Contacts of the strand formed by residues 31 - 38 (chain C) in PDB entry 3QHT
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 TYR 31 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 4.0 21.6 + - - +
69B GLY 4.0 12.3 - - - +
70B ILE* 4.0 16.8 - - + -
29C VAL* 3.4 9.3 - - - +
30C SER* 1.3 88.6 - - - +
32C TYR* 1.3 64.7 + - - +
33C ARG* 4.1 4.7 - - + -
49C THR* 3.7 32.3 - - + -
50C VAL 3.1 15.0 - - - +
52C GLY* 3.5 5.2 - - - +
75C TYR* 2.9 66.7 + + + -
82C TYR* 3.7 34.5 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 5.5 0.2 - - + -
5C PRO* 3.8 13.7 - - + -
22C TRP* 3.4 32.8 - + + -
23C ASP 4.0 0.3 + - - -
24C ALA* 3.6 10.7 - - + -
26C SER* 4.7 0.9 + - - -
29C VAL* 3.8 18.3 - - + +
31C TYR* 1.3 74.1 - - - +
33C ARG* 1.3 60.3 + - - +
34C ILE* 4.0 1.8 + - + -
49C THR* 3.2 4.0 - - - -
50C VAL* 2.8 44.9 + - + +
51C PRO 3.8 9.9 - - - -
52C GLY* 3.5 22.7 + - - -
54C SER 3.6 10.5 - - - -
72C VAL* 3.8 19.1 - - + -
73C TYR 3.2 14.1 - - - +
74C ALA* 3.6 22.2 - - + -
96C GOL 3.2 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.9 21.2 + - - +
36A PHE* 5.2 6.5 - - - +
38A LYS* 4.1 10.9 - - - +
99A GOL 5.7 0.8 + - - -
31C TYR* 4.1 9.3 + - + -
32C TYR* 1.3 73.5 - - - +
34C ILE* 1.3 61.3 + - - +
35C THR* 3.8 21.3 - - + +
47C GLU* 2.8 38.6 + - - +
48C PHE 3.6 5.4 - - - +
49C THR* 4.2 8.5 - - + -
71C THR 3.5 1.6 - - - +
72C VAL* 3.3 5.0 - - - -
73C TYR* 2.8 65.0 + - + -
75C TYR* 3.2 45.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 4.1 18.8 - - + -
22C TRP* 3.7 26.5 - - + -
32C TYR* 4.3 9.9 - - + +
33C ARG* 1.3 71.9 - - - +
35C THR* 1.3 66.4 + - - +
36C TYR* 4.8 0.2 - - + -
46C GLN 3.8 0.2 - - - +
47C GLU* 3.0 5.7 - - - +
48C PHE* 2.8 80.7 + - + +
50C VAL* 4.6 3.6 - - + -
57C ALA* 4.6 2.9 - - + -
59C ILE* 4.1 11.4 - - + -
70C ILE* 4.4 4.3 - - + -
71C THR 3.5 6.7 - - - +
72C VAL* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 3.8 29.8 - - + +
34C ILE* 1.3 75.3 - - - +
36C TYR* 1.3 66.5 + - - +
45C VAL* 4.8 15.6 - - + +
46C GLN 3.1 8.1 - - - -
47C GLU* 3.4 24.0 - - + -
69C THR 3.8 0.4 - - - +
70C ILE* 3.6 3.1 - - - +
71C THR* 3.0 51.1 + - - +
73C TYR* 3.9 9.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 4.6 0.7 - - + -
35C THR* 1.3 80.1 - - - +
37C GLY* 1.3 58.2 + - - +
44C PRO 4.1 1.0 - - - +
45C VAL* 3.4 5.3 - - - +
46C GLN* 2.9 88.1 + - + +
47C GLU 5.3 0.2 - - - -
48C PHE* 3.9 24.4 - + - -
59C ILE* 3.6 51.1 - - + +
60C SER 4.2 8.6 + - - -
62C LEU* 4.0 18.2 - - + -
68C TYR* 4.6 11.9 - + + -
69C THR 3.3 11.4 - - - +
70C ILE* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 1.3 75.2 - - - +
38C GLU* 1.3 62.8 + - - -
41C GLY 5.7 0.2 - - - -
43C SER* 4.1 7.2 - - - -
44C PRO 4.4 3.8 - - - -
45C VAL* 4.3 16.8 - - - +
68C TYR* 3.2 14.4 - - - +
69C THR* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLY* 1.3 73.7 - - - -
39C THR* 1.3 77.1 + - - +
40C GLY 3.3 2.4 + - - -
41C GLY* 3.4 30.1 + - - +
43C SER* 3.2 25.6 + - - +
66C VAL* 3.9 20.9 - - + +
67C ASP 3.3 11.4 - - - +
68C TYR* 3.9 8.3 - - + -
69C THR* 5.3 0.7 - - - -
----------------------------------------------------------
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