Contacts of the strand formed by residues 31 - 37 (chain D) in PDB entry 1XSK
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 GLU 31 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 3.6 4.3 - - - -
28D GLN* 2.9 37.3 + - - +
29D ASP 3.2 1.2 + - - -
30D ASN* 1.3 91.3 + - - +
32D MET* 1.3 60.9 + - - +
33D VAL* 4.2 0.7 - - - -
56D ARG* 2.8 48.8 + - + +
57D PHE 3.4 5.8 - - - +
58D PHE* 3.5 32.5 - - + +
88D GLN* 4.4 14.0 + - - +
94D ILE* 3.5 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 4.0 18.4 - - + -
26D GLU 3.6 4.7 - - - +
27D GLN* 4.8 0.2 - - - +
31D GLU* 1.3 71.9 - - - +
33D VAL* 1.3 62.9 + - - +
34D VAL* 4.4 9.9 - - + -
56D ARG* 3.5 1.4 - - - -
57D PHE* 2.8 47.5 + - + -
94D ILE* 3.2 30.2 - - + +
95D GLU 4.1 1.6 - - - +
101D ALA* 4.0 16.6 - - - +
102D GLU 2.8 50.0 - - - +
103D PHE* 3.5 21.5 - - + +
110D ALA 5.5 0.2 - - - +
112D VAL* 6.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLU 4.0 0.5 - - - +
25D VAL* 3.4 4.0 - - - +
26D GLU* 2.8 45.3 + - + +
28D GLN* 3.6 24.0 - - + +
32D MET* 1.3 75.8 - - - +
34D VAL* 1.3 64.5 + - - +
35D TYR* 3.8 30.5 - - + +
54D THR* 3.9 17.7 - - + -
55D LEU 3.3 9.4 - - - +
56D ARG* 3.4 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL* 4.1 33.0 - - + -
24D GLU 3.7 2.9 - - - +
25D VAL* 4.3 12.1 - - + +
32D MET* 4.4 12.6 - - + -
33D VAL* 1.3 77.2 - - - +
35D TYR* 1.3 66.2 + - - +
36D ALA 4.6 0.2 - - - +
54D THR* 3.7 0.5 - - - -
55D LEU* 2.7 51.2 + - + +
57D PHE* 3.8 24.2 - - + -
101D ALA* 5.0 1.1 - - + -
112D VAL* 4.5 12.8 - - + -
118D TRP* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LYS* 3.9 54.9 + - + +
22D VAL* 3.7 2.4 - - - +
23D PHE* 2.8 38.7 + - + +
24D GLU* 2.9 33.1 + - + +
26D GLU* 3.7 27.2 + - + -
28D GLN* 4.5 6.2 + - - -
33D VAL* 3.8 21.2 - - + +
34D VAL* 1.3 73.7 - - - +
36D ALA* 1.3 53.6 + - - +
52D LEU* 3.8 18.8 - - + -
53D PHE 3.5 3.1 - - - -
54D THR* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D PRO* 3.5 22.0 - - + -
21D GLN 3.3 5.4 - - - +
34D VAL* 3.7 1.3 + - + -
35D TYR* 1.3 72.8 - - - +
37D ALA* 1.3 60.8 + - - +
52D LEU* 2.9 21.6 - - - +
53D PHE* 2.9 24.7 + - - +
55D LEU* 4.0 8.5 - - + -
118D TRP* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C PHE* 5.6 2.5 - - + -
18D HIS 4.1 1.1 - - - -
19D PRO* 4.3 0.7 - - - -
20D LEU 2.7 29.0 + - - -
21D GLN 2.9 16.2 + - - +
23D PHE* 5.0 3.0 - - + +
35D TYR 4.4 0.4 + - - -
36D ALA* 1.3 73.9 - - - +
38D PRO* 1.3 63.4 - - + +
39D ARG 3.1 21.7 + - - +
41D VAL* 3.6 31.2 - - + -
50D THR* 5.6 0.4 - - + -
51D PRO 4.4 2.5 - - - +
52D LEU* 4.5 6.3 - - + -
53D PHE* 5.1 0.2 - - - -
----------------------------------------------------------
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