Contacts of the strand formed by residues 33 - 38 (chain L) in PDB entry 3GBN
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 33 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L CYS* 5.1 2.0 - - - -
28L ILE* 4.0 30.5 - - + -
31L ASP 4.2 3.6 - - - +
32L TYR* 1.3 79.4 - - - +
34L SER* 1.3 73.8 + - - +
35L TRP* 3.9 13.0 - - - +
48L ILE* 4.3 1.7 - - - +
49L TYR* 4.0 1.2 - - - -
50L ASP 3.6 3.7 + - - -
51L ASN* 2.9 43.1 + - - +
66L LYS* 4.3 2.0 - - + -
71L ALA* 3.7 27.4 - - + -
88L CYS* 4.2 11.0 - - + -
89L ALA 3.4 7.0 - - - +
90L THR* 4.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H GLU* 2.6 49.3 + - - -
32L TYR 4.3 0.2 + - - -
33L VAL* 1.3 77.1 - - - +
35L TRP* 1.3 65.6 + - - +
36L TYR* 4.0 12.6 - - - -
46L LEU* 4.3 1.6 - - - -
48L ILE 3.1 8.3 - - - -
49L TYR* 3.3 14.0 - - - +
50L ASP 4.1 0.9 + - - -
88L CYS* 3.3 4.3 - - - -
89L ALA 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 35 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 3.8 15.0 - - - -
21L ILE* 3.6 25.6 - - + -
22L SER 4.4 0.2 - - - -
23L CYS* 3.7 29.8 - - + -
33L VAL* 3.9 12.4 - - + +
34L SER* 1.3 76.1 - - - +
36L TYR* 1.3 67.3 + - - +
46L LEU* 3.7 2.1 - - - +
47L LEU* 2.8 29.8 + - + -
48L ILE* 2.8 50.2 + - + +
51L ASN 4.9 2.2 + - - -
64L GLY* 4.8 2.7 - - - -
65L SER 5.0 0.6 + - - -
71L ALA* 4.0 3.6 - - + +
72L THR 3.7 19.7 + - - -
73L LEU* 3.5 43.7 - - + -
86L TYR* 4.9 1.1 - - + -
87L TYR 3.4 23.3 - - - -
88L CYS* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H MET* 2.6 73.8 + + - +
103H TRP* 3.8 21.8 - + - -
34L SER* 4.0 9.0 - - - -
35L TRP* 1.3 77.8 - - - +
37L GLN* 1.3 60.2 + - - +
44L PRO* 4.2 16.2 - - + -
45L LYS 3.2 7.0 - - - +
46L LEU* 3.7 30.0 - - + +
47L LEU* 4.1 4.0 - - - -
85L ASN 3.8 0.2 - - - +
86L TYR* 3.2 8.1 - - - +
87L TYR* 2.7 50.9 + - + +
89L ALA* 3.8 18.2 - - + -
98L PHE* 4.1 17.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L TYR* 1.3 73.7 - - - +
38L GLN* 1.3 63.7 + - - +
39L LEU* 3.7 28.3 + - + +
43L ALA 4.1 0.9 - - - +
44L PRO* 4.4 0.7 - - - -
45L LYS* 2.8 57.1 + - + +
47L LEU* 3.7 29.7 - - + +
62L PHE* 4.2 10.6 - - - -
81L GLY 4.5 1.4 + - - -
82L ASP* 4.2 12.5 + - - +
84L ALA* 4.0 4.4 - - + +
85L ASN 3.5 3.8 - - - -
86L TYR* 2.7 35.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 2.8 41.4 + - - -
91H TYR* 3.5 10.1 + - - -
37L GLN* 1.3 75.8 - - - +
39L LEU* 1.3 69.5 + - - +
40L PRO* 4.6 0.2 - - - +
42L THR 2.8 29.9 + - - +
43L ALA 4.7 1.6 - - - -
44L PRO* 3.7 19.8 - - + +
84L ALA* 3.6 2.3 - - - +
85L ASN* 2.8 46.0 + - + +
87L TYR* 3.4 20.2 + - + -
----------------------------------------------------------
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