU* 1.3 57.9 + - - +
395B ARG* 3.6 27.8 + - - +
396B GLU 3.2 2.8 + - - -
397B ASP* 2.6 46.2 + - - +
398B LEU* 3.2 18.1 + - + +
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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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373B TYR* 4.1 40.1 - - + +
376B ILE* 4.4 3.8 - - + -
377B LYS* 4.1 41.7 - - + -
380B LEU* 4.3 10.3 - - + -
389B LEU 2.8 13.1 + - - +
390B LEU* 3.0 15.2 + - + +
392B LYS* 1.3 75.9 - - - +
394B ASN* 1.3 72.4 + - - +
396B GLU* 2.9 23.5 + - - +
398B LEU* 3.9 26.2 - - + +
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Residues in contact with ASN 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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377B LYS* 5.7 4.2 - - - +
390B LEU* 2.8 28.5 + - - +
391B VAL* 4.1 6.8 - - - +
393B LEU* 1.3 88.6 - - - +
395B ARG* 1.3 61.6 + - + +
396B GLU* 3.1 7.8 + - - +
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Residues in contact with ARG 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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215B ARG* 3.0 44.2 + - + +
216B LEU* 5.1 9.6 - - + -
307B ARG* 4.8 4.4 - - - +
323B LYS* 5.9 1.0 - - - +
327B GLU* 5.0 2.6 + - - -
388B GLU* 6.3 0.8 - - - +
391B VAL* 3.3 37.1 + - + +
392B LYS* 3.9 30.7 - - - +
393B LEU 3.2 0.2 - - - -
394B ASN* 1.3 76.5 - - + +
396B GLU* 1.3 68.2 + - - +
397B ASP* 3.6 30.3 + - + +
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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