Contacts of the strand formed by residues 33 - 38 (chain C) in PDB entry 2VL3
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 33 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 3.8 25.1 + - + +
147A THR* 4.7 6.9 + - - +
32C LYS* 1.3 75.8 - - - +
34C GLY* 1.3 61.3 + - - +
65C LYS* 2.7 29.8 + - - +
66C GLY* 3.6 21.7 + - - +
67C VAL* 3.5 12.2 - - + +
68C GLN* 2.8 30.5 + - - +
69C VAL 3.7 2.6 + - - -
131C VAL* 4.4 10.1 - - + -
132C VAL 3.3 4.5 - - - +
133C GLN* 3.9 24.9 - - + +
161C LEU* 4.2 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.8 9.9 - - - -
32C LYS 4.0 0.4 - - - -
33C LYS* 1.3 76.8 - - - +
35C VAL* 1.3 63.1 + - - +
67C VAL* 3.9 2.9 - - - -
69C VAL* 3.2 23.8 - - - -
131C VAL* 3.6 6.8 - - - +
132C VAL 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.9 4.5 - - - -
34C GLY* 1.3 77.9 - - - +
36C LEU* 1.3 68.6 + - - +
37C PHE* 4.7 2.0 - - + +
55C PHE* 3.9 29.8 - - + -
62C LEU* 4.7 8.7 - - + -
67C VAL* 3.8 27.6 - - + -
69C VAL 2.9 7.6 + - - +
70C VAL* 3.5 8.5 - - + -
71C ALA 2.9 26.0 + - - +
129C SER* 5.1 0.4 - - - -
130C MET 3.4 12.1 - - - +
131C VAL* 4.9 1.1 - - + -
157C ILE* 4.3 21.3 - - + -
161C LEU* 4.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 4.5 7.0 - - + -
25C LEU* 4.4 15.9 - - + -
29C PHE* 3.6 22.8 - - + -
34C GLY 4.2 0.2 - - - -
35C VAL* 1.3 77.2 - - - +
37C PHE* 1.3 68.1 + - - +
71C ALA* 3.5 22.9 - - + +
73C LEU* 4.4 15.7 - - + +
97C LEU* 4.9 1.1 - - + -
104C PHE* 3.8 33.2 - - + -
128C PHE* 3.7 9.2 - - + -
129C SER* 3.3 0.9 - - - -
130C MET* 2.8 58.9 + - + +
132C VAL* 4.4 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 4.8 1.1 - - + -
36C LEU* 1.3 76.2 - - - +
38C GLY* 1.3 59.9 + - - +
39C VAL* 3.9 16.6 - - + -
50C THR 4.5 2.2 - - - -
51C HIS 4.3 7.2 - - - -
52C LEU* 4.5 7.0 - - - -
55C PHE* 3.2 73.1 - + + -
70C VAL* 4.3 4.7 - - + -
71C ALA 3.0 29.7 + - - +
72C CYS* 3.1 42.6 - - + -
73C LEU* 2.9 27.4 + - - +
94C VAL* 4.1 8.5 - - + -
128C PHE* 3.0 23.8 - - - +
129C SER* 4.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 1.3 75.7 - - - +
39C VAL* 1.3 70.6 + - - +
50C THR 4.9 0.9 - - - +
73C LEU 3.4 10.1 - - - -
125C LEU* 4.7 1.8 - - - -
126C LYS 3.9 6.3 - - - -
127C ARG* 3.4 6.8 - - - +
128C PHE* 2.9 48.5 + - - +
----------------------------------------------------------
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