Contacts of the strand formed by residues 50 - 56 (chain D) in PDB entry 5SWW
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 GLN 50 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL 3.8 2.9 - - - -
38D GLU* 4.5 27.2 + - + +
39D ARG 5.2 3.6 + - - +
48D MET* 3.3 34.5 - - - +
49D ASP* 1.3 81.4 + - - +
51D HIS* 1.3 65.4 + - - +
52D ARG* 4.2 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 3.8 29.6 - + - +
36D GLU* 3.2 6.4 - - - +
37D VAL* 3.0 46.1 + - + +
38D GLU* 5.7 0.2 - - - +
49D ASP 5.6 0.2 - - - -
50D GLN* 1.3 77.8 - - - +
52D ARG* 1.3 76.8 + - - +
82D LEU* 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 3.5 10.7 + - - -
36D GLU* 2.8 38.9 + - + -
38D GLU* 4.6 8.2 + - - -
50D GLN* 4.2 26.8 - - - +
51D HIS* 1.3 91.4 + - - +
53D GLY* 1.3 59.8 + - - +
160D HIS* 4.5 11.5 - - - -
164D THR* 4.1 30.1 - - - +
165D PHE* 3.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D HIS 5.7 2.9 - - - -
34D CYS* 3.6 0.2 - - - -
35D TYR* 3.1 44.0 + - - -
52D ARG* 1.3 77.9 - - - +
54D PHE* 1.3 69.9 + - - +
165D PHE* 3.3 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D HIS* 3.4 36.8 - + - -
12D LEU* 3.3 36.1 - - - -
13D MET* 3.7 35.4 - - + -
14D ASP 5.2 0.4 - - - -
17D ILE* 6.3 0.2 - - + -
32D TYR* 4.5 15.7 - + + -
33D LEU 3.1 14.6 - - - +
34D CYS* 4.2 15.3 - - - -
35D TYR* 3.4 9.4 + - - -
53D GLY* 1.3 79.8 - - - +
55D LEU* 1.3 68.7 + - - +
56D HIS* 6.4 0.7 - + - -
165D PHE* 5.0 7.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 3.4 9.7 - - - -
33D LEU* 2.9 42.1 + - + +
35D TYR* 3.9 13.7 - - + -
54D PHE* 1.3 77.3 - - - +
56D HIS* 1.3 70.6 + - - +
71D ALA* 3.6 26.2 - - - +
74D ARG* 3.8 21.1 - - + +
75D PHE* 4.1 19.1 - - + -
78D LEU* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LYS* 5.9 1.5 - - + +
31D THR 3.2 14.6 - - - +
32D TYR* 3.7 36.1 - + + -
54D PHE* 6.4 0.9 - + - -
55D LEU* 1.3 87.1 - - - +
57D ASN* 1.3 92.5 + - - +
58D GLN* 5.6 0.4 - - - -
71D ALA* 4.6 0.7 - - - -
74D ARG* 4.1 18.2 + - - +
----------------------------------------------------------
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