Contacts of the helix formed by residues 25 - 34 (chain L) in PDB entry 2ZHX
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 LEU 25 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K ARG* 3.7 42.8 - - + +
171K ASP* 4.9 12.1 - - - +
174K THR* 5.6 8.5 - - + -
23L LEU* 5.3 6.5 - - + -
24L MET* 1.3 77.0 - - - +
26L PRO* 1.4 76.6 - - + +
27L GLU* 4.3 9.4 - - + +
28L GLU* 2.9 24.8 + - + +
29L VAL* 3.3 9.7 + - - +
40L ASP* 3.3 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L MET 4.0 0.2 - - - -
25L LEU* 1.4 84.4 - - + +
27L GLU* 1.3 62.9 + - + +
29L VAL* 2.9 4.5 + - + +
30L GLU* 2.9 26.9 + - - +
36L LYS* 4.2 15.7 - - + -
37L PRO* 3.6 44.6 - - + +
38L GLU 4.9 3.6 - - - +
39L SER* 4.1 15.0 - - - +
40L ASP* 3.4 17.3 - - - +
41L ILE 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K ARG* 4.6 16.2 - - - +
25L LEU* 4.5 11.4 - - + +
26L PRO* 1.3 80.5 - - + +
28L GLU* 1.3 60.1 + - - +
30L GLU* 3.9 12.7 - - - +
31L GLU* 3.8 15.9 + - - +
36L LYS* 5.1 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K GLY* 3.8 5.0 - - - -
170K ARG* 3.2 53.4 + - + +
171K ASP 4.3 0.5 + - - -
190K PRO* 4.9 6.8 - - - +
195K LEU* 6.2 0.2 - - - -
23L LEU 4.5 0.2 - - - +
24L MET* 3.2 44.1 - - + +
25L LEU* 2.9 31.5 + - + +
27L GLU* 1.3 75.4 - - + +
29L VAL* 1.3 64.8 + - - +
31L GLU* 3.5 20.3 + - - +
32L VAL* 3.6 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K LEU* 5.1 8.7 - - + -
24L MET* 4.4 12.3 - - + -
25L LEU 3.6 15.3 - - - +
26L PRO* 2.9 6.2 + - + +
28L GLU* 1.3 75.9 - - - +
30L GLU* 1.3 68.8 + - - +
32L VAL* 3.1 5.8 + - - +
33L ILE* 3.0 24.9 + - + +
37L PRO* 4.3 4.7 - - + -
41L ILE* 4.2 27.8 - - + -
43L VAL* 5.6 0.2 - - + -
58L LEU* 4.0 15.3 - - + -
68L TRP* 3.5 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L PRO 2.9 14.9 + - - +
27L GLU* 3.9 11.4 - - - +
29L VAL* 1.3 74.1 - - - +
31L GLU* 1.3 63.0 + - - +
32L VAL 2.9 0.2 + - - -
34L GLY* 2.6 33.9 + - - -
35L ASN 4.2 14.6 - - - +
36L LYS* 3.6 47.7 + - + +
37L PRO* 4.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 5.1 7.5 + - - +
61A ARG* 5.9 1.4 + - - -
190K PRO* 5.9 1.4 - - - +
199K ARG* 3.9 48.7 + - - +
27L GLU 3.8 9.2 + - - +
28L GLU* 3.5 14.3 + - - +
29L VAL 3.2 0.6 - - - -
30L GLU* 1.3 81.2 - - - +
32L VAL* 1.3 60.5 + - + +
34L GLY* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K LEU* 3.3 49.1 - - + +
196K SER* 5.0 4.0 - - - -
199K ARG* 3.7 30.5 - - + +
24L MET* 6.5 0.7 - - + -
28L GLU 3.6 15.9 - - - +
29L VAL* 3.1 5.2 + - - +
31L GLU* 1.3 79.6 - - + +
33L ILE* 1.3 62.0 + - + +
34L GLY 3.7 0.2 - - - -
79L ASN* 4.0 18.1 + - - +
81L ILE* 3.7 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K LEU* 4.4 10.1 - - + -
29L VAL* 3.0 17.1 + - + +
32L VAL* 1.3 80.3 - - + +
34L GLY* 1.3 60.5 + - - +
35L ASN* 4.4 5.7 - - + +
58L LEU* 3.6 32.1 - - + -
68L TRP* 3.8 21.8 - - + -
69L ALA* 4.4 3.6 - - + -
71L VAL* 3.8 27.6 - - + -
81L ILE* 3.8 31.6 - - + +
83L MET* 4.1 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L GLU* 2.6 27.1 + - - -
31L GLU 4.8 0.4 + - - -
32L VAL 3.7 0.8 - - - -
33L ILE* 1.3 73.3 - - - +
35L ASN* 1.3 72.3 + - - +
----------------------------------------------------------
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