Contacts of the strand formed by residues 50 - 53 (chain A) in PDB entry 2IHU
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 ASP 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.0 10.5 + - - +
29A LYS* 3.2 35.7 + - + +
30A VAL* 2.8 25.4 + - - -
43A PHE* 5.1 1.8 - - - -
48A GLY* 4.9 4.3 + - - -
49A ILE* 1.3 82.5 + - - +
51A PHE* 1.3 64.2 + - - +
52A VAL* 3.8 1.5 + - + +
510B PRO* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.3 15.5 - - + +
32A GLY* 3.4 37.9 - - - -
33A VAL 3.8 1.1 - - - -
34A VAL* 3.3 29.8 - - + -
43A PHE* 3.7 55.2 + + + +
49A ILE 4.4 0.4 + - - -
50A ASP* 1.3 76.9 - - - +
52A VAL* 1.3 62.9 + - - +
53A LEU* 3.8 17.6 + - + -
78A TRP* 3.9 16.2 - - + -
508B HIS* 5.3 1.4 + - - +
510B PRO* 3.7 42.5 - - + +
511B ALA* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 3.9 34.8 - - + +
30A VAL 2.8 10.5 + - - +
31A PHE* 3.4 35.6 - - + -
32A GLY 2.9 25.6 + - - -
50A ASP* 4.8 1.1 - - + -
51A PHE* 1.3 77.9 - - - +
53A LEU* 1.3 64.8 + - - +
54A THR* 3.7 6.3 + - + +
446A ILE* 5.7 0.7 - - + -
450A MET* 4.7 4.0 - - + -
475A THR* 5.1 0.4 - - + -
479A LEU* 3.8 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY 3.4 15.7 - - - +
33A VAL* 4.2 10.5 - - - -
34A VAL 4.7 0.2 - - - +
51A PHE* 3.8 7.3 - - + -
52A VAL* 1.3 70.8 - - - +
54A THR* 1.3 72.2 + - - +
475A THR* 3.7 7.3 - - - +
478A ARG* 2.8 36.6 + - - +
493B ASN* 4.1 15.3 - - - +
510B PRO 3.4 16.9 + - - +
511B ALA 3.7 15.0 - - - +
512B VAL 3.7 21.5 - - - +
513B LYS 3.6 20.9 - - - +
514B PHE* 3.4 27.1 - - + -
----------------------------------------------------------
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