Contacts of the helix formed by residues 41 - 53 (chain A) in PDB entry 3ZPL
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 PRO 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 4.1 19.7 - - + +
34A LEU* 4.6 1.3 - - - -
35A GLN* 5.3 1.8 - - + -
40A MET* 1.3 97.1 - - + +
42A HIS* 1.3 66.7 + - - +
43A VAL* 3.3 6.0 + - + +
44A TYR* 3.4 40.3 + - + +
45A TYR* 3.2 17.3 + - - +
81A ARG* 4.0 0.7 - - - +
12D T 4.0 26.0 - - - +
13D C 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 5.4 5.7 - - + +
30A LEU* 4.2 19.1 - - + +
31A ASP* 2.9 31.5 + - - +
34A LEU* 3.6 29.1 - - + +
41A PRO* 1.3 72.1 - - - +
43A VAL* 1.3 67.4 + - + +
45A TYR* 3.4 6.3 + + - +
46A GLY* 3.1 20.3 + - - -
119A HIS* 3.7 21.0 + + - -
16B TRP* 4.5 3.6 + + - -
20B ILE* 3.9 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 5.5 2.2 - - - +
41A PRO* 3.3 4.2 - - + -
42A HIS* 1.3 80.1 - - + +
44A TYR* 1.3 72.3 + - + +
46A GLY* 3.2 11.4 + - - -
47A LEU* 3.2 17.9 + - + +
68A ALA* 5.4 3.1 - - + +
70A ILE* 4.2 31.9 - - + -
74A ARG* 3.5 29.2 - - - +
24B THR* 6.6 0.2 - - + -
13D C 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.0 11.4 - - - -
41A PRO* 3.4 32.7 + - + +
42A HIS 3.3 0.2 - - - -
43A VAL* 1.3 78.9 - - + +
45A TYR* 1.3 57.7 + - - +
47A LEU* 2.7 34.4 + - + +
48A LEU* 3.2 12.0 + - - +
74A ARG* 5.8 0.2 - - - -
77A HIS* 4.7 2.1 + - - +
78A ALA* 3.4 34.4 + - + -
81A ARG* 3.6 37.0 - - + +
82A LEU* 3.9 22.2 - - + -
12D T 3.5 26.3 + - - +
13D C 3.3 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.6 31.6 - - + -
38A ALA* 5.0 0.2 - - + -
40A MET* 3.5 33.4 - - + -
41A PRO 3.2 10.6 + - - +
42A HIS* 3.6 11.0 - + - +
44A TYR* 1.3 77.2 - - - +
46A GLY* 1.3 62.5 + - - +
48A LEU* 3.2 6.3 + - - +
49A VAL* 3.0 47.4 + - + +
112A LEU* 4.4 13.5 + - + +
115A THR* 3.3 22.4 - - - -
116A ALA* 3.0 36.6 + - - +
119A HIS* 3.8 29.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 3.1 15.4 + - - -
43A VAL 3.5 5.4 - - - -
44A TYR 3.0 1.4 + - - -
45A TYR* 1.3 77.7 - - - +
47A LEU* 1.3 57.7 + - - +
49A VAL* 3.3 10.2 + - - +
50A LYS* 2.9 29.8 + - - +
68A ALA* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.2 15.0 + - + +
44A TYR* 2.7 24.8 + - + +
46A GLY* 1.3 71.4 - - - +
48A LEU* 1.3 61.7 + - + +
50A LYS* 3.2 3.9 + - - +
51A LEU* 3.1 29.5 + - + +
64A LEU* 4.1 29.0 - - + +
68A ALA* 3.7 30.1 - - + -
70A ILE* 4.2 12.1 - - + -
75A LEU* 3.8 19.7 - - + -
78A ALA* 4.0 21.3 - - + -
79A VAL* 5.0 1.6 - - + -
82A LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.6 32.3 - - + -
44A TYR 3.9 8.3 - - - +
45A TYR 3.2 8.0 + - - +
47A LEU* 1.3 78.7 - - + +
49A VAL* 1.3 56.1 + - - +
51A LEU* 3.3 6.3 + - + +
52A ALA* 2.9 31.2 + - - +
82A LEU* 4.1 17.9 - - + -
87A TRP* 4.3 19.7 - - + -
88A VAL* 3.7 29.4 - - + -
104A LEU* 4.0 12.8 - - + +
108A GLY 4.5 3.4 - - - +
111A VAL* 5.3 1.6 - - + -
112A LEU* 3.6 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.0 49.5 + - + +
46A GLY* 3.5 10.5 - - - +
47A LEU 3.3 0.2 - - - -
48A LEU* 1.3 76.1 - - - +
50A LYS* 1.3 63.2 + - - +
52A ALA* 3.6 2.1 - - - +
53A GLU* 3.1 37.2 + - + +
112A LEU* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 2.9 15.6 + - - +
47A LEU 3.2 4.0 + - - +
49A VAL* 1.3 79.0 - - - +
51A LEU* 1.3 55.4 + - - +
53A GLU* 3.4 27.0 + - - +
54A SER* 2.6 37.8 + - - +
59A LEU* 3.8 14.8 - - + -
64A LEU* 4.3 9.9 - - + -
67A TYR* 3.6 56.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.1 18.3 + - + +
48A LEU* 3.8 7.4 - - + +
50A LYS* 1.3 71.7 - - - +
52A ALA* 1.3 58.1 + - - +
53A GLU 3.0 1.6 - - - -
54A SER* 2.7 24.6 + - - -
57A ARG* 3.2 27.7 - - - +
58A ARG 4.2 0.7 - - - -
59A LEU* 3.5 33.0 - - + +
64A LEU* 3.9 20.9 - - + -
88A VAL* 4.2 21.1 - - + -
102A ALA* 3.6 29.8 - - + +
104A LEU* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 2.9 18.6 + - - +
49A VAL* 3.6 4.3 - - - +
51A LEU* 1.3 75.0 - - - +
53A GLU* 1.3 59.7 + - + +
54A SER 4.3 1.9 - - - +
57A ARG* 4.1 14.3 + - - +
104A LEU* 3.6 22.0 - - + +
109A TYR* 4.4 15.0 - - + -
112A LEU* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.1 29.5 + - + +
50A LYS* 3.5 37.0 + - + +
51A LEU 3.0 1.0 - - - -
52A ALA* 1.3 77.0 - - + +
54A SER* 1.3 63.5 + - - +
55A PRO* 4.0 1.6 - - - +
13B GLN* 4.3 13.2 - - - +
----------------------------------------------------------
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