Contacts of the helix formed by residues 33 - 44 (chain A) in PDB entry 4KLZ
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.3 0.8 + - - -
32A VAL* 1.3 78.1 - - - +
34A LYS* 1.3 65.5 + - - +
37A MET* 3.0 34.1 + - - +
134A ASN* 3.6 2.9 + - - -
501A GDP 3.1 43.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 4.1 16.3 - - + +
27A LEU 3.7 4.3 - - - -
28A GLY* 3.2 29.2 + - - +
29A ALA 2.8 26.5 + - - -
30A GLY* 3.9 2.8 - - - +
32A VAL* 4.3 3.1 - - + -
33A GLY* 1.3 72.7 - - - +
35A SER* 1.3 53.9 + - - +
37A MET* 3.5 7.1 - - - +
38A THR* 2.4 39.9 + - - -
75A ASP* 3.7 9.2 - - - +
76A THR* 3.1 33.8 + - - +
77A ALA* 5.5 0.2 - - - +
78A GLY* 4.4 4.3 - - - +
99A CYS* 4.2 24.7 - - + -
501A GDP 2.6 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 1.3 76.8 - - - +
36A ALA* 1.4 64.5 + - - +
37A MET 3.2 0.2 - - - -
38A THR* 3.5 0.7 + - - -
39A MET* 3.0 32.7 + - - +
47A PRO* 4.7 2.0 - - - -
50A HIS* 3.5 28.1 + - - -
75A ASP* 2.4 30.6 + - - -
501A GDP 3.2 11.6 + - - -
502A MG 2.4 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 3.5 0.6 + - - +
35A SER* 1.4 70.3 - - - +
37A MET* 1.3 53.3 + - - +
39A MET* 3.3 1.7 + - - +
40A GLN* 2.8 39.8 + - - +
45A ARG 4.0 0.5 - - - +
46A PHE* 3.3 40.2 - - + -
47A PRO* 3.6 15.9 - - + +
165A ALA* 3.8 12.1 - - + -
501A GDP 2.7 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 4.0 10.3 - - + -
33A GLY 3.0 26.5 + - - +
34A LYS* 3.5 4.0 - - - +
36A ALA* 1.3 78.4 - - - +
38A THR* 1.3 63.0 + - - +
40A GLN* 3.3 1.0 + - - -
41A PHE* 2.9 21.0 + - - +
97A ILE* 4.4 1.6 - - + -
99A CYS* 3.7 33.7 - - - -
132A VAL* 3.8 29.4 - - + -
134A ASN* 3.7 29.2 - - - +
163A THR* 4.2 3.8 - - + +
165A ALA* 3.7 7.1 - - + +
171A ILE* 3.5 34.7 - - + +
174A VAL* 4.8 5.6 - - + -
175A PHE* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 3.6 17.8 - - + +
34A LYS 2.4 31.4 + - - -
35A SER* 4.0 5.6 - - - -
37A MET* 1.3 72.8 - - - +
39A MET* 1.3 57.8 + - - +
41A PHE* 3.4 1.4 - - - +
42A ILE* 3.0 33.6 + - - +
58A TYR* 3.8 28.5 - - + -
73A ILE* 3.5 37.9 - - + -
75A ASP* 4.2 5.6 + - + -
175A PHE* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.0 23.9 + - - +
36A ALA 4.0 0.7 - - - +
38A THR* 1.3 74.2 - - - +
40A GLN* 1.3 66.9 + - - +
41A PHE 3.2 0.9 - - - -
42A ILE* 4.4 4.7 - - - +
43A SER* 3.0 29.0 + - - +
44A HIS 3.2 4.7 + - - -
45A ARG* 3.3 30.4 + - + +
47A PRO* 4.2 15.9 - - + -
50A HIS* 5.0 7.6 - - + +
56A ASP* 5.4 0.2 - - - -
58A TYR* 2.5 64.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 2.8 21.2 + - - +
37A MET* 3.8 5.2 - - - +
39A MET* 1.3 77.0 - - - +
41A PHE* 1.3 57.1 + - - +
44A HIS 3.1 17.0 + - - +
45A ARG* 3.2 25.1 + - - +
46A PHE* 3.4 21.2 - - - +
165A ALA 2.9 31.4 + - - +
166A ALA 4.1 4.2 + - - -
167A TYR 4.7 0.2 - - - -
168A ARG* 2.7 66.9 + - + +
171A ILE* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET 2.9 14.8 + - - +
38A THR* 3.4 9.2 - - - +
40A GLN* 1.3 80.4 - - - +
42A ILE* 1.3 81.9 + - + +
44A HIS* 4.7 3.6 - - - -
60A ILE* 4.6 1.1 - - + +
62A ILE* 4.1 24.8 - - + +
71A LEU* 3.6 23.6 - - + -
73A ILE* 4.2 0.7 - - + -
168A ARG* 3.6 8.9 + - - +
171A ILE* 3.7 8.2 - - + +
172A ASP* 3.4 31.6 - - - +
175A PHE* 3.4 49.4 - + + -
176A HIS* 4.0 21.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.0 19.4 + - + +
39A MET* 4.4 5.2 - - - +
41A PHE* 1.3 94.5 - - + +
43A SER* 1.3 68.9 + - - +
44A HIS* 5.4 1.1 - - - -
58A TYR* 4.2 20.2 - - + -
60A ILE* 2.5 75.2 - - + +
62A ILE* 6.5 0.2 - - - -
73A ILE* 3.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 3.0 15.6 + - - +
42A ILE* 1.3 84.7 - - - +
44A HIS* 1.3 77.9 + - - +
45A ARG* 3.1 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET 3.2 0.2 + - - -
40A GLN* 3.1 26.5 + - - +
41A PHE 4.7 4.7 - - - -
42A ILE 5.4 0.4 - - - -
43A SER* 1.3 82.6 - - - +
45A ARG* 1.4 57.3 + - - +
168A ARG* 3.3 48.4 + - - -
172A ASP* 5.1 0.8 + - - -
----------------------------------------------------------
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