Contacts of the helix formed by residues 386 - 394 (chain C) in PDB entry 3R2W
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C MET* 3.7 11.2 - - + +
384C VAL* 3.8 1.3 - - - +
385C LYS* 1.3 89.9 - - + +
387C THR* 1.3 54.7 + - - +
388C SER* 2.7 16.1 + - - -
389C ASP* 2.5 39.4 + - - +
390C LEU* 3.2 8.0 + - - +
426C THR* 5.2 14.1 - - + -
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Residues in contact with THR 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C MET* 4.0 4.6 - - - -
386C THR* 1.3 72.2 - - - +
388C SER* 1.3 57.8 + - - +
389C ASP 3.2 0.2 - - - -
390C LEU* 3.3 13.9 - - + +
391C LEU* 3.0 29.8 + - - +
421C LEU* 4.3 4.5 - - - +
425C PHE* 2.7 29.9 + - - +
426C THR* 3.2 27.3 + - - +
428C VAL* 4.1 19.1 - - + +
431C TYR* 3.8 33.4 - - + -
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Residues in contact with SER 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C THR* 2.7 12.6 + - - -
387C THR* 1.3 81.6 + - - +
389C ASP* 1.3 61.1 + - - +
391C LEU 4.2 0.8 + - - -
392C LEU* 3.9 6.6 + - - +
418C LEU* 5.4 0.4 - - - +
419C VAL* 2.9 41.4 - - - +
420C LYS* 3.6 1.9 - - - -
421C LEU* 2.9 49.0 + - - +
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Residues in contact with ASP 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C PRO* 3.4 23.4 - - - +
384C VAL* 4.0 18.1 - - + +
385C LYS* 3.8 13.0 + - - +
386C THR* 2.5 23.6 + - - +
388C SER* 1.3 74.4 - - - +
390C LEU* 1.3 63.7 + - - +
392C LEU* 3.0 25.3 - - - +
393C VAL* 3.0 22.2 + - - +
418C LEU* 4.2 11.7 - - - +
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C MET* 4.8 9.9 - - + -
119C ILE* 4.8 6.7 - - + -
120C GLY 4.5 7.6 - - - +
121C VAL* 4.7 9.4 - - + -
127C PHE* 4.7 13.0 - - + -
384C VAL* 3.7 21.7 - - + +
386C THR 3.2 4.2 + - - +
387C THR* 3.3 23.8 - - + +
389C ASP* 1.3 72.6 - - - +
391C LEU* 1.3 59.4 + - - +
392C LEU 3.0 1.1 - - - -
393C VAL* 2.5 33.7 + - + +
394C MET* 2.8 40.2 + - + +
428C VAL* 4.7 11.2 - - + -
431C TYR* 3.9 21.3 - - + -
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Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C THR 3.0 11.3 + - - +
388C SER 4.4 2.5 - - - +
390C LEU* 1.3 79.7 - - - +
392C LEU* 1.3 63.0 + - - +
394C MET* 3.8 2.4 + - - -
395C SER* 3.4 21.0 + - - -
419C VAL* 4.5 15.0 - - + -
421C LEU* 4.0 18.6 - - + -
431C TYR* 2.9 27.1 + - + +
435C PHE* 3.6 41.3 - - + -
438C ILE* 4.0 13.5 - - + +
439C PRO* 4.2 9.4 - - + -
441C MET* 3.9 20.5 - - + +
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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
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382C LEU* 6.2 0.4 - - + -
388C SER 3.9 3.9 + - - +
389C ASP* 3.0 34.4 + - - +
391C LEU* 1.3 83.0 - - - +
393C VAL* 1.3 61.9 + - + +
395C SER* 3.4 14.6 + - - -
397C LEU* 4.1 7.2 - - + +
398C TYR* 3.4 22.6 - - + +
416C VAL* 3.8 27.1 - - + -
417C PRO* 3.3 31.2 - - + +
418C LEU* 3.9 12.8 - - + -
419C VAL* 3.8 22.7 - - + -
441C MET* 4.2 11.2 - - + -
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Residues in contact with VAL 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C VAL* 4.1 23.8 - - + -
122C ARG* 3.2 20.4 + - - +
244C LEU* 3.8 26.0 - - + -
382C LEU* 5.3 5.2 - - + -
384C VAL* 5.1 5.8 - - + -
389C ASP 3.5 7.2 - - - +
390C LEU* 2.5 36.8 + - + +
392C LEU* 1.3 72.0 - - + +
394C MET* 1.3 57.4 + - + +
395C SER 3.3 4.3 - - - -
398C TYR* 3.5 17.8 - - + -
405C LEU* 3.8 27.1 - - + +
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Residues in contact with MET 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLY 3.9 5.6 - - - +
121C VAL 3.0 36.1 - - - +
122C ARG* 4.1 22.8 + - + +
123C ASN 5.5 0.9 - - - +
390C LEU* 2.8 55.1 + - + +
391C LEU 4.5 0.7 - - - +
393C VAL* 1.3 77.4 - - + +
395C SER* 1.3 62.0 + - - +
431C TYR* 3.8 19.7 - - + +
432C LEU* 5.2 5.6 - - - -
436C GLU* 5.8 0.7 - - - +
438C ILE* 3.4 36.0 - - + +
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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