Contacts of the strand formed by residues 31 - 37 (chain A) in PDB entry 5VLR
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 TYR 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 2.7 38.7 + - + -
24A PHE 3.4 14.4 - - - -
25A LEU* 3.6 15.0 - - + -
29A GLY 4.6 0.9 - - - +
30A VAL* 1.3 76.5 - - - +
32A LEU* 1.3 69.9 + - - +
33A ASN* 3.5 21.0 + - + +
56A GLU* 4.8 1.4 - - - +
494B PHE* 4.7 1.8 - + - -
497B GLN* 4.8 0.2 - - - +
527B ASN* 2.8 35.9 + - - +
530B LYS* 3.5 32.9 - - + +
531B LEU* 3.5 40.8 - - + -
534B ARG* 3.4 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 3.7 0.7 - - - -
24A PHE* 2.8 49.4 + - + +
26A LEU* 3.6 30.7 - - + +
30A VAL* 4.5 0.2 - - + -
31A TYR* 1.3 75.2 - - - +
33A ASN* 1.3 61.1 + - - +
34A PHE* 3.7 20.9 - - + -
49A LEU* 4.1 5.8 - - + -
52A ARG* 3.6 35.2 - - + +
53A ALA* 3.9 14.8 - - + +
56A GLU* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 3.1 27.8 - - - +
22A VAL 3.4 6.8 - - - +
23A ASP* 3.4 13.9 - - - +
31A TYR* 3.5 24.3 + - + +
32A LEU* 1.3 78.4 - - - +
34A PHE* 1.4 61.7 + - - +
534B ARG* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.4 4.7 - - - -
22A VAL* 3.2 28.9 + - - +
24A PHE* 3.4 30.9 - + - -
32A LEU* 3.7 31.6 - - + -
33A ASN* 1.4 75.6 - - - +
35A PRO* 1.4 76.2 - - + +
36A VAL* 3.5 27.6 + - + +
45A ILE 4.6 0.7 - - - -
48A LEU* 3.9 17.9 - - + -
49A LEU* 3.5 31.9 - - + -
52A ARG* 3.6 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 4.5 14.1 - - - +
20A VAL 3.7 8.7 - - - +
21A VAL* 4.2 19.7 - - + -
34A PHE* 1.4 92.9 - - + +
36A VAL* 1.3 64.6 + - - +
52A ARG* 3.7 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.1 7.0 + - - -
20A VAL* 2.8 38.1 + - + +
22A VAL* 3.7 24.2 - - + -
24A PHE* 4.7 4.7 - - + -
34A PHE* 3.5 29.4 - - + +
35A PRO* 1.3 79.5 - - - +
37A SER* 1.3 66.5 + - - +
40A ALA* 5.0 1.8 - - + -
45A ILE* 4.0 29.4 - - + -
48A LEU* 4.9 10.1 - - + -
89A LEU* 5.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.9 17.6 + - - +
19A SER* 3.6 13.5 + - - +
20A VAL* 4.7 0.2 - - - -
36A VAL* 1.3 80.9 - - - +
38A ARG* 1.4 61.9 + - - +
39A ASN* 3.6 14.4 + - - +
40A ALA* 3.1 34.2 + - - +
89A LEU* 4.6 2.3 - - - +
----------------------------------------------------------
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