Contacts of the helix formed by residues 33 - 42 (chain D) in PDB entry 4KYI
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 GLY 33 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ALA 3.4 0.8 - - - -
32D VAL* 1.3 81.9 - - - +
34D LYS* 1.3 59.9 + - - +
36D SER* 3.8 0.5 - - - -
37D LEU* 2.9 37.2 + - - +
100D VAL* 5.1 0.2 - - - -
134D ASN* 3.2 11.4 + - - -
301D GNP 3.2 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 4.0 14.7 - - + +
27D LEU 3.7 28.3 - - - +
28D GLY* 3.8 5.4 - - - +
29D GLU 3.0 18.0 + - - -
32D VAL* 3.6 13.2 - - + +
33D GLY* 1.3 79.7 - - - +
35D SER* 1.3 62.8 + - - +
37D LEU* 3.4 14.4 + - - +
38D VAL* 3.3 20.8 - - - +
76D ASP* 3.7 11.0 - - - +
77D THR* 3.6 21.3 - - - -
79D GLY* 3.7 9.6 - - - +
100D VAL* 3.8 13.5 - - + -
301D GNP 2.4 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LYS* 1.3 75.2 - - - +
36D SER* 1.3 65.4 + - - +
38D VAL* 3.4 6.1 + - - +
39D LEU* 3.1 20.8 + - - +
50D GLN* 4.3 14.5 + - - -
51D GLU 5.7 2.0 - - - -
53D THR* 2.9 5.2 + - - +
76D ASP* 2.7 21.7 + - - -
301D GNP 3.1 12.7 + - - -
302D MG 2.0 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLY 3.9 4.3 - - - -
35D SER* 1.3 74.4 - - - +
37D LEU* 1.3 55.5 + - - +
39D LEU* 3.2 4.7 + - - +
40D ARG* 2.8 35.0 + - - +
45D GLN 4.2 1.7 - - - +
46D PHE* 4.3 8.9 - - - -
47D HIS 4.3 3.6 + - - -
50D GLN* 3.3 30.0 + - - +
165D ALA* 3.9 10.7 - - - +
301D GNP 3.0 40.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 4.7 8.3 - - + -
33D GLY 2.9 23.5 + - - +
34D LYS* 3.4 7.4 - - - +
35D SER 3.2 0.4 - - - -
36D SER* 1.3 76.3 - - - +
38D VAL* 1.3 58.1 + - + +
40D ARG* 3.1 5.6 + - - +
41D PHE* 2.9 29.8 + - - +
98D ILE* 5.4 2.5 - - + -
100D VAL* 4.0 35.0 - - + -
132D ALA* 5.1 4.7 - - + -
134D ASN* 3.5 22.2 - - - +
163D THR* 4.0 18.6 - - + +
165D ALA* 4.1 8.0 - - + +
171D VAL* 3.8 30.3 - - + +
174D ILE* 6.4 0.7 - - + -
175D PHE* 5.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.7 28.9 - - + -
34D LYS 3.3 16.8 + - - +
35D SER* 3.4 6.3 + - - +
36D SER 3.4 0.2 - - - -
37D LEU* 1.3 74.0 - - - +
39D LEU* 1.3 57.7 + - - +
41D PHE* 4.2 6.1 - - - -
42D VAL* 3.0 30.6 + - + +
59D LEU* 4.0 25.7 - - + +
74D ILE* 3.7 33.2 - - + -
76D ASP* 4.2 13.5 - - + -
175D PHE* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER 3.1 13.9 + - - +
36D SER* 3.3 9.6 - - - +
37D LEU 3.1 0.4 - - - -
38D VAL* 1.3 76.2 - - - +
40D ARG* 1.3 59.6 + - - +
42D VAL* 5.2 0.4 - - - -
43D LYS* 3.0 45.3 + - + +
44D GLY 2.9 21.8 + - - -
45D GLN* 3.3 35.1 + - + +
46D PHE* 4.2 2.5 - - - +
47D HIS* 3.6 24.5 - - + +
50D GLN* 3.3 25.6 - - - +
59D LEU* 5.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER 2.8 17.0 + - - +
37D LEU 3.5 7.9 - - - +
39D LEU* 1.3 72.9 - - - +
41D PHE* 1.3 62.9 + - - +
44D GLY* 3.2 41.7 + - - -
45D GLN 3.4 9.3 + - - +
46D PHE* 3.3 23.1 - - - +
165D ALA* 2.5 36.1 + - + +
166D LYS 3.2 17.8 + - - -
168D ALA* 3.6 23.7 - - + +
171D VAL* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU 2.9 15.1 + - - +
38D VAL* 3.7 4.0 - - - +
40D ARG* 1.3 80.5 - - - +
42D VAL* 1.3 68.2 + - + +
44D GLY 4.6 0.3 + - - -
61D GLN* 3.6 35.8 + - + -
63D VAL* 4.1 18.4 - - + -
72D PHE* 4.2 10.5 - + - -
74D ILE* 3.7 27.1 - - + -
171D VAL* 4.2 6.5 - - + -
172D ASN* 4.1 26.5 - - + +
175D PHE* 3.8 52.7 - + + -
176D MET* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 3.0 23.5 + - + +
41D PHE* 1.3 87.7 - - + +
43D LYS* 1.3 74.3 + - + +
59D LEU* 3.9 27.8 - - + -
60D THR 4.8 5.6 - - - +
61D GLN* 3.6 47.6 + - + +
74D ILE* 4.6 3.6 - - + -
----------------------------------------------------------
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