Contacts of the strand formed by residues 40 - 44 (chain B) in PDB entry 2HDH
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 40 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 2.9 13.3 + - - +
17B HIS* 3.5 28.6 - - + +
18B VAL* 2.9 27.2 + - - +
38B GLY 4.2 0.7 + - - -
39B HIS* 1.3 72.6 - - - +
41B VAL* 1.3 65.7 + - - +
42B VAL* 5.5 1.6 - - + -
87B THR* 4.0 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.4 10.1 - - + +
20B VAL* 4.3 7.2 - - + -
31B ALA* 3.8 29.2 - - + +
34B ALA* 3.5 31.4 - - + -
35B ALA* 3.7 13.2 - - - +
39B HIS* 3.8 5.2 - - + +
40B THR* 1.3 80.6 - - - +
42B VAL* 1.3 73.4 + - - +
43B LEU 4.1 2.0 - - - +
87B THR 3.0 13.8 + - - +
88B ILE* 3.3 11.5 - - + -
89B ALA* 2.6 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 3.5 31.2 - - + +
18B VAL 3.0 8.8 + - - +
19B THR* 3.4 5.5 - - - +
20B VAL 2.9 24.8 + - - +
40B THR* 5.5 2.0 - - + -
41B VAL* 1.3 80.1 - - - +
43B LEU* 1.3 60.2 + - - +
44B VAL* 3.7 8.3 + - + -
89B ALA* 3.4 21.8 - - + +
90B THR 4.6 0.7 - - - +
91B SER* 4.3 9.4 - - - -
97B VAL* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.3 28.7 - - + +
22B GLY 3.6 23.1 - - - +
23B GLY* 3.9 7.4 - - - -
27B GLY 4.5 1.6 - - - +
28B ALA* 5.0 1.3 - - - -
31B ALA* 4.3 11.7 - - + -
41B VAL* 4.0 1.2 - - - +
42B VAL* 1.3 70.5 - - - +
44B VAL* 1.3 60.0 + - - +
51B LEU* 3.6 16.2 - - + +
54B SER* 4.1 25.8 - - - -
55B LYS* 5.0 3.6 - - - +
58B ILE* 4.4 19.5 - - + -
88B ILE* 4.4 11.4 - - + -
89B ALA 2.7 15.2 + - - +
90B THR* 3.2 12.1 - - + -
91B SER 3.1 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 4.2 22.9 - - + -
20B VAL 2.7 13.1 + - - +
21B ILE* 3.5 14.7 - - + +
22B GLY* 2.6 33.6 + - - -
23B GLY 4.1 0.2 + - - -
42B VAL* 4.2 7.4 - - + +
43B LEU* 1.3 77.7 - - - +
45B ASP* 1.3 69.1 + - - +
51B LEU* 4.0 0.7 - - - -
91B SER* 3.2 24.9 - - - +
92B THR 4.3 2.9 - - - +
94B ALA* 3.8 38.4 - - + +
97B VAL* 4.5 2.0 - - + -
750B NAD 5.1 2.7 - - + -
----------------------------------------------------------
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