Contacts of the helix formed by residues 391 - 402 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C LEU* 4.4 9.9 - - + -
390C TYR* 1.3 94.1 - - - +
392C LEU* 1.3 63.6 + - - +
393C TYR* 3.3 32.6 + - + +
394C ASP* 2.9 20.2 + - - +
395C LEU 3.2 12.3 + - - -
419C VAL* 5.9 1.8 - - - -
455C GLN* 4.9 6.3 - - + +
456C GLY* 4.2 17.3 - - - +
458C ALA 4.4 1.3 + - - +
459C GLN* 6.2 1.3 - - - +
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C TYR* 4.4 2.2 - - + -
380C PHE* 3.8 23.8 - - + +
381C LYS* 4.0 9.6 - - - -
382C LEU* 4.2 28.8 - - + +
390C TYR* 4.3 4.5 - - + -
391C THR* 1.3 72.3 - - - +
393C TYR* 1.3 56.4 + - - +
395C LEU* 3.2 22.2 + - + -
396C SER* 2.8 35.3 + - - -
408C ALA* 3.8 9.4 - - + -
419C VAL* 3.7 37.0 - - + +
420C VAL 4.1 0.2 - - - -
421C MET* 3.5 30.1 - - + +
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Residues in contact with TYR 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C THR* 3.3 14.1 - - + +
392C LEU* 1.3 77.9 - - - +
394C ASP* 1.3 61.7 + - - +
396C SER* 3.3 5.2 + - - -
397C GLU* 3.1 22.9 + - - +
400C ARG* 4.8 1.6 + - - -
408C ALA* 3.7 31.3 - - + +
410C THR* 3.6 19.2 + - - +
419C VAL* 3.7 25.1 - - + +
458C ALA* 3.3 35.8 - - + +
459C GLN* 4.1 22.4 + - + -
460C GLN 3.8 23.1 - - - -
461C ASN* 2.7 28.9 + - - -
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Residues in contact with ASP 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C TYR* 3.6 1.0 - - + -
391C THR* 2.9 30.8 + - - +
393C TYR* 1.3 75.2 - - - +
395C LEU* 1.3 58.2 + - - +
397C GLU* 3.4 5.6 + - - +
398C ARG* 3.1 32.5 + - - +
448C LEU* 3.9 19.5 - - + -
454C LEU* 3.4 17.6 - - + +
455C GLN* 3.5 5.5 - - - -
456C GLY 2.9 22.5 + - - -
457C ILE 3.6 0.2 + - - -
458C ALA* 3.3 29.7 + - - +
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Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C TYR* 4.5 4.0 - - - +
390C TYR* 4.3 9.2 - - + -
391C THR 3.2 10.7 + - - +
392C LEU* 3.2 16.6 + - + +
394C ASP* 1.3 75.5 - - - +
396C SER* 1.3 60.9 + - - +
398C ARG* 3.1 4.6 + - - +
399C LEU* 2.9 36.9 + - + +
421C MET* 3.7 22.0 - - + -
441C TYR* 3.4 39.9 - - + +
444C SER* 3.9 24.7 - - - -
445C LEU* 4.2 16.2 - - + -
448C LEU* 4.1 8.7 - - + +
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Residues in contact with SER 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LEU 2.8 17.3 + - - -
393C TYR* 3.4 7.0 - - - -
395C LEU* 1.3 75.8 - - - +
397C GLU* 1.3 62.5 + - - -
399C LEU* 3.1 7.7 + - - +
400C ARG* 2.9 48.9 + - - +
404C TRP 4.6 0.7 - - - +
406C VAL 2.7 26.5 + - - -
408C ALA* 4.1 13.4 + - - -
421C MET* 3.7 8.9 - - - +
462C SER* 4.2 2.1 + - - -
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Residues in contact with GLU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C TYR 3.1 13.4 + - - +
394C ASP* 3.6 10.8 - - - +
395C LEU 3.3 0.2 - - - -
396C SER* 1.3 73.4 - - - +
398C ARG* 1.3 86.1 + - - +
400C ARG* 3.1 31.2 + - - +
401C LEU* 3.3 12.9 + - + +
454C LEU* 5.1 1.9 - - - +
458C ALA* 4.4 15.5 - - + +
398D ARG* 2.8 43.8 + - - -
401D LEU* 3.8 18.7 - - + +
447D TYR* 4.6 4.7 + - - -
454D LEU* 5.0 2.9 - - - +
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Residues in contact with ARG 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ASP 3.1 16.4 + - - +
395C LEU* 3.1 8.5 + - - +
397C GLU* 1.3 103.1 + - - +
399C LEU* 1.3 62.6 + - - +
401C LEU* 3.2 36.0 + - - +
402C ARG* 3.6 10.7 + - - +
444C SER* 3.6 24.9 + - - +
447C TYR* 3.7 40.1 - - - -
448C LEU* 3.8 22.8 - - + +
454C LEU* 3.8 24.3 - - - +
397D GLU* 3.1 35.8 + - - -
398D ARG* 3.8 0.6 - - - +
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Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C LEU* 2.9 31.5 + - + +
396C SER* 3.1 8.5 + - - +
398C ARG* 1.3 78.0 - - - +
400C ARG* 1.3 58.4 + - - +
402C ARG* 3.2 11.1 + - - +
403C GLY 3.3 0.2 + - - -
404C TRP* 3.0 34.8 + - + +
406C VAL* 4.1 32.3 - - + -
421C MET* 4.4 3.1 - - + -
437C LEU* 4.3 15.0 - - + -
440C ASP* 3.8 25.6 - - + +
441C TYR* 3.9 22.4 - - + +
444C SER* 3.7 15.9 - - - +
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Residues in contact with ARG 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 3.6 37.2 - - - +
393C TYR 4.8 1.6 + - - -
396C SER* 2.9 32.0 + - - +
397C GLU* 3.1 37.8 + - - +
399C LEU* 1.3 77.0 - - - +
401C LEU* 1.3 56.3 + - - +
402C ARG 3.1 0.2 - - - -
403C GLY* 3.1 17.5 + - - -
404C TRP 3.1 19.2 + - - +
405C GLN* 3.2 26.9 + - + +
406C VAL 5.2 0.4 - - - +
458C ALA* 5.8 2.2 - - - +
462C SER* 3.8 5.7 + - - -
400D ARG 5.4 3.3 - - - +
401D LEU* 3.7 27.3 - - + +
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Residues in contact with LEU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C GLU* 3.3 8.2 + - + +
398C ARG* 3.2 52.6 + - - +
400C ARG* 1.3 75.5 - - - +
402C ARG* 1.3 63.2 + - + +
403C GLY 3.3 1.3 - - - -
397D GLU* 3.7 37.9 - - + +
400D ARG* 3.7 35.0 - - + +
401D LEU* 3.7 23.3 - - + +
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Residues in contact with ARG 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 3.7 11.6 + - - +
398C ARG 3.6 7.6 + - - +
399C LEU 3.2 9.4 + - - +
400C ARG 3.1 0.6 - - - -
401C LEU* 1.3 83.3 - - + +
403C GLY* 1.3 56.0 + - - +
404C TRP* 3.5 8.7 + - + -
439C GLU* 4.7 1.6 + - - +
440C ASP* 2.5 65.0 + - + +
443C ALA* 3.7 27.1 - - - +
444C SER* 4.4 7.2 - - - -
307E GLY* 5.1 13.3 + - - -
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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
------------------------------------------------------------
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