Contacts of the strand formed by residues 50 - 54 (chain M) in PDB entry 6VEN
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 LEU 50 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M ALA* 4.8 4.0 - - + -
43M LEU 3.1 29.8 - - - +
44M GLY* 4.1 6.7 - - - -
48M GLY 3.4 4.1 + - - +
49M ALA* 1.3 73.8 - - - +
51M VAL* 1.3 64.0 + - - +
52M ILE* 5.5 1.6 - - + -
63M VAL* 3.5 15.2 - - - +
64M PRO* 3.2 47.0 + - + +
71M HIS* 5.4 2.7 - - + -
75M ILE* 4.0 14.1 - - + -
78M ILE* 4.2 14.1 - - + -
87M LEU* 4.4 11.4 - - + -
89M THR* 3.9 30.3 - - + +
99M TRP* 4.6 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M ASN* 4.8 2.5 - - - +
42M ALA* 3.5 3.8 - - - -
43M LEU* 2.9 35.0 + - + +
45M CYS* 3.9 24.5 - - - -
49M ALA* 4.8 3.1 - - + -
50M LEU* 1.3 80.7 - - - +
52M ILE* 1.3 72.2 + - - +
53M TYR* 3.4 35.2 - - + +
60M PRO* 3.7 19.1 - - + -
62M CYS 3.8 2.9 - - - +
63M VAL* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M TYR* 3.7 23.1 - - + -
41M LEU 3.4 5.6 - - - +
42M ALA* 4.4 9.4 - - + -
50M LEU* 5.5 2.2 - - + -
51M VAL* 1.3 79.4 - - - +
53M TYR* 1.3 63.7 + - - +
61M ILE* 3.0 25.1 + - + +
62M CYS* 2.9 23.4 + - + +
64M PRO* 4.1 17.0 - - + -
80M TRP* 4.5 4.7 - - + -
87M LEU* 4.3 16.6 - - + -
101M LEU* 3.8 29.4 - - + -
413M ILE* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M ILE* 3.3 39.9 - - + -
24M GLU 4.3 3.9 + - - -
25M ASN* 3.2 32.3 + - - +
26M PRO* 4.5 4.9 - - - +
40M TYR* 3.4 7.8 - - - +
41M LEU* 2.9 40.1 + - + +
43M LEU* 3.5 23.3 - - + -
51M VAL* 3.4 28.0 - - + +
52M ILE* 1.3 77.4 - - - +
54M ASP* 1.3 64.7 + - - +
55M MET* 5.3 1.3 - - - -
58M PHE* 4.0 15.0 - - - -
59M ARG 4.1 6.3 - - - +
60M PRO* 3.4 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L LYS* 3.2 19.8 + - - -
109L ASN* 2.8 34.1 + - - +
39M ASP 3.0 10.5 - - - +
40M TYR* 3.2 16.7 - - + -
53M TYR* 1.3 75.6 - - - +
55M MET* 1.3 73.4 + - - +
56M ASP* 3.2 10.2 + - - +
57M THR* 3.2 7.1 + - - +
58M PHE* 2.7 35.5 + - - -
59M ARG 3.7 6.1 + - - -
61M ILE* 3.6 21.5 - - + +
----------------------------------------------------------
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