Contacts of the helix formed by residues 391 - 401 (chain B) in PDB entry 3FZ7
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 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B LEU* 4.3 6.1 - - - -
390B TYR* 1.3 92.7 - - - +
392B LEU* 1.3 63.5 + - - +
393B TYR* 3.1 34.0 + - + +
394B ASP* 2.8 19.3 + - - +
395B LEU 3.2 12.1 + - - -
419B VAL* 6.2 0.9 - - - -
455B GLN* 5.0 4.3 - - + +
456B GLY* 4.2 18.2 - - - +
458B ALA 4.5 2.1 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B TYR* 4.3 2.9 - - + -
380B PHE* 3.8 32.1 - - + +
381B LYS* 3.9 11.2 - - - -
382B LEU* 3.9 30.7 - - + +
390B TYR* 4.3 3.4 - - + -
391B THR* 1.3 71.0 - - - +
393B TYR* 1.3 59.6 + - - +
395B LEU* 3.8 23.6 - - + -
396B SER* 2.9 25.1 + - - -
408B ALA* 3.8 12.2 - - + +
419B VAL* 3.7 32.6 - - + +
420B VAL 4.2 0.2 - - - -
421B MET* 3.3 26.6 - - + +
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Residues in contact with TYR 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B THR* 3.1 18.5 + - + +
392B LEU* 1.3 74.0 - - - +
394B ASP* 1.3 55.7 + - - +
396B SER* 3.1 4.9 + - - -
397B GLU* 2.8 34.3 + - - +
400B ARG* 4.8 1.4 + - - -
408B ALA* 3.6 24.4 - - + +
410B THR* 3.5 16.8 + - - +
419B VAL* 3.7 29.7 - - + +
458B ALA* 3.5 31.8 - - + +
459B GLN* 4.5 11.0 + - + -
460B GLN 3.4 33.7 - - - -
461B ASN* 2.5 27.9 + - - -
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Residues in contact with ASP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B TYR* 3.5 15.2 - - + -
391B THR* 2.8 32.8 + - - +
393B TYR* 1.3 75.2 - - - +
395B LEU* 1.3 63.5 + - - +
397B GLU* 3.1 5.3 + - - +
398B ARG* 3.0 30.3 + - - +
448B LEU* 4.0 10.3 - - + -
454B LEU* 3.6 9.9 - - + +
455B GLN* 3.6 1.8 - - - -
456B GLY 3.0 20.8 + - - -
457B ILE* 3.6 7.1 + - - +
458B ALA* 3.4 28.0 + - - +
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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
----------------------------------------------------------
363B TYR* 4.4 3.8 - - - +
390B TYR* 4.3 9.6 - - + -
391B THR 3.2 10.2 + - - +
392B LEU* 3.6 20.4 - - + +
394B ASP* 1.3 78.0 - - - +
396B SER* 1.3 62.7 + - - +
398B ARG* 3.4 1.9 + - - +
399B LEU* 3.0 32.2 + - + +
421B MET* 3.7 20.4 - - + -
441B TYR* 3.1 39.5 - - + +
444B SER* 4.0 24.2 - - - -
445B LEU* 4.1 17.7 - - + -
448B LEU* 4.3 9.3 - - + +
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Residues in contact with SER 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU 2.9 18.9 + - - -
393B TYR* 3.1 6.9 + - - -
395B LEU* 1.3 76.9 - - - +
397B GLU* 1.3 56.7 + - - +
399B LEU* 3.3 7.1 + - - +
400B ARG* 3.0 49.0 + - - +
404B TRP 4.8 0.2 - - - +
406B VAL 2.8 28.6 + - - +
408B ALA* 4.2 13.9 + - - -
421B MET* 3.6 7.6 - - - +
462B SER* 4.3 1.7 + - - -
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Residues in contact with GLU 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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398A ARG* 2.9 37.2 + - - -
401A LEU* 3.7 22.0 - - + +
447A TYR* 4.4 5.0 + - - -
454A LEU* 5.1 1.2 - - - +
393B TYR 2.8 16.2 + - - +
394B ASP* 3.1 8.0 + - - +
396B SER* 1.3 70.5 - - - +
398B ARG* 1.3 90.5 + - - +
400B ARG* 3.1 34.4 + - - +
401B LEU* 3.3 10.5 + - + +
454B LEU* 4.9 4.2 - - - +
457B ILE* 6.0 1.9 - - - +
458B ALA* 4.3 17.6 - - + +
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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
----------------------------------------------------------
397A GLU* 3.0 36.6 + - - -
394B ASP* 3.0 14.2 + - - +
395B LEU 3.4 6.7 + - - +
397B GLU* 1.3 102.6 + - - +
399B LEU* 1.3 63.1 + - - +
401B LEU* 3.1 37.5 + - - +
402B ARG* 3.7 10.9 + - - +
444B SER* 3.6 26.3 + - - +
447B TYR* 3.7 26.8 - - + -
448B LEU* 3.9 28.3 - - + -
454B LEU* 3.5 29.2 - - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU* 3.0 36.3 + - + +
396B SER* 3.6 5.4 - - - +
397B GLU 3.2 0.4 - - - -
398B ARG* 1.3 75.7 - - - +
400B ARG* 1.3 63.0 + - - +
402B ARG* 3.1 13.2 + - - +
403B GLY 3.3 0.5 + - - -
404B TRP* 3.1 40.3 + - + +
406B VAL* 4.1 28.9 - - + -
421B MET* 4.5 4.5 - - + -
437B LEU* 3.7 23.1 - - + -
440B ASP* 4.2 2.9 - - + -
441B TYR* 4.1 30.5 - - + +
444B SER* 4.1 14.6 - - - +
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG 5.4 2.8 - - - +
401A LEU* 3.8 24.5 - - + +
393B TYR 4.8 2.0 + - - -
396B SER* 3.0 33.9 + - - +
397B GLU* 3.1 36.1 + - - +
399B LEU* 1.3 76.6 - - - +
401B LEU* 1.3 55.9 + - - +
402B ARG 3.0 0.4 - - - -
403B GLY* 2.9 18.8 + - - -
404B TRP 3.1 20.1 + - - +
405B GLN* 3.1 28.6 + - + +
406B VAL 5.4 0.4 - - - +
458B ALA* 5.8 2.4 - - - +
462B SER* 4.1 0.2 + - - -
306C LEU* 3.6 40.7 - - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLU* 3.9 20.4 - - + +
400A ARG* 3.7 47.0 - - + +
401A LEU* 3.8 28.3 - - + +
397B GLU* 3.3 6.3 + - + +
398B ARG* 3.1 54.7 + - - +
400B ARG* 1.3 74.8 - - - +
402B ARG* 1.3 60.6 + - + +
403B GLY 3.3 0.9 - - - -
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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