Contacts of the strand formed by residues 28 - 36 (chain D) in PDB entry 3IT8
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 28 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D HIS* 3.4 3.3 - - - -
25D TYR* 2.8 38.7 + - + +
26D ASN 3.2 0.2 - - - -
27D ASP* 1.3 103.8 - - - +
29D LEU* 1.3 65.2 + - - +
30D VAL* 3.2 2.8 + - - +
50D TRP* 4.2 21.0 - - + +
177D LYS 4.7 2.2 + - - -
178D ILE* 3.7 38.2 - - + +
179D PRO* 4.0 16.5 - - - +
208D TYR* 4.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D TYR* 3.9 18.6 - - + -
23D ASP 3.6 3.8 - - - +
24D HIS* 3.4 31.5 + - + +
27D ASP 3.8 2.4 + - - -
28D GLN* 1.3 74.2 - - - +
30D VAL* 1.3 61.3 + - - +
31D THR 3.5 24.5 - - - +
32D LYS* 4.6 7.9 - - + -
46D PHE* 3.6 44.0 - - + -
48D ALA* 3.6 15.4 - - - +
50D TRP* 5.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASP* 2.7 27.7 + - - +
25D TYR* 3.8 23.6 - - + +
28D GLN 3.5 13.9 - - - +
29D LEU* 1.3 74.8 - - - +
31D THR* 1.3 66.4 + - - +
46D PHE* 4.3 2.7 - - - -
47D ARG* 3.3 4.0 - - - -
48D ALA* 2.9 28.7 + - + -
50D TRP* 3.9 15.0 - - + -
51D PHE* 3.5 42.0 - - + -
170D TYR* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE* 3.7 3.3 - - + +
22D TYR* 3.4 5.0 - - - -
23D ASP* 2.9 32.4 + - - -
29D LEU* 3.5 7.4 - - - +
30D VAL* 1.3 84.8 + - - +
32D LYS* 1.3 62.8 + - - +
33D ILE* 3.8 21.8 - - + -
44D VAL* 4.5 1.6 - - + -
46D PHE* 3.3 9.4 - - - +
47D ARG* 2.3 41.2 + - - +
64D TYR* 3.0 28.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 4.5 13.0 - - + -
21D PHE 3.3 4.9 - - - +
22D TYR* 3.7 42.3 + - + -
29D LEU* 4.6 6.1 - - + -
31D THR* 1.3 75.7 - - - +
33D ILE* 1.3 71.1 + - - +
34D SER* 5.0 1.3 - - - -
44D VAL* 3.5 1.7 - - - +
45D ASN* 2.8 49.9 + - + +
46D PHE* 3.1 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 3.1 6.1 - - - +
21D PHE* 2.7 48.7 + - + +
31D THR* 3.8 12.3 - - + -
32D LYS* 1.3 82.0 - - - +
34D SER* 1.3 64.5 + - - +
42D GLY* 4.2 1.1 - - - -
43D ASN 3.3 19.5 - - - +
44D VAL* 4.0 15.5 - - + -
45D ASN* 3.7 2.0 - - - +
63D ASP* 3.6 38.6 - - + +
64D TYR* 3.8 17.5 - - + -
66D PHE* 3.6 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLY 3.1 11.9 - - - -
20D VAL* 4.0 11.2 - - - -
32D LYS* 5.0 1.6 - - - -
33D ILE* 1.3 76.8 - - - +
35D TYR* 1.3 65.5 + - - +
36D ASN 3.4 1.4 + - - -
42D GLY* 3.3 0.2 - - - -
43D ASN* 3.0 28.3 + - - +
45D ASN* 2.5 32.5 + - - -
66D PHE* 4.1 5.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
18D ASP* 4.7 3.1 - - - +
19D GLY 2.9 18.2 + - - +
34D SER* 1.3 72.2 - - - +
36D ASN* 1.3 65.8 + - - +
37D HIS* 3.5 41.2 + + - +
40D ARG* 3.2 54.0 + - - +
41D HIS* 3.5 13.5 - - - -
42D GLY 4.3 0.2 - - - -
66D PHE* 3.8 9.7 - + + -
67D ASN* 5.4 1.8 - - - -
70D TYR* 3.5 66.8 - + + -
74D LYS* 5.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D SER 3.4 1.8 + - - -
35D TYR* 1.3 71.7 - - - +
37D HIS* 1.3 53.7 + - - +
38D GLU* 2.8 14.7 + - - +
39D THR* 2.6 41.9 + - - -
40D ARG* 2.6 36.9 + - - -
41D HIS 2.9 16.4 + - - +
43D ASN* 2.9 32.4 - - - +
----------------------------------------------------------
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