Contacts of the helix formed by residues 392 - 401 (chain B) in PDB entry 5NC5
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 392 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA 3.9 0.2 + - - -
34B GLN* 3.0 30.5 + - - +
35B TYR* 3.7 20.5 - - + +
332B PHE* 5.4 5.1 - - + -
333B VAL* 5.8 0.5 - - - +
336B SER* 4.6 8.4 + - - +
391B ASN* 1.3 73.3 - - - +
393B LEU* 1.3 64.3 + - - +
395B MET* 3.5 19.6 - - + +
396B PHE* 3.0 37.1 + - + -
926B TYR* 3.5 24.0 - - - +
999B ALA* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 4.0 22.2 - - + -
36B PRO* 3.7 23.6 - - + -
38B ILE* 4.9 3.6 - - + -
391B ASN* 2.8 12.8 + - - +
392B THR* 1.3 72.3 - - - +
394B THR* 1.3 60.8 + - - +
395B MET 3.2 0.3 + - - -
396B PHE* 3.2 2.0 + - - -
397B GLY 2.9 18.9 + - - -
466B ILE* 4.1 26.7 - - + -
469B GLN* 3.7 27.8 - - + -
470B PHE* 3.4 29.1 - - + -
564B LEU* 4.7 7.4 - - + -
671B ILE* 5.3 0.7 - - + -
926B TYR* 3.7 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 4.4 11.7 - - + -
388B PHE* 4.1 11.2 - - + -
389B SER 2.9 16.6 + - - +
390B ILE* 3.8 2.0 - - - -
391B ASN* 2.8 35.4 + - - +
393B LEU* 1.3 74.7 - - - +
395B MET* 1.3 59.3 + - - +
397B GLY 3.4 0.6 + - - +
398B MET* 3.1 26.2 + - - +
469B GLN* 3.7 28.0 - - + +
473B THR* 3.5 27.9 - - - +
1117B D10 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 6.5 0.2 - - + -
33B ALA 5.5 0.7 - - - +
34B GLN* 6.3 0.4 - - - -
333B VAL* 5.0 7.0 - - + +
336B SER* 3.4 48.7 - - - +
337B ILE* 3.9 23.8 - - + +
340B VAL* 3.9 18.7 - - + +
390B ILE* 3.7 18.8 - - + -
391B ASN* 2.7 21.7 + - - +
392B THR* 3.5 29.6 - - - +
394B THR* 1.3 75.3 + - - +
396B PHE* 1.3 62.0 + - + +
398B MET* 3.4 15.0 + - - +
399B VAL* 3.4 16.3 - - - +
1117B D10 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 5.0 9.9 - - + -
392B THR* 3.0 29.0 + - + +
393B LEU 4.0 2.2 - - - +
395B MET* 1.3 72.8 - - + +
397B GLY* 1.3 68.3 + - - +
398B MET 3.1 1.6 - - - -
399B VAL* 3.1 21.4 + - + +
400B LEU* 2.9 26.6 + - + +
470B PHE* 4.2 5.2 - - + -
926B TYR* 3.5 35.7 - + + -
989B LEU* 5.2 3.8 - - + -
996B GLY* 4.8 1.6 - - - -
999B ALA* 3.2 32.3 - - + -
1000B GLN* 3.9 32.8 - - + -
1003B VAL* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU 2.9 12.0 + - - -
394B THR 3.8 4.7 - - - -
395B MET 3.4 0.2 - - - -
396B PHE* 1.3 77.1 - - - +
398B MET* 1.3 62.2 + - - +
400B LEU* 3.3 3.6 + - - -
401B ALA* 3.2 22.2 + - - +
470B PHE* 3.7 21.0 - - - -
473B THR* 4.1 13.9 - - - -
474B ILE* 3.7 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 5.1 1.6 - - + -
344B LEU* 4.8 14.7 - - + +
376B LEU* 3.8 21.7 - - + +
379B THR* 3.5 36.8 - - + -
380B PHE* 3.3 45.5 - - + -
383B LEU* 5.7 3.8 - - + -
394B THR 3.1 17.0 + - - +
395B MET* 3.5 10.3 - - - +
396B PHE 3.1 0.6 - - - -
397B GLY* 1.3 74.2 - - - +
399B VAL* 1.3 62.3 + - + +
401B ALA* 3.2 15.2 + - - +
402B ILE* 3.4 13.4 + - - +
405B LEU* 5.5 1.7 - - - +
473B THR* 3.9 11.4 - - + +
477B ALA* 4.8 9.0 - - - -
1117B D10 4.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 4.2 22.4 - - + +
343B THR* 4.2 15.5 - - + +
344B LEU* 5.5 1.3 - - + -
395B MET 3.4 17.0 - - - +
396B PHE* 3.1 15.8 + - + +
398B MET* 1.3 75.0 - - + +
400B LEU* 1.3 65.3 + - + +
402B ILE* 3.2 36.2 + - + +
982B PHE* 4.3 8.5 - - - -
986B VAL* 5.5 5.4 - - + +
989B LEU* 4.0 26.9 - - + -
1003B VAL* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B PHE 2.9 19.9 + - - +
397B GLY 3.9 5.2 - - - +
398B MET 3.3 0.4 - - - -
399B VAL* 1.3 78.3 - - + +
401B ALA* 1.3 57.6 + - - +
402B ILE 3.4 0.2 - - - -
403B GLY* 4.5 4.3 + - - -
404B LEU* 4.8 2.4 - - - +
470B PHE* 4.5 11.2 - - + -
474B ILE* 4.6 4.3 - - + -
926B TYR* 4.3 7.2 - - + +
929B VAL* 3.3 33.9 - - + -
930B GLY* 3.9 10.3 - - - +
933B THR* 3.4 34.2 + - + +
982B PHE* 4.7 7.3 - - + -
1003B VAL* 3.7 36.8 - - + -
1007B VAL* 4.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLY 3.2 10.7 + - - +
398B MET* 3.2 11.8 + - - +
399B VAL 3.1 0.4 - - - -
400B LEU* 1.3 75.3 - - - +
402B ILE* 1.3 65.7 + - - +
403B GLY 3.2 2.9 - - - -
404B LEU* 3.2 15.3 + - + +
405B LEU* 3.1 25.9 + - + +
474B ILE* 4.4 17.0 - - + +
477B ALA* 4.1 25.8 - - + -
478B MET* 5.7 1.1 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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