Contacts of the strand formed by residues 45 - 51 (chain C) in PDB entry 3VA2
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 GLN 45 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.6 3.6 - - - +
41C THR* 2.8 51.5 + - - +
42C GLY* 3.2 13.3 + - - +
43C LEU 3.7 1.1 - - - +
44C ALA* 1.3 78.9 - - - +
46C VAL* 1.3 61.9 + - - +
85C LYS* 3.3 44.0 + - + +
86C CYS 3.7 4.0 - - - -
87C VAL* 4.1 10.8 - - + +
88C THR 4.0 0.4 + - - -
90C LEU* 4.3 3.2 - - - +
174C ARG* 3.6 38.4 + - - +
176C GLY 4.7 4.5 + - - +
177C SER* 6.2 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
38C ILE* 4.0 6.7 - - + -
39C LYS 3.3 11.4 - - - +
40C VAL* 4.3 5.2 - - - -
41C THR* 4.3 3.8 - - - -
45C GLN* 1.3 79.0 - - - +
47C LEU* 1.3 59.6 + - - +
48C LEU* 4.1 7.9 - - + -
85C LYS* 3.5 6.6 - - - +
86C CYS* 2.9 57.8 + - + +
88C THR* 4.3 3.1 - - + -
90C LEU* 3.6 29.6 - - + -
94C PHE* 4.1 21.3 - - + -
118C LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C THR* 3.8 1.4 + - - +
38C ILE* 3.6 2.9 - - - -
39C LYS* 2.9 47.9 + - + +
41C THR* 3.6 20.1 - - + +
46C VAL* 1.3 72.6 - - - +
48C LEU* 1.3 73.1 + - - +
49C GLN* 3.6 31.7 + - + +
83C GLU* 4.2 17.3 - - + +
84C SER* 3.6 28.5 - - - +
85C LYS* 3.8 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 4.0 11.0 - - + -
37C THR 3.5 2.2 - - - -
38C ILE* 3.6 36.3 - - + -
46C VAL* 4.1 5.6 - - + -
47C LEU* 1.3 74.2 - - - +
49C GLN* 1.3 59.9 + - - +
50C TRP* 3.8 13.7 - - + -
67C VAL* 3.6 33.4 - - + -
69C ILE* 5.1 4.0 - - + -
77C TYR* 4.3 7.6 - - - +
83C GLU* 3.2 6.9 - - - +
84C SER 2.7 43.2 + - - +
86C CYS* 4.8 7.2 - - + -
94C PHE* 3.9 15.7 - - + -
96C ALA* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASN 3.3 2.0 - - - +
36C PHE* 3.1 3.8 - - - -
37C THR* 2.5 60.5 + - + +
39C LYS* 3.6 23.6 - - - +
47C LEU* 3.6 23.7 + - + +
48C LEU* 1.3 78.8 - - - +
50C TRP* 1.3 61.9 + - - +
51C LYS* 4.7 19.4 - - - +
82C THR 3.8 3.1 - - - -
83C GLU* 3.5 24.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PRO* 3.9 24.9 - - + -
34C VAL 3.8 6.7 - - - +
35C ASN 3.6 8.3 - - - -
36C PHE* 3.9 26.9 - + + -
48C LEU* 3.8 28.5 - - + -
49C GLN* 1.3 81.2 - - - +
51C LYS* 1.3 76.7 + - - +
65C TYR* 3.4 28.0 - + + -
67C VAL* 3.8 25.1 - - + -
79C THR* 3.5 15.7 - - + -
81C ILE 3.3 18.4 - - - -
82C THR* 2.9 52.5 + - + +
83C GLU* 3.9 13.7 - - - -
84C SER* 4.1 2.7 - - - -
98C VAL* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PRO* 3.6 2.9 - - - +
34C VAL* 2.9 35.3 + - + +
35C ASN* 4.4 26.7 + - + +
37C THR* 5.9 2.2 - - - +
49C GLN* 4.7 23.8 - - - +
50C TRP* 1.3 95.6 + - - +
52C PRO* 1.3 78.6 - - + +
53C ASN 3.4 0.2 + - - -
82C THR* 5.5 3.1 - - - +
----------------------------------------------------------
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