Contacts of the helix formed by residues 391 - 402 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E LEU* 4.6 6.5 - - + -
390E TYR* 1.3 82.9 - - - +
392E LEU* 1.3 57.9 + - - +
393E TYR* 3.1 30.4 + - + +
394E ASP* 2.6 48.9 + - - +
395E LEU 2.9 9.9 + - - -
419E VAL* 6.1 0.9 - - - -
455E GLN* 5.3 5.4 - - + +
456E GLY* 4.7 11.9 - - - +
458E ALA 4.4 2.0 + - - +
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Residues in contact with LEU 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E TYR* 4.5 1.1 - - + -
380E PHE* 3.9 23.1 - - + +
381E LYS* 4.0 1.1 - - - -
382E LEU* 3.9 39.5 - - + +
390E TYR* 4.4 2.9 - - + -
391E THR* 1.3 74.5 - - - +
393E TYR* 1.3 57.0 + - - +
395E LEU* 3.8 23.8 - - + -
396E SER* 2.8 25.8 + - - -
408E ALA* 3.9 12.6 - - + -
419E VAL* 3.7 30.2 - - + +
420E VAL 4.2 0.4 - - - -
421E MET* 3.2 38.4 - - + +
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Residues in contact with TYR 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391E THR* 3.0 18.5 + - + +
392E LEU* 1.3 75.3 - - - +
394E ASP* 1.3 60.1 + - - +
396E SER* 3.2 5.2 + - - -
397E GLU* 2.9 28.1 + - - +
400E ARG* 5.0 1.6 + - - -
408E ALA* 3.7 24.4 - - + +
410E THR* 3.4 21.7 + - - +
419E VAL* 3.3 30.6 - - + +
458E ALA* 3.3 29.4 - - + +
459E GLN* 4.3 8.3 - - + -
460E GLN 3.8 27.4 - - - -
461E ASN* 2.8 31.8 + - - -
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Residues in contact with ASP 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E TYR* 3.6 10.5 - - + -
391E THR* 2.6 41.2 + - - +
393E TYR* 1.3 72.0 - - - +
395E LEU* 1.3 59.6 + - - +
397E GLU* 3.1 7.4 + - - +
398E ARG* 3.0 26.2 + - - -
448E LEU* 4.1 11.9 - - + -
454E LEU* 3.5 9.9 - - + +
455E GLN* 3.6 4.4 - - - -
456E GLY 2.9 23.1 + - - -
457E ILE* 3.4 7.1 + - - +
458E ALA* 3.3 28.6 + - - +
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Residues in contact with LEU 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E TYR* 4.3 0.7 - - - +
390E TYR* 4.2 17.0 - - + -
391E THR 2.9 9.7 + - - +
392E LEU* 3.8 19.3 - - + +
394E ASP* 1.3 73.9 - - - +
396E SER* 1.3 65.2 + - - +
398E ARG* 3.0 12.8 + - - +
399E LEU* 3.1 33.6 + - + +
421E MET* 4.3 6.3 - - + -
441E TYR* 3.1 38.8 - - + +
444E SER* 3.7 29.4 - - - -
445E LEU* 3.9 24.2 - - + -
448E LEU* 4.2 9.3 - - + +
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Residues in contact with SER 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E LEU 2.8 21.7 + - - -
393E TYR* 3.2 8.0 + - - -
395E LEU* 1.3 72.2 - - - +
397E GLU* 1.3 64.0 + - - +
399E LEU* 3.6 6.7 + - - +
400E ARG* 3.1 46.4 + - - +
404E TRP 4.7 0.5 - - - +
406E VAL 2.7 29.7 + - - -
408E ALA* 4.1 10.0 + - - -
421E MET* 3.9 6.2 - - - +
462E SER* 4.3 1.9 + - - -
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Residues in contact with GLU 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E TYR 2.9 13.2 + - - +
394E ASP* 3.1 10.7 + - - +
396E SER* 1.3 75.5 - - - +
398E ARG* 1.3 91.3 + - - +
400E ARG* 3.1 29.3 + - - +
401E LEU* 3.5 9.9 + - + +
454E LEU* 4.9 4.5 - - - +
458E ALA* 4.5 15.6 - - + +
398F ARG* 2.7 37.1 + - - -
401F LEU* 3.5 20.7 - - + +
447F TYR* 4.7 4.5 + - - -
454F LEU* 5.0 2.1 - - - +
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Residues in contact with ARG 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E ASP 3.0 17.8 + - - +
395E LEU 3.0 6.4 + - - +
397E GLU* 1.3 103.2 + - - +
399E LEU* 1.3 58.1 + - - +
401E LEU* 3.0 44.9 + - - +
402E ARG* 3.6 10.0 + - - +
444E SER* 3.5 28.9 - - - +
447E TYR* 3.7 28.6 - - + -
448E LEU* 3.8 24.5 - - + -
454E LEU* 4.0 29.4 - - - +
397F GLU* 2.8 37.8 + - - -
457F ILE* 6.0 0.6 - - - +
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Residues in contact with LEU 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E LEU* 3.1 35.7 + - + +
396E SER* 3.8 6.1 - - - +
398E ARG* 1.3 76.3 - - - +
400E ARG* 1.3 62.6 + - - +
401E LEU 3.2 0.2 - - - -
402E ARG* 3.2 10.6 + - - +
403E GLY 3.4 0.2 + - - -
404E TRP* 2.9 37.9 + - + +
406E VAL* 4.2 25.1 - - + -
421E MET* 4.8 1.8 - - - -
437E LEU* 3.9 22.4 - - + -
440E ASP* 3.9 8.5 - - + +
441E TYR* 3.9 35.0 - - + +
444E SER* 3.9 15.5 - - - +
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Residues in contact with ARG 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D LEU* 3.6 40.7 - - - +
393E TYR 5.0 1.4 + - - -
396E SER* 3.1 35.0 + - - +
397E GLU* 3.1 34.5 + - - +
399E LEU* 1.3 78.9 - - - +
401E LEU* 1.3 55.4 + - - +
402E ARG 3.0 0.2 - - - -
403E GLY* 2.8 21.4 + - - -
404E TRP 3.1 17.5 - - - +
405E GLN* 3.2 27.5 + - + +
406E VAL 5.3 0.2 - - - +
460E GLN 5.6 0.2 + - - -
462E SER* 3.8 4.4 + - - -
400F ARG 5.6 1.6 - - - +
401F LEU* 3.8 29.0 - - + +
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Residues in contact with LEU 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E GLU* 3.5 7.4 + - + +
398E ARG* 3.0 53.6 + - - +
400E ARG* 1.3 76.1 - - - +
402E ARG* 1.3 63.2 + - + +
403E GLY 3.4 0.8 + - - -
397F GLU* 3.8 28.0 - - + +
400F ARG* 3.9 40.3 - - + +
401F LEU* 3.9 22.0 - - + +
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Residues in contact with ARG 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLY* 5.6 8.1 - - - -
58E GLN* 3.4 16.3 + - - +
398E ARG 3.6 9.8 + - - +
399E LEU* 3.2 9.4 + - - +
400E ARG 3.0 0.8 - - - -
401E LEU* 1.3 84.5 - - + +
403E GLY* 1.3 55.5 + - - +
404E TRP* 3.5 7.5 + - + -
439E GLU 5.5 0.4 + - - -
440E ASP* 3.0 52.3 + - + +
443E ALA* 3.6 28.1 + - - +
444E SER* 4.9 2.6 + - - -
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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