Contacts of the strand formed by residues 51 - 55 (chain L) in PDB entry 4ADV
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 VAL 51 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L VAL* 3.6 1.6 - - - +
37L TYR* 2.9 49.1 + - + +
39L THR* 3.5 23.3 - - + +
49L ARG 4.7 0.7 - - - +
50L LYS* 1.3 80.1 - - - +
52L CYS* 1.3 67.3 + - - +
63L THR* 3.6 8.5 - - - +
64L SER 3.6 8.5 - - - +
65L TYR* 4.2 7.6 - - + -
66L ILE* 3.5 9.5 - - - +
89L LEU* 4.4 11.4 - - + -
92L VAL* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L CYS* 3.6 25.4 - - - -
35L ARG 2.8 24.5 - - - +
36L VAL* 4.1 2.5 - - + -
37L TYR* 4.4 4.3 - - - +
51L VAL* 1.3 80.5 - - - +
53L ARG* 1.3 62.1 + - - +
54L VAL* 3.5 4.1 + - - +
63L THR* 3.1 5.7 + - - -
64L SER 2.8 38.9 + - - -
66L ILE* 3.4 25.6 - - + -
73L LEU* 4.2 0.2 - - - -
96L THR* 4.0 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L CYS* 3.2 5.0 - - - -
34L THR* 2.6 66.3 + - + +
35L ARG* 3.7 7.0 + - + +
37L TYR* 4.6 27.4 + - + -
52L CYS* 1.3 73.9 - - - +
54L VAL* 1.3 56.3 + - - +
55L ARG* 6.0 1.0 - - - +
61L GLU* 2.8 41.1 + - - +
62L VAL* 3.8 1.6 - - - -
63L THR* 3.7 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLY* 3.3 29.6 - - - -
32L VAL 3.8 3.4 - - - +
33L CYS* 4.1 4.5 - - - +
34L THR* 4.7 0.4 - - - -
52L CYS* 3.6 17.0 - - - +
53L ARG* 1.3 79.4 - - - +
55L ARG* 1.3 62.3 + - - +
56L LEU* 3.3 20.5 + - + +
61L GLU* 3.1 9.2 - - - +
62L VAL 2.6 41.6 + - - +
64L SER* 4.0 13.5 - - - -
79L ILE* 3.6 29.2 - - + -
81L ILE* 4.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLY* 4.1 2.3 - - - -
32L VAL* 3.8 37.6 - - + +
33L CYS 4.1 2.2 - - - +
34L THR* 4.6 13.9 + - - +
53L ARG* 4.4 1.0 + - - +
54L VAL* 1.3 75.0 - - - +
56L LEU* 1.3 70.4 + - - +
57L THR* 3.5 1.0 + - - -
59L GLY* 4.6 9.2 - - - +
60L PHE 4.6 0.2 - - - -
61L GLU* 3.8 30.7 + - + +
----------------------------------------------------------
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