Contacts of the strand formed by residues 27 - 36 (chain B) in PDB entry 6MZL
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 LYS 27 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG 5.5 4.0 - - - +
25B PRO 3.6 2.0 - - - -
26B TYR* 1.3 75.8 - - - +
28B LEU* 1.3 61.1 - - - +
29B THR* 5.6 0.4 - - + -
54B PHE* 2.8 46.6 + - + +
56B THR* 3.9 10.7 + - - +
198B GLU* 5.4 3.4 - - - -
488B PHE* 5.2 16.8 - - + -
491B HIS* 3.2 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.3 28.5 - - + +
27B LYS* 1.3 79.3 - - - +
29B THR* 1.3 67.6 + - - +
30B HIS 5.3 0.2 - - - +
51B LEU* 5.5 14.1 - - + -
52B THR 3.6 6.3 - - - +
53B ILE* 3.6 30.1 - - + -
65B LEU* 6.2 2.0 - - + -
193B VAL* 3.7 29.2 - - + -
198B GLU* 4.2 16.6 + - + +
199B LEU 3.2 18.4 - - - +
200B CYS* 3.6 18.4 - - - -
488B PHE* 4.8 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 6.4 0.2 - - + -
28B LEU* 1.3 79.3 - - - +
30B HIS* 1.3 70.9 + - - +
52B THR* 3.0 32.8 + - + +
54B PHE* 4.3 31.9 - - + -
199B LEU 4.5 0.9 - - - -
200B CYS* 3.1 9.2 - - - -
201B THR* 2.9 30.5 + - - +
488B PHE* 4.4 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 5.3 0.4 - - - +
29B THR* 1.3 86.9 + - - +
31B GLN* 1.3 74.2 + - - +
32B VAL* 3.4 27.7 - - + +
51B LEU* 3.7 0.9 - - - +
52B THR* 3.0 40.4 + - + +
200B CYS* 4.5 3.6 - - - -
201B THR* 2.7 32.8 + - + +
202B TRP 3.4 8.7 - - - -
203B LYS* 3.3 30.1 + - + +
237B MET* 5.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS* 1.3 79.1 + - - +
32B VAL* 1.3 68.3 + - - +
49B VAL* 3.3 19.5 - - + +
50B GLU 3.3 14.8 - - - +
51B LEU* 4.2 15.4 - - + +
52B THR* 5.1 0.2 - - - -
190B PHE* 3.2 28.6 - - - -
191B PRO 4.0 4.8 + - - -
192B CYS* 3.5 18.7 - - - -
200B CYS* 5.5 3.7 - - + +
201B THR 2.9 5.5 + - - -
202B TRP* 2.6 49.7 + - + +
203B LYS 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS* 3.4 28.9 - - + +
31B GLN* 1.3 74.6 - - - +
33B VAL* 1.3 72.6 + - - +
34B CYS* 5.4 3.4 - - + -
48B PHE* 3.9 8.4 - - + +
49B VAL* 3.3 13.1 - - - +
50B GLU* 3.1 42.7 + - + +
202B TRP* 5.5 0.4 - - - -
203B LYS* 2.9 28.5 - - + +
205B GLU* 5.3 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 1.3 83.2 - - - +
34B CYS* 1.3 69.7 + - - +
35B ILE* 4.6 4.5 - - + +
47B GLY* 6.3 0.7 - - - -
48B PHE 4.0 4.5 - - - +
49B VAL* 5.0 2.2 - - + -
150B PHE* 5.3 8.5 - - + -
189B TRP* 5.6 11.0 - - + -
190B PHE* 4.8 32.1 - - + -
202B TRP* 5.5 0.6 - - + -
203B LYS 3.0 6.5 + - - -
204B LEU* 3.6 26.2 - - + +
205B GLU* 2.8 24.4 + - - +
206B PHE* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 5.4 0.4 - - + -
33B VAL* 1.3 80.8 - - - +
35B ILE* 1.3 64.6 + - - +
36B ASN* 3.0 40.3 + - - -
47B GLY* 3.2 23.3 - - - -
48B PHE* 3.4 38.0 + - + +
205B GLU* 3.1 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.6 6.6 - - + +
34B CYS* 1.3 72.9 - - - +
36B ASN* 1.3 60.0 + - - +
38B ILE* 4.0 25.8 - - + -
45B VAL* 3.7 38.1 - - + -
46B VAL 3.7 3.8 - - - -
47B GLY* 4.7 0.9 - - - -
189B TRP* 6.2 3.6 - - + +
205B GLU 2.9 13.9 + - - +
206B PHE* 3.5 26.9 - - + -
207B THR* 2.5 41.5 + - - +
208B VAL* 6.2 0.4 - - + -
249B LEU* 4.3 7.9 - - + -
251B ILE* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B CYS* 3.0 34.7 + - - -
35B ILE* 1.3 77.9 - - - +
37B ASN* 1.3 76.1 + - - +
38B ILE* 3.2 4.4 + - - -
46B VAL* 2.8 40.2 + - + +
47B GLY* 4.9 1.8 - - - -
48B PHE* 3.8 15.2 - - - -
205B GLU* 5.3 0.9 - - - +
207B THR* 2.4 31.7 + - + +
----------------------------------------------------------
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