Contacts of the helix formed by residues 391 - 401 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A LEU* 4.5 8.1 - - + -
390A TYR* 1.3 88.7 - - - +
392A LEU* 1.3 64.6 + - - +
393A TYR* 3.4 21.0 + - + +
394A ASP* 3.0 33.6 + - - +
395A LEU 3.1 16.8 + - - -
419A VAL* 6.1 2.9 - - - -
455A GLN* 5.0 5.4 - - + +
456A GLY* 4.4 15.2 + - - +
458A ALA 4.4 2.3 + - - +
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 4.2 3.6 - - + -
380A PHE* 3.9 22.2 - - + +
381A LYS* 3.8 20.2 - - - +
382A LEU* 4.0 28.2 - - + +
390A TYR* 4.5 3.4 - - + -
391A THR* 1.3 72.6 - - - +
393A TYR* 1.3 56.6 + - - +
395A LEU* 4.1 19.5 - - + -
396A SER* 2.7 31.5 + - - -
408A ALA* 3.8 11.2 - - + -
419A VAL* 3.8 32.7 - - + +
420A VAL 4.1 0.9 - - - -
421A MET* 3.3 34.4 - - + +
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Residues in contact with TYR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A THR* 3.4 12.6 - - + +
392A LEU* 1.3 77.7 - - - +
394A ASP* 1.3 62.1 + - - +
396A SER* 3.2 4.7 + - - -
397A GLU* 3.0 18.0 + - - +
400A ARG* 4.8 2.1 + - - -
408A ALA* 3.6 35.8 - - + +
410A THR* 3.6 19.3 + - + +
419A VAL* 3.9 26.9 - - + -
458A ALA* 3.3 41.1 - - + +
459A GLN* 4.4 10.9 + - + -
460A GLN 4.1 23.1 - - - -
461A ASN* 2.8 24.9 + - - -
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Residues in contact with ASP 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TYR* 3.8 1.2 - - + -
391A THR* 3.0 32.6 + - - +
393A TYR* 1.3 75.1 - - - +
395A LEU* 1.3 61.8 + - - +
397A GLU* 3.1 15.8 + - - +
398A ARG* 3.2 19.5 + - - +
448A LEU* 4.1 18.2 - - + -
454A LEU* 3.4 16.0 - - + +
455A GLN* 3.4 6.7 - - - -
456A GLY 3.0 21.4 + - - -
457A ILE* 4.6 0.2 - - - +
458A ALA* 3.1 32.5 + - - +
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 4.3 4.0 - - - +
390A TYR* 4.5 7.2 - - + -
391A THR 3.1 11.6 + - - +
392A LEU* 3.2 18.6 + - + +
394A ASP* 1.3 75.5 - - - +
396A SER* 1.3 63.5 + - - +
398A ARG* 3.3 2.9 + - - +
399A LEU* 3.1 30.4 + - + +
421A MET* 4.1 14.8 - - + -
441A TYR* 3.3 41.7 - - + +
444A SER* 3.9 25.6 - - - -
445A LEU* 4.0 17.7 - - + -
448A LEU* 4.1 13.2 - - + -
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU 2.7 17.6 + - - -
393A TYR* 3.2 6.0 + - - -
395A LEU* 1.3 77.2 - - - +
397A GLU* 1.3 60.8 + - - +
399A LEU* 3.3 7.3 + - - +
400A ARG* 2.9 46.1 + - - +
404A TRP 4.8 0.5 - - - +
406A VAL 2.9 27.8 + - - -
408A ALA* 4.0 12.9 + - - -
421A MET* 3.7 9.8 - - - +
462A SER* 4.3 1.9 + - - -
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A TYR 3.0 12.1 + - - +
394A ASP* 3.1 11.2 + - - +
396A SER* 1.3 73.7 + - - +
398A ARG* 1.3 89.8 + - - +
400A ARG* 3.1 31.1 + - - +
401A LEU* 3.2 11.5 + - + +
454A LEU* 4.9 2.3 - - - +
457A ILE* 6.0 1.9 - - - +
458A ALA* 4.4 16.6 - - + +
398B ARG* 3.0 37.8 + - - -
401B LEU* 3.9 18.2 - - + +
447B TYR* 4.5 5.7 + - - -
454B LEU* 4.8 4.9 - - - +
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Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ASP* 3.2 14.7 + - - +
395A LEU 3.6 4.5 - - - +
397A GLU* 1.3 104.8 + - - +
399A LEU* 1.3 61.5 + - - +
401A LEU* 3.2 32.8 + - - +
402A ARG* 3.5 9.5 + - - +
444A SER* 3.3 32.4 + - - +
447A TYR* 3.3 30.0 - - + -
448A LEU* 3.8 25.1 - - + -
454A LEU* 3.7 30.7 - - + +
397B GLU* 2.9 37.2 + - - -
457B ILE* 5.9 0.4 - - - +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.1 29.7 + - + +
396A SER* 3.3 5.8 + - - +
397A GLU 3.2 0.2 - - - -
398A ARG* 1.3 75.8 - - - +
400A ARG* 1.3 59.0 + - - +
402A ARG* 3.0 13.5 + - + +
404A TRP* 2.9 38.2 + - + +
406A VAL* 4.0 29.2 - - + -
421A MET* 5.0 1.6 - - + -
437A LEU* 4.3 10.8 - - + -
440A ASP* 3.8 40.2 - - + +
441A TYR* 4.0 27.6 - - + +
444A SER* 3.8 7.6 - - - +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A TYR 4.8 1.8 + - - -
396A SER* 2.9 39.8 + - - -
397A GLU* 3.1 29.4 + - - +
399A LEU* 1.3 76.3 - - - +
401A LEU* 1.3 60.0 + - - +
402A ARG 3.1 0.4 - - - -
403A GLY* 3.1 14.0 + - - -
404A TRP 3.1 18.3 + - - +
405A GLN* 3.1 28.4 + - + +
406A VAL 5.1 0.8 - - - +
462A SER* 4.0 4.2 + - - -
400B ARG 5.4 3.3 - - - +
401B LEU* 3.7 30.4 - - + +
306F LEU* 3.4 41.0 - - - +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLU* 3.2 6.2 + - + +
398A ARG* 3.2 49.0 + - - +
400A ARG* 1.3 76.7 - - - +
402A ARG* 1.3 62.3 + - + +
403A GLY 3.3 1.2 + - - -
397B GLU* 3.7 22.9 - - + +
400B ARG* 3.8 41.3 - - + +
401B LEU* 3.8 28.0 - - + +
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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