Contacts of the strand formed by residues 18 - 23 (chain B) in PDB entry 2VTX
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 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 1.3 78.6 - - - +
19B TRP* 1.3 66.3 + - - +
48B ARG* 5.4 1.6 - - + -
114B SER* 5.1 2.0 - - - +
115B GLY 3.5 15.7 - - - +
116B GLN* 4.0 15.8 - - + +
117B HIS* 5.5 0.7 - - - -
65C ILE* 3.9 38.4 - - + +
67C ASP* 3.9 27.7 + - - +
74C LYS* 5.2 6.9 - - + +
76C VAL* 3.9 30.1 - - + +
78C ILE* 4.9 6.1 - - + -
94C ILE* 4.7 8.7 - - + -
96C LEU* 4.3 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU 3.8 0.4 + - - -
18B ILE* 1.3 74.6 - - - +
20B GLY* 1.3 70.0 + - - +
21B CYS* 3.7 28.9 - - + -
30B PHE* 4.0 19.5 - + - -
32B PHE* 3.3 37.7 - + + -
45B LEU* 3.7 30.3 - - + -
47B LEU* 4.5 1.8 - - + -
102B PHE* 3.6 23.8 - + - -
113B ILE* 3.8 25.8 - - + -
114B SER* 3.3 3.7 - - - -
115B GLY* 2.7 46.5 + - - +
117B HIS* 4.2 18.8 - - + +
76C VAL* 3.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 1.3 91.4 + - - +
21B CYS* 1.3 60.8 + - - +
30B PHE* 5.1 1.6 - - - -
113B ILE 3.1 12.8 - - - -
75C SER 5.8 0.4 - - - -
76C VAL* 3.7 22.1 - - - +
77C PRO* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 3.7 24.1 - - + -
20B GLY* 1.3 73.1 - - - +
22B GLU* 1.3 61.0 + - - +
23B LEU* 4.1 9.0 - - - -
30B PHE* 3.8 37.7 - - + -
102B PHE* 4.5 1.8 - - - -
111B LEU 3.8 0.2 - - - +
112B TYR* 3.4 6.9 - - - +
113B ILE* 3.0 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B CYS* 1.3 75.7 - - - +
23B LEU* 1.3 73.8 + - - +
24B ASN* 2.8 28.9 + - - +
27B ASN* 4.5 6.2 - - - +
30B PHE* 4.7 9.3 - - - +
110B PRO* 3.7 21.7 - - + +
111B LEU 3.4 4.5 - - - +
112B TYR* 3.5 34.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B CYS* 4.1 6.7 - - - -
22B GLU* 1.3 78.2 - - - +
24B ASN* 1.3 64.3 + - - +
27B ASN 3.7 6.7 - - - +
28B LYS 4.1 9.4 - - - +
30B PHE* 3.6 32.8 - - + +
63B VAL* 4.0 18.6 - - + -
102B PHE* 4.2 7.6 - - + +
103B ARG 4.0 2.7 - - - -
104B LEU* 4.0 33.4 - - + +
109B GLY* 4.2 0.5 - - - -
110B PRO* 3.6 1.0 - - - +
111B LEU* 2.8 45.9 + - + +
113B ILE* 3.8 24.7 - - + -
----------------------------------------------------------
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