Contacts of the helix formed by residues 41 - 50 (chain A) in PDB entry 3ZVU
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
----------------------------------------------------------
40A ALA* 1.4 91.2 - - + +
42A PRO* 1.3 74.4 - - + +
43A GLU* 4.3 7.0 - - + +
44A LEU* 2.9 33.3 + - + +
45A VAL* 3.2 10.8 + - - +
135A ILE* 4.6 10.3 - - + +
179A ALA* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 1.3 84.9 - - + +
43A GLU* 1.3 55.9 + - + +
45A VAL* 3.4 1.3 + - + -
46A TRP* 2.9 32.1 + - - +
104A ARG* 3.7 22.7 - - - +
126A VAL* 3.8 7.2 - - + +
128A ARG* 3.6 32.5 - - + +
135A ILE* 3.9 18.2 - - + -
137A THR* 2.8 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.1 5.5 + - + +
42A PRO* 1.3 80.9 - - - +
44A LEU* 1.3 57.7 + - - +
46A TRP* 4.0 7.5 - - + +
47A SER* 3.1 26.3 + - - -
104A ARG* 3.9 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.1 6.7 - - + -
41A PRO* 2.9 21.9 + - + +
43A GLU* 1.3 78.2 - - - +
45A VAL* 1.3 64.9 + - - +
47A SER* 2.4 25.5 + - - +
48A ILE* 3.4 8.2 + - - +
175A ALA* 3.7 14.8 - - + +
178A MET* 3.5 34.5 - - + +
179A ALA* 3.6 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.8 25.1 - - + -
40A ALA* 4.1 11.2 - - + +
41A PRO 3.2 13.2 + - - +
42A PRO 3.8 5.2 - - - +
44A LEU* 1.3 74.8 - - - +
46A TRP* 1.3 56.2 + - - +
48A ILE* 3.1 14.8 + - - +
49A VAL* 2.9 28.6 + - + +
126A VAL* 4.3 9.2 - - + -
137A THR* 4.5 5.4 - - + -
139A VAL* 3.5 32.3 - - + -
171A LEU* 4.2 9.0 - - + -
175A ALA* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO 2.9 18.2 + - - +
43A GLU* 4.0 6.1 - - + +
45A VAL* 1.3 72.1 - - - +
47A SER* 1.3 61.9 + - - +
48A ILE 3.0 1.8 - - - -
49A VAL* 3.9 21.1 - - + -
50A ARG* 2.8 54.8 + - + +
99A LEU* 3.9 9.9 - - + -
100A ASP 3.7 12.6 - - - -
101A ASP* 2.8 39.1 + - - +
104A ARG* 3.4 51.8 - - + +
105A VAL 3.4 29.8 - - - -
106A THR* 3.9 11.0 - - + -
124A THR 4.8 0.4 - - - -
126A VAL* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU 3.1 15.7 + - - -
44A LEU* 2.4 35.6 + - - +
46A TRP* 1.3 76.7 - - - +
48A ILE* 1.3 61.0 + - - +
50A ARG* 3.7 15.1 - - - +
51A ARG* 3.3 25.8 + - - +
178A MET* 4.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 3.6 13.9 - - - +
45A VAL 3.1 6.2 + - - +
46A TRP 3.0 0.6 - - - -
47A SER* 1.3 78.6 - - - +
49A VAL* 1.3 65.8 + - - +
51A ARG* 3.1 21.2 + - - +
54A LYS 5.4 0.3 - - - +
57A THR* 3.9 15.5 + - - +
58A TYR* 3.8 24.6 - - + -
171A LEU* 3.7 20.2 - - + -
174A VAL* 4.0 11.0 - - + -
175A ALA* 3.9 29.4 - - + +
178A MET* 3.9 32.5 - - + -
----------------------------------------------------------
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 VAL* 2.9 25.6 + - + +
46A TRP* 3.9 20.2 - - + +
48A ILE* 1.3 78.1 - - - +
50A ARG* 1.3 60.2 + - - +
51A ARG 3.3 3.1 + - - -
52A PHE* 4.8 1.0 + - - -
58A TYR* 4.6 20.7 + - + +
106A THR* 3.6 30.3 + - + +
124A THR* 3.9 20.0 - - + -
126A VAL* 4.2 7.0 - - + -
139A VAL* 5.0 0.2 - - + -
171A LEU* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 2.8 56.4 + - + +
47A SER* 3.7 16.6 - - - +
49A VAL* 1.3 72.8 - - - +
51A ARG* 1.3 70.6 + - + +
52A PHE* 2.8 10.7 + - - +
73A MET* 3.0 49.3 - - - +
99A LEU* 4.1 15.6 - - + +
101A ASP* 2.8 36.4 + - - -
106A THR* 5.1 2.4 + - - -
----------------------------------------------------------
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