Contacts of the helix formed by residues 21 - 31 (chain D) in PDB entry 3Q2K
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 ILE 21 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ARG* 1.3 71.6 - - - +
22D SER* 1.3 69.3 + - - +
23D LYS 3.1 3.4 - - - -
24D ASN* 2.8 49.0 + - + +
25D HIS* 3.5 10.4 + - + -
79D ALA* 3.8 18.8 - - + -
102D GLU* 3.9 13.5 - - + +
301D HIS* 4.5 5.6 - - + +
500D NAI 2.7 80.0 + - + +
550D HP7 5.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 3.4 27.3 - - - +
17D GLY 3.6 6.3 - - - -
18D CYS* 3.0 28.0 + - - +
19D GLY 2.8 20.0 + - - +
21D ILE* 1.3 83.5 - - - +
23D LYS* 1.3 58.0 + - - +
25D HIS* 3.1 11.8 + - - +
26D ILE* 2.8 34.6 + - - +
79D ALA* 4.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLY 4.5 4.7 - - - +
20D ARG* 3.2 45.9 + - - +
22D SER* 1.3 76.4 + - - +
24D ASN* 1.3 61.2 + - - +
26D ILE* 3.9 15.2 - - + +
27D GLY* 2.7 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ARG 4.9 2.3 - - - +
21D ILE* 2.8 35.6 + - + +
23D LYS* 1.3 86.9 - - - +
25D HIS* 1.3 52.6 + - - +
27D GLY* 3.9 1.1 - - - -
28D ALA* 2.8 33.6 + - - +
131D GLN* 5.8 0.2 - - - +
298D GLY 3.0 27.4 + - - +
299D PHE* 3.3 33.3 - - - +
301D HIS* 3.7 25.0 + - + +
302D PRO* 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.0 14.1 - - + -
21D ILE* 3.6 21.8 - - + -
22D SER* 3.1 9.2 + - - +
24D ASN* 1.3 78.3 - - - +
26D ILE* 1.3 56.7 + - - +
28D ALA* 2.9 7.6 + - - +
29D ILE* 2.8 42.2 + - + +
77D VAL* 3.1 24.8 - - + +
79D ALA* 4.8 1.8 - - + -
102D GLU* 2.6 40.2 + - + +
129D VAL* 4.3 11.0 - - + -
301D HIS* 3.5 16.9 - + - -
305D TYR* 2.6 28.2 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.4 11.2 - - + +
18D CYS* 6.1 0.2 - - + -
22D SER* 2.8 24.4 + - - +
23D LYS* 3.4 17.9 - - + +
25D HIS* 1.3 66.6 - - - +
27D GLY* 1.3 70.2 + - - +
28D ALA 2.7 5.0 + - - -
29D ILE* 3.0 4.1 + - - +
30D ALA* 3.0 26.1 + - + +
38D LEU* 3.9 27.6 - - + +
41D ILE* 6.0 0.2 - - + -
52D ALA* 5.4 8.7 - - + -
55D ALA* 5.1 9.4 - - + -
56D THR* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LYS 2.7 15.8 + - - -
24D ASN* 3.9 2.0 - - - -
26D ILE* 1.3 82.8 - - - +
28D ALA* 1.3 58.9 + - - -
30D ALA* 4.0 5.8 - - - +
31D GLN* 3.2 27.2 + - - +
302D PRO* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASN 2.8 22.5 + - - +
25D HIS* 2.9 8.9 + - - +
26D ILE 2.7 6.5 + - - -
27D GLY* 1.3 73.5 - - - +
29D ILE* 1.3 63.5 + - - +
31D GLN* 3.6 6.1 + - - +
32D HIS* 3.3 21.7 - - - -
301D HIS* 3.8 11.7 - - + -
302D PRO* 3.9 18.6 - - + +
305D TYR* 3.7 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PHE* 3.5 49.4 - - + -
15D LEU* 6.2 2.2 - - + -
25D HIS* 2.8 24.9 + - + +
26D ILE 4.0 1.3 - - - +
28D ALA* 1.3 68.9 - - - +
30D ALA* 1.3 58.7 + - - +
31D GLN 2.9 1.6 - - - -
32D HIS* 2.5 41.3 + - + +
33D GLY* 4.4 0.2 - - - -
36D ALA* 4.1 10.8 - - + +
37D GLU* 4.0 22.7 - - - -
38D LEU* 3.9 27.4 - - + +
77D VAL* 5.4 2.0 - - + -
305D TYR* 4.1 23.3 - - + +
309D ILE* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 3.0 17.5 + - + +
27D GLY* 4.0 6.7 - - - +
29D ILE* 1.3 78.6 - - - +
31D GLN* 1.3 57.5 + - - +
32D HIS 2.9 6.2 + - - -
33D GLY* 2.9 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLY 3.2 16.4 + - - +
28D ALA* 3.7 8.1 - - - +
29D ILE 2.9 1.2 + - - -
30D ALA* 1.3 76.3 - - - +
32D HIS* 1.3 61.8 + - + +
33D GLY 3.6 1.1 - - - -
302D PRO* 3.8 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