Contacts of the strand formed by residues 41 - 50 (chain A) in PDB entry 4ZIN
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 THR 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY* 3.2 1.0 - - - -
36A ARG* 2.9 50.8 + - - +
39A GLU* 4.2 11.5 + - + +
40A GLY* 1.3 83.5 - - - +
42A GLN* 1.3 65.9 + - - +
72A TYR* 3.6 3.8 - - - +
214A TYR* 3.2 31.4 - - + +
215A GLU 3.5 3.4 - - - -
216A ARG* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.3 17.2 - - + -
34A GLU 3.3 14.1 - - - +
35A GLY* 3.9 0.9 - - - -
40A GLY 5.5 0.4 - - - +
41A THR* 1.3 78.8 - - - +
43A THR* 1.3 64.5 + - - +
66A CH6 4.1 11.4 - - + +
69A SER* 2.6 53.8 + - - -
72A TYR* 3.5 24.4 + - + +
214A TYR* 3.3 9.6 - - - -
215A GLU* 2.9 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.8 4.6 - - - -
33A GLY* 3.1 3.2 - - - -
34A GLU* 2.8 50.4 + - - +
42A GLN* 1.3 79.0 - - - +
44A ALA* 1.3 63.5 + - - +
45A LYS* 5.8 4.5 - - - -
66A CH6 4.8 1.6 - - - -
202A THR* 6.1 0.9 - - + +
213A GLN 3.2 12.1 - - - +
214A TYR* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.8 14.1 - - + -
32A GLU 3.5 8.5 - - - +
43A THR* 1.3 77.4 - - - +
45A LYS* 1.3 62.9 + - - +
46A LEU* 4.0 20.4 - - + -
65A PHE* 5.3 0.2 - - + -
66A CH6 3.5 25.4 - - + -
211A VAL 4.0 0.2 - - - +
212A GLU* 3.3 5.7 - - - +
213A GLN* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.2 2.8 - - - -
32A GLU* 2.9 37.1 + - + +
34A GLU* 6.2 2.2 - - - -
43A THR* 5.8 5.4 - - - -
44A ALA* 1.3 74.4 - - - +
46A LEU* 1.3 62.0 + - - +
210A ILE* 6.3 2.5 - - + -
211A VAL 3.5 4.9 - - - +
212A GLU* 3.5 36.9 + - + +
169C ASP* 4.7 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.8 20.0 - - + -
29A ILE* 4.1 5.4 - - + -
30A GLU 3.4 2.0 - - - -
31A GLY* 3.9 7.6 - - - -
44A ALA* 4.0 18.8 - - + +
45A LYS* 1.3 75.5 - - - +
47A LYS* 1.3 63.2 + - - +
58A TRP* 4.0 25.5 - - + -
65A PHE* 3.8 34.1 - - + -
210A ILE* 3.5 5.7 - - - +
211A VAL* 2.8 39.7 + - - +
213A GLN* 3.9 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.3 5.5 - - - -
30A GLU* 2.7 55.5 + - - +
46A LEU* 1.3 76.4 - - - +
48A VAL* 1.3 64.4 + - - +
49A THR* 3.4 18.9 + - + +
58A TRP* 5.7 0.9 - - - -
209A THR 3.2 11.7 - - - +
210A ILE* 4.7 9.4 - - + -
201B ILE* 5.6 5.1 + - - +
204B HIS* 3.0 36.8 + - + +
208B TYR* 3.4 12.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 3.5 7.4 - - - +
29A ILE* 4.0 13.7 - - + -
47A LYS* 1.3 72.7 - - - +
49A THR* 1.3 60.4 + - - +
50A LYS 3.3 25.6 - - - +
52A GLY* 3.8 21.5 - - - +
54A LEU* 4.1 22.7 - - + -
58A TRP* 4.2 7.6 - - + -
208A TYR 3.8 21.8 - - - +
209A THR* 3.0 26.8 + - + +
204B HIS* 5.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.0 29.1 + - - +
29A ILE 3.9 0.9 + - - -
30A GLU* 3.7 39.8 + - + +
47A LYS* 3.8 23.6 - - + +
48A VAL* 1.3 77.0 - - - +
50A LYS* 1.3 69.1 + - - +
52A GLY 5.7 0.2 - - - -
204B HIS* 5.2 10.8 - - + -
206B GLU* 3.4 26.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
27A PHE* 3.2 5.7 - - - -
28A GLU* 3.0 57.0 + - + +
48A VAL* 3.3 11.1 - - - +
49A THR* 1.3 91.8 + - - +
51A GLY* 1.3 60.4 + - - +
52A GLY 3.4 2.2 - - - -
206B GLU* 3.8 20.6 - - + +
----------------------------------------------------------
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