Contacts of the helix formed by residues 42 - 53 (chain C) in PDB entry 1TAD
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 LYS 42 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.5 35.6 - - + +
35C LEU* 4.1 6.3 - - - +
36C GLY 3.2 22.8 + - - +
37C ALA 2.9 24.7 + - - -
40C SER* 3.5 7.7 + - - +
41C GLY* 1.3 75.9 - - - +
43C SER* 1.3 61.6 + - - +
45C ILE* 3.3 3.1 + - - +
46C VAL* 3.2 25.2 + - - +
196C ASP* 4.7 6.3 - - + -
197C VAL* 3.1 27.6 - - + +
199C GLY* 3.9 2.7 - - - +
220C ILE* 3.7 19.0 - - + +
351C GDP 2.7 26.3 + - - +
355C ALF 2.9 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 1.3 70.0 - - - +
44C THR* 1.3 60.6 + - - +
46C VAL* 3.2 12.8 + - - +
47C LYS* 3.0 42.9 + - - +
175C VAL 5.5 1.1 - - - -
177C THR* 3.6 14.6 + - - +
181C ILE* 5.3 1.4 - - - +
196C ASP* 3.8 9.7 + - - -
351C GDP 2.9 24.5 + - - -
352C CA 2.5 22.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLY 3.6 6.3 - - - -
42C LYS 3.2 0.4 - - - -
43C SER* 1.3 74.3 - - - +
45C ILE* 1.3 65.0 + - - +
47C LYS* 3.1 13.0 + - - +
48C GLN* 3.0 22.1 + - - +
171C LEU* 3.7 27.1 + - + +
173C SER 5.3 0.5 + - - -
322C ALA* 3.5 33.7 - - + +
323C THR* 3.9 10.3 - - + -
351C GDP 2.7 42.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.1 21.8 - - + -
41C GLY 3.3 13.7 + - - +
42C LYS 3.3 7.8 + - - +
44C THR* 1.3 77.2 - - - +
46C VAL* 1.3 63.0 + - - +
48C GLN* 3.1 7.2 + - - +
49C MET* 3.1 36.6 + - + +
194C MET* 4.9 4.9 - - + -
218C ILE* 5.7 0.7 - - + -
220C ILE* 3.8 16.8 - - + -
263C PHE* 4.3 24.7 - - + -
265C ASN* 5.4 2.0 - - - +
320C THR* 5.4 2.9 - - - +
322C ALA* 3.7 21.3 - - + -
328C VAL* 3.9 24.9 - - + -
332C PHE* 5.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.5 18.6 - - + -
42C LYS 3.2 14.7 + - - +
43C SER* 3.3 12.1 - - - +
44C THR 3.1 0.2 - - - -
45C ILE* 1.3 76.8 - - - +
47C LYS* 1.3 63.0 + - + +
49C MET* 3.1 19.7 + - - +
50C LYS* 3.3 10.9 + - - +
181C ILE* 5.2 5.2 - - + -
183C THR* 3.3 26.3 - - + +
194C MET* 4.5 6.5 - - + -
196C ASP* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER* 3.0 32.3 + - - +
44C THR* 3.4 11.5 + - - +
46C VAL* 1.3 75.4 - - + +
48C GLN* 1.3 63.0 + - - +
50C LYS* 3.1 9.1 + - - +
51C ILE* 3.0 25.2 + - - +
57C TYR* 3.2 22.6 + - + +
65C PHE* 4.0 17.5 - - - -
170C VAL* 3.6 28.5 - - + +
171C LEU* 3.8 22.9 + - + +
173C SER* 3.9 19.0 + - - -
175C VAL* 6.1 2.2 - - - +
351C GDP 5.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR 3.0 15.2 + - - +
45C ILE* 3.1 8.7 + - - +
47C LYS* 1.3 77.0 - - - +
49C MET* 1.3 54.7 + - + +
51C ILE* 3.2 9.4 + - - +
52C ILE* 2.7 40.7 + - + +
171C LEU* 3.5 12.0 - - + +
322C ALA 2.7 29.6 + - - +
323C THR 3.3 10.9 + - - -
324C ASP 3.4 1.2 - - - -
325C THR* 2.9 53.4 + - - +
328C VAL* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.1 17.4 + - + +
46C VAL* 3.1 9.5 + - - +
48C GLN* 1.3 78.9 - - - +
50C LYS* 1.3 55.8 + - - +
52C ILE* 4.7 3.1 - - + -
53C HIS* 2.6 50.3 + - + +
54C GLN* 3.3 5.4 + - - +
183C THR* 4.2 9.0 - - + -
185C PHE* 3.6 34.8 - - + -
194C MET* 3.8 23.6 - - + -
328C VAL* 3.8 27.6 - - + -
332C PHE* 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL 3.3 6.7 + - - +
47C LYS* 3.1 10.9 + - - +
49C MET* 1.3 75.7 - - - +
51C ILE* 1.3 63.4 + - - +
54C GLN* 3.2 41.2 + - + +
56C GLY 2.9 43.6 + - - +
57C TYR* 3.4 35.9 - - + +
61C GLU* 2.9 40.2 + - - -
183C THR* 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LYS 3.0 13.1 + - - +
48C GLN* 3.2 21.5 + - - +
50C LYS* 1.3 79.0 - - - +
52C ILE* 1.3 61.7 + - + +
54C GLN 4.1 6.2 - - - +
55C ASP 5.1 0.3 - - - -
56C GLY* 3.9 11.9 + - - -
57C TYR* 3.6 26.0 - - + -
167C GLU* 3.8 37.2 - - + +
171C LEU* 4.0 29.6 - - + -
325C THR* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLN* 2.7 27.7 + - + +
49C MET* 4.7 4.0 - - + -
51C ILE* 1.3 75.2 - - + +
53C HIS* 1.3 87.3 + - + +
54C GLN 3.6 2.5 - - - +
325C THR* 3.6 33.4 - - + +
328C VAL* 4.3 10.5 - - + -
329C LYS* 3.6 60.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C MET* 2.6 31.7 + - + +
52C ILE* 1.3 98.7 - - + +
54C GLN* 1.3 62.6 + - - +
185C PHE* 3.5 39.0 - + + +
186C SER 4.5 10.2 + - - +
187C PHE* 3.6 41.2 - + + -
329C LYS* 5.8 2.9 - - - +
332C PHE* 3.6 31.9 - + + -
----------------------------------------------------------
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