Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 5EEZ
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 PHE 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.4 36.3 - - + -
23A GLY 3.4 5.2 - - - -
24A LEU* 3.8 21.8 - - + -
31A ARG* 1.3 84.7 - - - +
33A HIS* 1.3 57.8 + - - +
34A HIS 4.8 2.9 - - - +
35A SER* 6.4 0.4 - - - -
56A LYS* 4.2 17.7 - - + -
58A ARG* 4.2 18.6 - - - -
36B GLU* 3.3 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.0 30.4 + - - -
24A LEU 3.9 0.2 - - - -
25A THR* 3.8 25.6 - - + -
31A ARG* 3.6 2.2 + - + +
32A PHE* 1.3 72.7 - - - +
34A HIS* 1.3 78.6 + - + +
51A HIS* 3.7 22.4 + - + -
52A THR* 2.8 29.2 + - - -
28K ALA* 4.5 16.1 + - - +
30K THR* 4.3 1.4 + - - -
101K TRP* 4.0 24.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.4 5.8 - - - +
23A GLY 2.9 26.4 + - - -
32A PHE* 3.7 2.3 - - - +
33A HIS* 1.3 101.7 + - + +
35A SER* 1.3 86.2 + - - +
36A GLU* 2.6 33.8 + - + -
24K LEU* 5.7 0.4 - - + -
30K THR* 3.5 44.6 + - + +
101K TRP* 3.9 15.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 3.6 31.4 + - - +
21A VAL 3.5 4.5 - - - -
22A ILE* 3.7 13.3 - - - +
32A PHE* 6.4 0.4 - - - -
34A HIS* 1.3 89.0 + - - +
36A GLU* 1.3 58.5 + - - +
37A LYS* 3.8 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL 3.5 0.5 - - - +
20A ASN* 3.5 4.2 - - - -
21A VAL* 2.8 42.3 + - + +
34A HIS* 2.6 39.8 + - + +
35A SER* 1.3 71.4 - - - +
37A LYS* 1.3 62.9 + - - +
38A LEU* 3.7 18.4 + - + +
44A LEU* 4.2 24.7 - - + -
24K LEU* 4.0 16.9 - - + +
30K THR* 4.5 0.5 - - - +
32K PHE* 3.5 18.8 - - - -
56K LYS* 3.5 20.6 + - + +
101K TRP* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY* 4.2 17.2 - - - -
19A VAL 3.3 9.9 - - - +
20A ASN* 4.1 13.9 - - - +
35A SER 3.8 3.6 + - - +
36A GLU* 1.3 73.2 - - - +
38A LEU* 1.3 60.8 + - - +
39A ASP* 3.6 28.2 + - - +
42A GLU* 4.1 0.9 - - - +
56K LYS* 3.4 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.8 32.1 - - + +
14A ALA* 3.7 16.6 - - + +
18A GLY 3.3 3.6 + - - -
19A VAL* 2.8 41.2 + - + +
21A VAL* 3.9 22.2 - - + -
36A GLU* 4.2 10.3 - - + +
37A LYS* 1.3 79.0 - - - +
39A ASP* 1.3 66.3 + - - +
42A GLU* 3.4 16.4 - - + +
44A LEU* 3.8 28.0 - - + +
56K LYS* 4.1 21.5 - - + -
----------------------------------------------------------
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