Contacts of the strand formed by residues 34 - 41 (chain D) in PDB entry 3UYO
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 34 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 3.6 21.8 - - + -
243A THR 3.3 27.4 - - - -
244A VAL 3.9 6.5 - - - +
245A TYR 5.1 1.1 - - - -
246A GLY* 3.6 20.2 - - - +
247A VAL* 3.8 10.8 - - + -
32D VAL* 3.3 6.1 - - - +
33D ASP* 1.3 84.9 - - + +
35D TYR* 1.3 63.3 + - - +
36D VAL* 3.7 28.7 - - + -
52D THR* 4.3 6.1 - - + +
53D VAL 3.3 15.9 - - - +
54D PRO* 4.6 1.3 - - + -
55D GLY 3.6 4.5 - - - +
78D GLY* 2.8 38.8 + - - +
79D TYR 3.6 29.2 - - - -
85D TRP* 4.0 4.5 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
8D PRO* 3.8 22.9 - - + -
25D TRP* 3.4 29.5 + + + -
27D ALA* 4.3 4.3 - - - +
28D PRO* 3.4 27.0 - - - +
32D VAL* 3.7 25.1 - - + +
34D PHE* 1.3 75.0 - - - +
36D VAL* 1.3 62.2 + - - +
37D ILE* 3.8 3.0 - - + +
52D THR* 3.1 6.4 - - - -
53D VAL* 2.9 40.5 + - + -
54D PRO 3.9 10.1 - - - -
55D GLY* 3.6 20.1 + - - -
57D LYS 3.3 21.7 + - - -
75D VAL* 3.9 21.3 - - + -
76D TYR 3.2 15.7 - - - +
77D ALA* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.6 28.0 - - + -
247A VAL* 3.9 12.8 - - + -
34D PHE* 3.7 28.7 - - + -
35D TYR* 1.3 72.4 - - - +
37D ILE* 1.3 66.9 + - - +
38D THR* 4.0 7.9 - - + -
50D GLU* 4.3 7.4 - - + +
51D PHE 3.5 9.4 - - - +
52D THR* 4.0 6.7 - - + -
74D THR 3.6 1.4 - - - +
75D VAL* 3.3 6.4 - - - +
76D TYR* 2.9 42.5 + - + +
78D GLY* 5.3 0.4 - - - -
85D TRP* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 4.3 9.2 - - + -
25D TRP* 4.3 7.4 - - + -
35D TYR* 3.8 18.2 - - + +
36D VAL* 1.3 77.9 - - - +
38D THR* 1.3 70.8 + - - +
39D TYR* 4.5 0.6 - - + -
50D GLU* 3.2 5.0 - - - +
51D PHE* 2.8 74.2 + - + +
53D VAL* 4.0 20.4 - - + -
60D ALA* 4.6 0.9 - - + -
62D ILE* 3.9 22.0 - - + -
73D ILE* 4.2 7.0 - - + -
74D THR 3.4 5.4 - - - +
75D VAL* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 4.6 2.7 - - + -
161A SER* 4.3 19.6 - - - +
36D VAL* 4.4 7.9 - - + -
37D ILE* 1.3 76.8 - - - +
39D TYR* 1.3 64.1 + - - +
48D VAL* 4.1 15.3 - - + +
49D GLN 3.3 7.9 - - - +
50D GLU* 3.9 15.9 - - + -
72D THR 4.4 0.8 + - - -
73D ILE* 3.3 4.0 - - - +
74D THR* 2.8 53.4 + - - +
76D TYR* 4.1 20.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 4.5 0.7 - - + -
38D THR* 1.3 81.2 - - - +
40D GLY* 1.3 60.3 + - - +
48D VAL* 3.4 4.8 - - - +
49D GLN* 2.9 71.8 + - + +
50D GLU 4.5 0.7 - - - -
51D PHE* 3.8 30.2 - + - -
62D ILE* 3.7 31.4 - - + +
63D SER 3.7 12.1 + - - -
64D GLY 5.9 0.4 - - - -
65D LEU* 3.7 27.4 - - + -
71D TYR* 5.0 5.6 - + + -
72D THR 3.3 9.4 - - - +
73D ILE* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR* 1.3 76.8 - - - +
41D GLU* 1.3 65.5 + - - -
46D SER* 5.1 4.5 - - - -
47D PRO 5.2 0.4 - - - -
48D VAL* 4.3 18.2 - - - +
71D TYR* 3.4 10.6 - - - -
72D THR* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLY* 1.3 71.6 - - - -
42D THR* 1.3 68.8 + - - +
43D GLY 3.5 2.6 + - - +
44D GLY 2.9 25.3 - - - +
45D ASN* 5.1 3.3 + - - +
46D SER* 4.3 19.0 + - - +
69D VAL* 3.7 25.1 - - + +
70D ASP* 3.4 14.8 - - + +
71D TYR* 3.8 9.9 - - + -
----------------------------------------------------------
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