Contacts of the strand formed by residues 15 - 22 (chain D) in PDB entry 3CHB
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 THR 15 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D CYS* 2.8 31.6 + - - +
12D TYR* 3.3 28.1 + - + -
13D HIS 3.7 1.1 - - - +
14D ASN* 1.3 80.3 - - - +
16D GLN* 1.3 65.8 + - - +
86D CYS* 4.4 5.8 - - - -
87D VAL 3.0 13.7 - - - +
88D TRP* 3.5 31.4 - - + +
89D ASN* 3.9 6.0 + - - -
97D ALA* 5.5 0.2 - - + -
109D UNX 3.0 12.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D CYS* 3.8 6.7 - - - -
15D THR* 1.3 77.5 - - - +
17D ILE* 1.3 64.8 + - - +
18D HIS* 3.5 36.4 + - + -
85D LEU 3.7 0.9 - - - +
86D CYS* 3.6 0.5 - - - -
87D VAL* 2.9 33.9 + - + +
89D ASN* 2.9 31.2 + - - +
94D ARG* 5.5 0.5 + - - -
109D UNX 3.9 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 3.9 23.1 - - + +
6D THR* 4.1 24.0 - - + +
9D CYS* 3.8 31.2 - - + -
16D GLN* 1.3 80.2 + - - +
18D HIS* 1.3 79.9 + - - +
19D THR* 4.1 6.4 + - - +
84D LYS* 3.9 23.3 - - + +
85D LEU 3.4 11.0 - - - +
86D CYS* 4.0 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 3.5 36.8 + - + +
17D ILE* 1.3 77.2 - - - +
19D THR* 1.3 62.3 + - - +
20D LEU* 3.5 16.6 - - + +
48D PHE* 3.9 25.4 - + + -
84D LYS* 3.2 4.9 - - - +
85D LEU* 2.9 35.0 + - + +
87D VAL* 3.8 23.5 - - + +
89D ASN* 5.0 1.1 - - - -
94D ARG* 5.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 4.1 4.8 + - - +
18D HIS* 1.3 71.8 - - - +
20D LEU* 1.3 65.4 + - - +
21D ASN* 3.4 29.6 - - + +
83D GLU* 3.6 8.1 - - + +
84D LYS* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D HIS* 3.5 25.8 - - + +
19D THR* 1.3 77.8 - - - +
21D ASN* 1.4 69.5 + - - +
22D ASP* 3.2 8.4 + - + +
42D PHE* 3.7 50.3 - - + -
44D ASN* 4.7 13.7 - - - +
46D ALA* 4.8 3.4 - - + -
48D PHE* 4.5 8.5 - - + -
82D VAL* 3.7 12.3 - - + +
83D GLU 2.8 10.7 + - - +
85D LEU* 4.0 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D THR* 3.4 24.3 - - - +
20D LEU* 1.4 75.6 - - - +
22D ASP* 1.3 57.8 + - - +
81D LYS* 3.6 29.8 - - + +
82D VAL 2.8 14.3 + - - -
83D GLU* 3.1 28.4 + - - +
102D ALA* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.2 10.5 - - + +
21D ASN* 1.3 78.5 - - - +
23D LYS* 1.3 94.9 + - - +
42D PHE* 3.6 12.5 - - + +
43D LYS* 3.1 45.1 + - - +
81D LYS* 3.5 7.7 - - - +
82D VAL* 2.9 30.8 + - - +
----------------------------------------------------------
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