Contacts of the strand formed by residues 28 - 32 (chain K) in PDB entry 1VCB
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 GLU 28 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LYS* 2.8 14.2 + - - +
12J THR* 3.5 10.3 + - + +
13J THR* 2.9 28.6 + - - +
20K LYS* 2.7 46.4 + - + +
21K LEU 3.6 2.9 - - - -
22K ILE* 3.6 24.6 - - + +
26K GLY 3.7 11.5 - - - +
27K HIS* 1.3 75.1 - - - +
29K PHE* 1.3 62.1 + - - +
30K ILE* 3.8 4.8 - - + +
59K GLU* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J THR* 3.2 28.5 - - + +
15J PHE* 3.5 24.2 - + + -
93J PHE* 3.6 31.6 - + - -
19K VAL 3.4 2.8 - - - +
20K LYS* 3.5 0.8 - - - -
21K LEU* 3.0 44.8 + - + +
23K SER* 4.5 4.0 - - - -
27K HIS* 3.7 26.2 - - + -
28K GLU* 1.3 72.2 - - - +
30K ILE* 1.3 62.5 + - - +
31K VAL* 3.6 1.5 + - + +
67K SER* 4.1 13.0 - - - -
70K LEU* 3.8 26.7 - - + -
71K SER* 4.1 12.8 - - - -
74K CYS* 4.0 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J THR* 3.8 29.4 - - + -
13J THR 3.0 6.9 + - - +
14J ILE* 3.6 15.3 - - + +
15J PHE* 3.0 28.2 + - - +
34J ILE* 3.6 22.4 - - + -
35J LEU* 4.9 5.8 - - + -
18K TYR* 3.4 38.6 - - + -
19K VAL 3.2 7.6 - - - +
20K LYS* 4.3 25.1 - - + -
28K GLU* 3.8 8.5 - - + +
29K PHE* 1.3 76.5 - - - +
31K VAL* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE* 4.1 22.0 - - + +
18K TYR* 3.4 6.6 - - - -
19K VAL* 2.8 38.4 + - + +
21K LEU* 4.2 8.7 - - + -
29K PHE 4.2 7.0 - - - +
30K ILE* 1.3 79.3 - - - +
32K LYS* 1.3 75.0 + - - +
35K HIS* 3.7 21.8 - - + -
36K ALA* 4.4 4.3 - - + +
74K CYS* 3.6 31.6 - - + -
77K PHE* 4.7 10.1 - - + -
78K THR* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE 4.5 3.2 + - - +
16J THR* 4.1 15.7 + - - +
17J ASP* 2.7 32.0 + - - -
17K MET* 3.5 20.0 - - + +
18K TYR* 3.6 36.2 - - + -
31K VAL* 1.3 81.3 - - - +
33K ARG* 1.3 64.0 + - - +
34K GLU* 3.0 23.1 - - + +
35K HIS* 3.2 31.6 + - + +
36K ALA* 3.1 19.1 + - - +
----------------------------------------------------------
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