Contacts of the helix formed by residues 47 - 58 (chain C) in PDB entry 5W5T
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 ILE 47 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 5.7 1.1 - - + -
36C LYS* 3.5 27.1 - - + +
37C PRO 3.4 7.1 + - - +
39C VAL* 2.9 33.6 + - + +
41C PHE* 4.5 7.4 - - + +
46C ARG* 1.3 72.4 - - - +
48C ILE* 1.3 64.4 + - - +
49C ASP 3.0 1.7 + - - -
50C PHE* 3.2 25.6 + - - +
51C ALA* 4.4 0.7 + - - +
135C GLY 4.4 0.3 - - - +
136C ASP* 3.5 36.6 - - - +
137C HIS 3.8 12.4 - - - +
138C ILE* 4.2 15.9 - - + -
271C VAL* 3.7 25.6 - - + -
277C TYR* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 4.5 9.9 - - + -
20C ALA* 3.9 21.8 - - + -
37C PRO* 2.9 22.9 + - + +
46C ARG* 4.5 2.5 - - + -
47C ILE* 1.3 75.0 - - - +
49C ASP* 1.3 73.8 + - - +
50C PHE 3.1 2.8 + - - -
51C ALA* 3.4 4.4 + - - +
52C LEU* 3.2 27.7 + - + +
65C VAL* 3.9 12.8 - - + -
74C LEU* 3.7 28.5 - - + -
77C HIS* 4.1 14.8 - - + +
78C LEU* 3.9 18.4 - - + -
135C GLY* 3.6 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 4.3 2.7 - - + -
46C ARG 2.9 28.8 + - - +
48C ILE* 1.3 76.6 - - - +
50C PHE* 1.3 57.3 + - + +
52C LEU* 4.5 4.5 - - - -
53C SER* 2.6 36.1 + - - -
77C HIS* 2.8 25.4 + - - -
82C TRP* 2.9 19.1 + - - -
300C ILE* 3.6 11.6 - - + +
301C TRP 3.3 19.1 - - - +
302C THR* 2.6 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.8 30.1 - + + -
45C ALA* 4.7 8.3 - - + -
46C ARG 3.9 11.7 - - - -
47C ILE* 3.2 17.9 + - - +
48C ILE 3.1 1.0 + - - -
49C ASP* 1.3 78.4 - - - +
51C ALA* 1.3 61.4 + - - +
53C SER* 3.3 0.9 + - - -
54C ASN* 2.8 38.0 + - - +
137C HIS 4.0 11.0 - - - +
138C ILE* 3.7 31.9 - - + -
139C TYR 3.8 20.6 - - - +
140C LYS* 4.8 5.2 - - + -
291C LEU* 4.5 14.4 - - + -
300C ILE* 3.8 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 4.7 9.0 - - + -
47C ILE 4.4 1.0 + - - -
48C ILE 3.4 8.0 + - - +
50C PHE* 1.3 77.3 - - - +
52C LEU* 1.3 64.3 + - - +
54C ASN* 3.3 5.7 + - - +
55C ALA* 3.0 22.9 + - - +
133C LEU* 4.0 16.7 - - + +
134C ALA 4.0 20.9 - - - +
135C GLY* 4.5 10.1 - - - -
137C HIS 4.9 2.7 + - - +
139C TYR* 4.4 8.7 - - + +
143C TYR* 3.9 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 3.9 17.5 - - + -
48C ILE* 3.2 26.8 + - + +
50C PHE 3.2 0.8 - - - -
51C ALA* 1.3 77.7 - - + +
53C SER* 1.3 58.2 + - - +
55C ALA* 3.2 6.5 + - + +
56C LEU* 3.0 27.9 + - - +
63C ILE* 3.7 32.4 - - + +
65C VAL* 4.0 7.4 - - + -
78C LEU* 3.6 24.5 - - + -
82C TRP* 3.5 48.8 - - + +
93C PHE* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASP 2.6 24.6 + - - -
50C PHE 3.9 1.8 - - - -
52C LEU* 1.3 73.2 - - - +
54C ASN* 1.3 60.3 + - - +
56C LEU* 3.7 4.7 - - - +
57C ASN* 2.8 38.2 + - - +
82C TRP* 3.5 9.6 - - - -
299C PRO 3.7 20.0 - - - -
300C ILE* 3.5 11.2 - - - -
301C TRP* 2.9 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PHE 2.8 19.6 + - - +
51C ALA 3.5 0.7 - - - +
53C SER* 1.3 75.3 - - - +
55C ALA* 1.3 64.7 + - - +
58C SER* 2.9 30.3 + - - -
139C TYR* 2.8 49.6 + - - +
140C LYS* 3.4 5.5 - - - +
141C MET 3.3 15.3 + - - +
143C TYR* 3.3 23.3 + - + +
298C TRP* 2.8 29.3 + - - +
300C ILE* 5.0 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 3.8 23.6 - - + -
18C VAL* 6.1 0.2 - - + -
51C ALA 3.0 13.1 + - - +
52C LEU* 3.2 8.9 + - + +
54C ASN* 1.3 77.5 - - - +
56C LEU* 1.3 60.9 + - - +
58C SER* 3.3 1.6 + - - -
59C GLY 3.3 3.3 + - - -
60C ILE* 2.9 33.7 + - + +
63C ILE* 3.8 20.6 - - + -
133C LEU* 4.8 1.3 - - + -
143C TYR* 3.5 14.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG* 3.8 32.8 - - + -
91A GLU* 5.6 5.4 - - - +
52C LEU 3.0 15.7 + - - +
53C SER* 3.7 6.1 - - - +
55C ALA* 1.3 78.8 - - - +
57C ASN* 1.3 64.6 + - - +
59C GLY* 3.0 18.9 + - - -
60C ILE 4.1 8.7 - - - +
61C ARG* 6.1 0.9 - - - -
63C ILE* 4.6 1.0 - - + +
82C TRP* 3.9 24.0 - - + -
84C PHE* 3.9 7.9 - - + -
85C PHE* 4.2 22.0 - - + -
301C TRP* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 4.0 13.5 + - - -
89A ARG* 5.2 5.7 - - - +
90A ASN* 5.6 0.3 + - - -
53C SER* 2.8 23.6 + - - +
56C LEU* 1.3 80.2 - - - +
58C SER* 1.3 59.6 + - - +
59C GLY* 3.2 1.4 + - - -
298C TRP* 3.3 62.4 - - + -
299C PRO* 2.9 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 5.9 0.2 - - - +
12A ARG* 3.4 22.7 + - - +
11C ALA* 3.3 19.1 - - - +
54C ASN 2.9 21.7 + - - -
55C ALA* 3.7 4.9 - - - -
56C LEU 3.2 0.2 - - - -
57C ASN* 1.3 76.7 - - - +
59C GLY* 1.3 57.5 + - - +
60C ILE* 3.4 4.7 - - - -
141C MET 3.6 1.0 + - - -
142C ASP* 3.3 12.4 - - - -
143C TYR* 2.8 41.9 + - - -
144C GLU* 4.4 2.6 - - - +
298C TRP* 3.6 1.6 - - - -
----------------------------------------------------------
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