Contacts of the helix formed by residues 394 - 404 (chain V) in PDB entry 1I84
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 ASN 394 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92T LEU 2.7 4.8 + - - -
93T ARG* 1.4 78.1 - - - +
96T ASP* 1.5 68.8 + - + +
99T GLY* 2.8 18.0 - - - -
101T GLY* 1.9 8.4 - - - +
102T THR 4.2 0.2 - - - +
140T TYR* 1.7 35.9 - - + +
393V ILE* 1.3 58.2 - - - +
395V VAL* 1.3 63.3 + - - +
396V THR* 2.6 1.6 + - - -
397V ASP* 2.4 4.2 + - - +
398V PHE* 2.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89T VAL* 6.3 0.9 - - + -
90T GLU* 4.2 12.8 - - - +
93T ARG* 0.5 290.1 - - + +
94T VAL 3.8 0.2 - - - +
381V ASN* 6.3 1.6 - - + -
384V ALA* 5.6 0.4 - - + -
385V GLN* 3.9 26.2 - - + +
388V CYS* 4.4 0.2 - - + -
394V ASN* 1.3 58.5 - - - +
396V THR* 1.3 58.0 + - + +
398V PHE* 2.5 29.3 + - - +
399V THR* 2.7 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 396 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90T GLU 4.6 0.7 - - - +
93T ARG* 1.8 35.4 + - + -
94T VAL* 2.0 85.1 + - + +
95T PHE 2.9 0.2 + - - -
394V ASN* 2.6 3.1 + - - -
395V VAL* 1.3 73.7 - - + +
397V ASP* 1.3 67.6 + - - +
399V THR* 3.2 8.2 + - - -
400V ARG* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 397 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94T VAL 4.7 0.8 - - - +
95T PHE 3.2 2.6 - - - -
96T ASP* 0.9 200.1 + - + +
97T LYS* 1.4 27.6 + - - -
98T GLU 2.8 14.4 - - - +
99T GLY 2.8 10.8 - - - +
394V ASN* 2.4 2.5 + - - +
395V VAL 2.8 2.8 + - - -
396V THR* 1.3 83.1 + - - +
398V PHE* 1.3 58.6 + - - +
400V ARG* 3.0 12.8 + - - +
401V SER* 2.5 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 398 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T ARG* 3.0 24.2 - - - +
99T GLY* 2.3 34.2 - - - +
362V LEU* 4.8 0.2 - - + -
365V ILE* 3.9 3.8 - - + -
384V ALA* 3.9 19.1 - - + -
387V VAL* 4.6 8.1 - - + -
388V CYS* 3.2 5.8 - - - -
391V MET* 4.3 10.1 - - + -
393V ILE* 3.4 13.5 - - + -
394V ASN 2.9 9.9 - - - +
395V VAL 2.5 4.2 + - - -
397V ASP* 1.3 67.5 - - - +
399V THR* 1.3 54.1 + - + -
401V SER* 3.1 3.6 + - - -
402V ILE* 2.5 59.0 + - + +
427V ILE* 3.3 35.0 - - + -
430V LEU* 4.1 10.5 - - + -
609V VAL* 3.3 26.7 - - + -
612V LEU* 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 399 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732S GLN* 5.9 3.6 - - - +
93T ARG* 4.1 2.8 + - - +
378V MET* 3.8 26.7 - - + -
381V ASN* 6.1 0.7 - - - +
384V ALA* 5.8 2.7 - - + -
395V VAL* 2.7 27.1 + - - +
396V THR* 3.2 9.5 + - - -
398V PHE* 1.3 75.9 - - + +
400V ARG* 1.3 53.6 + - - +
402V ILE* 2.9 9.1 + - + +
403V LEU* 2.6 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165S LEU 5.8 3.2 + - - -
168S ARG* 2.4 53.3 - - - +
258S VAL* 5.2 0.4 - - - +
94T VAL 5.4 4.0 + - - -
97T LYS* 2.3 33.9 + - - +
98T GLU* 4.9 0.8 - - - +
396V THR* 2.9 15.6 + - - +
397V ASP* 3.5 21.9 + - - +
399V THR* 1.3 69.6 - - - +
401V SER* 1.3 56.8 + - - +
403V LEU* 2.6 11.9 + - - -
404V THR* 2.4 58.2 + - + +
406V ARG* 4.5 19.5 - - - +
608V ASN* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97T LYS 4.1 1.9 + - - -
98T GLU* 3.2 20.7 - - - +
397V ASP 2.5 21.9 + - - -
398V PHE 3.3 4.9 - - - -
400V ARG* 1.3 78.1 + - - +
402V ILE* 1.3 58.0 + - - +
403V LEU 3.5 0.2 + - - -
404V THR 3.9 2.0 - - - -
405V PRO* 4.0 5.7 - - - +
418V GLN* 4.0 3.8 - - - +
606V ASN* 2.5 27.1 + - - -
608V ASN* 3.4 36.9 + - - +
609V VAL* 3.9 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367V PHE* 3.3 29.4 - - + -
378V MET* 5.5 0.7 - - - -
398V PHE* 2.5 52.1 + - + +
399V THR* 3.3 12.6 - - + +
401V SER* 1.3 73.5 - - - +
403V LEU* 1.3 65.8 + - + +
418V GLN* 2.9 17.0 + - - +
423V ALA* 4.1 13.6 - - - +
426V ALA* 5.3 4.4 - - + +
427V ILE* 3.5 29.2 - - + +
430V LEU* 4.5 4.5 - - + -
606V ASN* 4.3 4.0 - - + +
609V VAL* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367V PHE* 3.4 23.8 - - + -
376V ALA 3.5 24.0 - - - +
377V SER* 3.7 17.5 - - - +
378V MET* 4.4 5.6 - - + +
399V THR* 2.6 54.6 + - + +
400V ARG* 2.6 4.4 + - - +
402V ILE* 1.3 78.8 - - + +
404V THR* 1.3 66.4 + - + +
405V PRO* 3.3 4.2 - - - +
417V ALA* 3.7 2.8 - - - +
418V GLN* 2.9 33.6 + - - +
423V ALA* 5.2 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 404 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168S ARG* 1.8 74.8 + - - -
729S GLU* 5.2 10.8 - - - +
400V ARG* 2.4 45.2 + - + +
401V SER 4.1 0.4 - - - -
403V LEU* 1.3 77.4 - - + +
405V PRO* 1.3 56.0 - - - +
415V GLN* 4.2 5.4 - - - -
416V LYS 3.2 7.2 - - - -
417V ALA* 4.0 12.6 - - + +
----------------------------------------------------------
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