Contacts of the strand formed by residues 47 - 53 (chain C) in PDB entry 1INL
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 ARG 47 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 3.9 2.8 + - - -
41C GLY 3.5 10.5 - - - +
42C GLN* 3.5 16.1 - - - +
46C GLN* 1.3 73.2 - - - +
48C ILE* 1.3 64.6 + - - +
49C ASP* 2.8 37.5 + - - +
62C LEU* 3.3 8.0 - - - +
63C ASP* 2.9 41.8 + - - +
11D LEU* 3.4 21.7 - - + +
12D GLN 2.8 37.0 + - - -
13D PRO* 4.0 4.0 - - - +
14D ARG* 3.9 20.8 - - - +
16D HIS* 3.6 8.3 - - - -
17D LEU* 3.6 15.6 - - - +
34D MET 4.6 0.6 + - - -
35D ASN* 2.8 38.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
39C TYR* 4.2 14.4 - - + -
40C SER* 3.3 4.3 - - - -
41C GLY 2.7 36.5 + - - +
46C GLN* 4.8 4.9 - - + +
47C ARG* 1.3 74.4 - - - +
49C ASP* 1.3 67.1 + - - +
50C ILE* 4.0 17.9 - - + -
60C PHE* 3.7 20.4 - - + -
61C ALA 3.6 3.6 - - - -
62C LEU* 3.6 19.1 - - + -
123C ASP* 4.9 1.8 - - - +
125C LEU* 3.8 45.3 - - + +
126C VAL* 3.9 20.2 - - + +
129C ALA* 4.5 5.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
37C VAL* 5.1 2.1 - - + +
39C TYR 3.5 2.5 - - - +
40C SER* 2.9 24.8 + - - -
47C ARG* 2.8 31.5 + - - +
48C ILE* 1.3 75.9 - - - +
50C ILE* 1.3 64.5 + - - +
51C PHE* 4.8 10.2 - - + -
59C VAL 3.7 0.9 - - - +
60C PHE* 3.6 0.5 - - - -
61C ALA* 2.8 46.6 + - + +
63C ASP 5.6 0.2 + - - -
64C GLY 5.3 2.4 + - - -
16D HIS* 2.5 37.6 + - + +
17D LEU* 3.7 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 3.7 3.1 - - - +
38C ILE* 2.8 34.1 + - + -
39C TYR* 2.8 27.4 + - + +
48C ILE* 4.0 15.9 - - + -
49C ASP* 1.3 79.6 - - - +
51C PHE* 1.3 62.4 + - - +
58C VAL* 3.5 28.7 - - + -
59C VAL 3.2 4.7 - - - +
60C PHE* 4.0 14.1 - - + -
129C ALA* 4.2 15.9 - - + -
133C TYR* 3.9 27.4 - - + -
134C LEU* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.5 48.2 - + + -
32C MET* 3.8 8.1 - - + -
33C LYS 4.2 9.4 - - - -
34C MET* 3.5 35.7 - - + -
36C ARG 3.3 15.7 - - - +
37C VAL* 4.0 8.7 - - + -
38C ILE* 4.0 7.6 - - - +
49C ASP* 4.8 9.2 - - + -
50C ILE* 1.3 78.8 - - - +
52C GLU* 1.3 66.1 + - - +
53C ASN* 4.4 1.8 - - + -
57C GLY 3.6 0.2 - - - +
58C VAL* 3.4 4.0 - - - +
59C VAL* 2.8 72.9 + - + +
61C ALA* 5.0 4.7 - - + -
17D LEU* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C MET* 3.5 5.2 - - - -
35C ASN* 2.8 63.8 + - + +
36C ARG* 2.9 36.6 + - + +
38C ILE* 4.2 10.8 - - + +
51C PHE* 1.3 74.9 - - - +
53C ASN* 1.3 65.0 + - - +
54C PRO* 5.7 0.7 - - + +
57C GLY* 3.5 10.5 - - - +
58C VAL* 4.6 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN* 3.0 24.7 + - - +
28B VAL* 3.8 3.7 - - - +
32C MET* 3.7 6.6 - - + +
33C LYS 2.8 26.8 + - - +
51C PHE* 4.1 3.6 + - + -
52C GLU* 1.3 79.7 - - - +
54C PRO* 1.3 68.5 - - - +
55C ASP* 2.9 13.0 + - - +
56C LEU* 2.9 43.0 + - + +
57C GLY* 2.8 38.8 + - - +
59C VAL* 4.2 9.4 - - + -
----------------------------------------------------------
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