Contacts of the helix formed by residues 409 - 417 (chain C) in PDB entry 3U1K
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 ASP 409 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ILE 5.0 8.1 - - - +
407C LYS* 4.4 1.6 - - - +
408C SER* 1.3 77.6 - - - +
410C GLN* 1.3 63.3 + - - +
411C VAL* 3.0 16.4 + - - +
412C ILE* 2.8 51.8 + - + +
413C THR* 2.8 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B LYS 4.8 1.6 - - - +
632B GLN* 2.8 55.7 + - - +
633B ALA* 4.7 1.4 + - - +
637B VAL 3.5 3.2 + - - -
638B THR* 3.3 29.7 + - + +
112C ILE* 4.4 14.9 - - + +
407C LYS 5.6 0.4 - - - -
408C SER 3.5 5.3 + - - -
409C ASP* 1.3 71.7 - - - +
411C VAL* 1.3 73.1 + - + +
413C THR* 3.4 7.6 + - - +
414C ALA* 3.2 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B SER* 5.0 16.2 - - - +
112C ILE* 4.0 18.7 - - + +
113C PRO 3.9 19.7 - - - +
114C THR* 4.0 6.1 - - + -
116C TYR* 4.1 15.3 - - - +
117C LEU* 4.0 22.4 - - + -
409C ASP* 3.0 12.4 + - - +
410C GLN* 1.3 82.3 - - + +
412C ILE* 1.3 69.5 + - + +
414C ALA* 3.1 13.0 + - - +
415C ILE* 3.2 13.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 3.7 27.6 - - + -
407C LYS* 3.3 42.3 - - + +
409C ASP* 2.8 46.4 + - + +
411C VAL* 1.3 73.4 - - + +
413C THR* 1.3 63.8 + - - +
415C ILE* 3.4 25.5 + - + +
416C ASN* 4.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B LYS 5.2 2.5 - - - +
633B ALA* 4.0 11.9 - - + -
406C ILE* 3.7 11.9 - - + +
407C LYS* 2.9 44.9 + - + +
409C ASP 2.8 15.7 + - - -
410C GLN* 3.5 9.6 - - - +
411C VAL 3.1 0.2 - - - -
412C ILE* 1.3 78.3 - - - +
414C ALA* 1.3 52.1 + - - +
415C ILE 3.2 0.3 + - - -
416C ASN* 3.5 1.4 + - - +
417C GLY* 2.8 33.4 + - - +
418C ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B GLN 5.0 1.1 - - - +
633B ALA* 4.7 17.0 - - - +
107C ALA* 3.5 12.9 - - + +
108C ALA* 4.4 11.5 + - + +
112C ILE* 4.0 32.1 - - + -
410C GLN* 3.2 10.0 + - - +
411C VAL 3.1 9.0 + - - +
413C THR* 1.3 80.2 - - - +
415C ILE* 1.3 65.7 + - - +
417C GLY* 3.2 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLN* 4.6 6.3 + - - +
107C ALA* 3.6 13.0 - - + +
114C THR* 3.8 23.6 - - + -
117C LEU* 4.1 23.6 - - + -
122C GLY 6.2 0.4 - - - +
124C SER* 3.6 33.4 - - - +
126C LYS* 5.8 2.1 - - - +
411C VAL 3.2 13.9 + - - +
412C ILE* 3.5 22.7 - - + +
413C THR 3.2 1.0 - - - -
414C ALA* 1.3 79.7 - - - +
416C ASN* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C SER* 3.7 8.6 - - - +
125C ASP* 3.2 49.5 + - - +
126C LYS 4.7 0.3 + - - -
407C LYS* 5.9 6.1 - - + +
412C ILE 4.0 3.5 + - - +
413C THR 3.5 3.9 + - - +
415C ILE* 1.3 83.7 - - - +
417C GLY* 1.3 66.8 + - - +
418C ILE 5.1 0.9 - - - -
419C LYS* 5.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ALA* 5.0 8.1 - - - -
405C GLY 4.4 4.3 - - - +
413C THR* 2.8 18.7 + - - +
414C ALA* 3.2 12.7 + - - -
416C ASN* 1.3 84.4 - - - +
418C ILE* 1.3 69.8 + - - +
419C LYS* 4.0 2.6 + - - +
----------------------------------------------------------
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