Contacts of the helix formed by residues 444 - 453 (chain C) in PDB entry 5UH6
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 444 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ASP 4.4 0.7 - - - +
442C GLN* 4.4 4.9 - - - -
443C ASN* 1.3 76.0 + - - +
445C PRO* 1.3 77.9 - - + +
446C LEU* 2.9 16.3 + - - +
447C SER* 2.6 39.0 + - - -
448C GLY* 3.5 3.8 + - - -
612C GLN 3.3 6.0 + - - -
613C ARG 2.6 34.4 + - - -
615C ALA* 3.0 23.4 + - - +
617C PRO* 4.9 1.3 - - + -
640C ASP* 5.1 2.2 - - - +
706C PRO* 5.8 0.7 - - - -
707C CYS* 4.3 6.7 - - - -
715C LEU* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ASN* 1.3 86.9 - - + +
446C LEU* 1.3 64.1 + - - +
448C GLY* 3.0 14.4 + - - -
449C LEU* 3.2 10.0 + - - +
635C ALA* 5.6 0.7 - - - +
638C ALA* 4.0 24.8 - - + +
640C ASP* 4.0 32.1 - - + +
641C VAL* 6.3 0.7 - - + -
706C PRO* 3.2 40.4 - - + +
707C CYS* 4.1 8.7 - - + -
708C THR* 4.6 4.7 - - - +
713C MET* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ASN* 2.9 10.7 + - - +
445C PRO* 1.3 75.7 - - - +
447C SER* 1.3 58.1 + - - +
449C LEU* 3.1 24.1 + - + +
450C THR* 2.7 41.5 + - - +
589C VAL* 5.0 2.5 - - + +
590C ALA* 4.7 12.3 - - + +
593C MET* 3.7 35.2 - - + -
612C GLN* 3.7 33.9 - - + +
613C ARG* 4.5 2.2 - - + +
634C ALA* 5.0 7.0 - - + -
638C ALA* 5.4 0.9 - - - -
713C MET* 3.5 21.2 - - + +
715C LEU* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ASP* 2.8 43.6 + - - +
443C ASN 3.8 2.2 + - - -
444C ASN* 2.6 24.9 + - - -
445C PRO 3.2 0.2 - - - -
446C LEU* 1.3 73.5 - - - +
448C GLY* 1.3 59.1 + - - +
450C THR* 3.4 7.7 + - - -
451C HIS* 3.2 21.0 + - - +
454C ARG* 4.7 0.9 + - - -
613C ARG* 3.3 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C MET* 4.0 16.9 - - - +
441C ASP 3.2 16.6 + - - -
442C GLN* 5.5 0.2 - - - -
444C ASN 3.5 2.7 + - - -
445C PRO 3.0 8.8 + - - -
447C SER* 1.3 76.5 + - - +
449C LEU* 1.3 64.6 + - - +
451C HIS* 3.1 15.5 + - - +
452C LYS* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.7 39.3 - - + -
54C LEU* 3.6 27.8 - - + -
445C PRO 3.2 9.1 + - - +
446C LEU* 3.1 17.6 + - + +
448C GLY* 1.3 76.3 - - - +
450C THR* 1.3 61.8 + - - +
452C LYS* 3.1 17.5 + - - +
453C ARG* 3.4 23.2 + - - +
589C VAL* 4.0 16.2 - - + -
634C ALA* 4.0 22.4 - - + +
637C ASP* 4.9 4.9 - - + +
638C ALA* 4.6 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 2.7 36.6 + - - +
447C SER* 3.7 8.5 - - - -
449C LEU* 1.3 77.6 - - - +
451C HIS* 1.3 62.2 + - - +
453C ARG* 3.2 15.6 + - - +
454C ARG* 3.2 29.2 + - + +
487C GLU* 3.2 35.7 - - - +
499C SER* 4.4 7.6 - - - +
589C VAL* 6.5 0.9 - - - -
590C ALA* 4.6 7.0 - - + +
613C ARG* 5.0 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C VAL* 3.8 22.2 - - + +
176C VAL* 4.0 10.3 - - + +
438C GLN* 2.3 35.4 + - + +
439C PHE 3.4 18.4 - - - -
440C MET* 4.1 3.1 - - + -
441C ASP* 3.1 28.3 + - + +
447C SER 3.2 12.7 + - - +
448C GLY* 3.1 12.5 + - - +
449C LEU 3.1 0.4 - - - -
450C THR* 1.3 77.8 - - - +
452C LYS* 1.3 61.8 + - + +
453C ARG 3.1 1.3 + - - -
454C ARG* 3.5 26.5 + - - +
1201C RFP 3.1 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.6 27.6 - - + +
56C VAL* 4.6 8.7 - - - +
57C GLN* 3.2 38.2 + - + +
163C LYS* 3.2 27.0 + - - +
164C GLY 4.6 3.4 - - - +
165C THR* 3.6 16.4 - - - +
174C VAL* 4.2 22.9 - - + -
176C VAL* 5.9 0.8 - - - -
177C SER* 5.2 1.6 + - - -
440C MET* 3.3 27.1 - - - +
448C GLY 3.3 18.2 + - - +
449C LEU* 3.1 8.8 + - - +
451C HIS* 1.3 77.3 - - - +
453C ARG* 1.3 61.1 + - + +
454C ARG 3.6 1.5 - - - +
638C ALA 3.6 21.2 + - - -
640C ASP* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PRO* 6.0 0.2 - - - +
52C GLY 5.1 1.0 + - - -
53C LEU* 3.2 53.7 + - - +
54C LEU* 5.7 0.4 - - + -
56C VAL* 4.3 10.1 - - + +
449C LEU* 3.4 28.5 + - + +
450C THR* 3.2 8.3 + - - +
451C HIS 3.1 1.0 - - - -
452C LYS* 1.3 83.0 - - + +
454C ARG* 1.3 62.3 + - - +
455C LEU* 3.8 3.2 - - - +
499C SER* 3.7 8.8 - - - +
500C LEU* 2.7 84.5 + - + +
501C SER 3.1 6.0 + - - -
502C VAL 3.4 15.6 + - - -
504C ALA 4.6 2.6 + - - -
589C VAL* 3.8 21.2 - - - +
----------------------------------------------------------
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