Contacts of the strand formed by residues 44 - 52 (chain C) in PDB entry 3VG9
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 SER 44 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 5.1 0.2 - - - -
100B GLY* 4.9 10.5 - - - -
38C LYS 3.3 2.1 - - - +
39C GLN* 3.2 4.9 - - - -
40C SER* 3.0 39.1 + - - -
41C HIS* 4.2 10.7 + - - -
43C LYS* 1.3 82.8 - - - +
45C LEU* 1.3 60.3 + - - +
46C GLU* 4.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 5.6 0.4 - - + -
44B PRO* 4.4 19.5 - - + -
87B TYR* 3.8 32.7 - - + -
98B PHE* 3.5 59.0 + - + +
99B GLY 4.8 2.5 + - - +
37C VAL* 3.6 20.9 - - + -
38C LYS 3.4 0.2 - - - -
39C GLN* 3.6 34.1 - - + +
43C LYS 3.4 7.8 + - - +
44C SER* 1.3 75.9 + - - +
46C GLU* 1.3 66.4 + - - +
95C TYR* 4.9 2.7 - - + -
114C TRP* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 6.2 0.4 - - - +
98B PHE* 4.2 2.7 - - - +
37C VAL* 3.1 9.2 - - - +
38C LYS* 2.8 52.9 + - + +
40C SER* 4.3 8.3 + - - -
44C SER* 4.5 12.1 + - - +
45C LEU* 1.3 81.0 - - - +
47C TRP* 1.3 62.0 + - - +
48C ILE* 3.5 0.7 + - - +
61C ASN* 5.5 2.5 + - - +
63C LYS* 3.2 36.6 + - - +
64C PHE* 3.8 26.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLN* 5.0 0.4 - - - -
94B SER 3.7 15.5 - - - -
95B THR* 3.6 20.2 - - - -
96B TRP* 3.5 59.0 + + + +
97B ALA* 5.4 1.2 - - - +
98B PHE* 4.0 15.5 - - + -
35C ASN* 2.7 26.4 + - + -
36C TRP 3.8 6.5 - - - -
37C VAL* 4.6 1.3 - - + +
46C GLU* 1.3 71.5 - - - +
48C ILE* 1.3 57.4 + - - +
49C GLY* 3.4 25.6 + - - -
50C ASN* 3.7 12.6 - - - -
59C ARG* 3.7 22.7 - - - -
60C TYR 3.9 3.1 - - - -
61C ASN* 3.0 55.8 + - + +
64C PHE* 3.7 3.0 - - - -
111C PHE* 4.0 14.8 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
36C TRP* 2.8 23.9 + - + +
37C VAL 3.8 4.0 - - - -
38C LYS* 3.8 24.7 - - + +
47C TRP* 1.3 75.2 - - - +
49C GLY* 1.3 57.5 + - - +
60C TYR* 3.8 7.3 - - + +
61C ASN* 2.9 23.0 + - - +
64C PHE* 3.7 27.6 - - + +
68C ALA* 3.6 30.7 - - + -
70C LEU* 5.1 3.4 - - + -
81C ILE* 3.9 15.9 - - + -
83C LEU* 5.7 0.9 - - + -
94C TYR* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASN* 3.2 3.5 - - - -
36C TRP 3.0 24.1 + - - -
47C TRP* 3.4 21.6 + - - -
48C ILE* 1.3 81.7 - - - +
50C ASN* 1.3 62.7 + - - +
59C ARG 3.1 14.4 - - - -
60C TYR* 4.1 1.1 - - - -
70C LEU* 3.7 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TRP* 4.5 0.6 - - - -
33C ASN* 3.4 23.6 - - + +
34C MET 3.1 7.4 - - - +
35C ASN* 3.0 30.7 + - - +
47C TRP* 4.0 6.1 - - - -
49C GLY* 1.3 69.8 - - - +
51C ILE* 1.3 62.9 + - - +
57C SER 4.0 0.2 - - - +
58C THR* 3.2 5.2 - - - -
59C ARG* 2.9 69.8 + - - +
70C LEU* 3.6 6.6 - - - +
99C GLU* 3.3 21.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
33C ASN* 3.2 7.8 - - - -
34C MET* 2.9 50.5 + - + +
36C TRP* 5.4 2.5 - - - +
50C ASN* 1.3 76.8 - - - +
52C ASN* 1.3 68.6 + - - +
53C PRO* 3.6 1.6 - - - +
56C GLY* 3.8 18.2 - - - +
57C SER 3.2 5.6 - - - +
58C THR* 3.5 23.6 - - + -
70C LEU* 3.9 10.8 - - + +
71C THR* 3.6 28.5 - - - +
72C VAL* 3.5 33.9 - - + +
79C ALA* 4.8 3.1 - - + -
80C TYR 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.4 29.3 + - - +
33C ASN* 3.4 17.2 + - - +
51C ILE* 1.3 72.0 - - - +
53C PRO* 1.3 65.4 - - - +
54C TYR* 3.5 12.4 + - - +
55C TYR* 4.5 11.2 - - - -
56C GLY* 2.6 36.6 + - - -
57C SER* 2.7 31.8 + - - +
----------------------------------------------------------
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