Contacts of the strand formed by residues 52 - 59 (chain B) in PDB entry 1Z9N
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 GLY 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER* 2.7 41.1 + - - -
50B ALA 3.7 0.6 - - - -
51B TYR* 1.3 80.6 - - - +
53B LEU* 1.3 67.7 + - - -
133B LEU* 3.6 2.9 - - - +
134B ALA 3.6 5.6 - - - -
135B PRO 4.3 3.1 - - - -
137B LEU 3.1 15.7 - - - -
138B LYS* 4.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.1 9.9 - - + -
47B THR 3.3 7.2 - - - +
48B GLU* 3.6 31.9 - - + -
52B GLY* 1.3 72.3 - - - -
54B VAL* 1.3 59.4 + - - +
55B PHE* 3.9 14.8 - - + -
133B LEU* 3.5 3.1 - - - +
134B ALA* 2.8 33.1 + - - +
137B LEU* 2.9 38.5 + - + +
138B LYS 3.8 13.0 - - - +
139B LYS 3.8 18.8 - - - +
140B LEU* 4.0 6.1 - - + -
143B VAL* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TRP* 3.6 52.7 - - + +
45B GLU 3.3 1.9 - - - +
46B ILE* 3.2 7.1 - - - +
47B THR* 2.7 47.1 + - - +
48B GLU 5.1 0.2 - - - -
49B SER* 3.8 17.5 - - - -
53B LEU* 1.3 76.7 - - - +
55B PHE* 1.3 63.2 + - - +
56B THR* 3.7 19.1 - - - +
131B PRO* 4.1 3.4 - - + -
132B VAL 3.5 6.7 - - - +
133B LEU* 3.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 4.1 9.4 - - + -
45B GLU 3.5 3.1 - - - -
46B ILE* 3.6 39.5 - - + -
53B LEU* 3.9 29.4 - - + -
54B VAL* 1.3 74.7 - - - +
56B THR* 1.3 60.3 + - - +
57B PRO* 3.5 5.0 - - - +
69B PHE* 4.0 17.5 - + + -
71B ILE* 4.1 22.7 - - + -
117B LEU* 3.9 26.2 - - + -
131B PRO* 3.2 3.1 - - - +
132B VAL* 2.9 40.9 + - + +
134B ALA* 3.9 15.7 - - + -
137B LEU* 4.4 5.6 - - + -
143B VAL* 4.9 0.4 - - + -
148B LEU* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 5.7 0.7 - - - +
44B VAL* 3.6 1.5 - - - +
45B GLU* 2.8 47.4 + - - +
47B THR* 4.8 3.9 + - - +
54B VAL* 3.7 18.4 + - - +
55B PHE* 1.3 72.3 - - - +
57B PRO* 1.3 70.9 - - + +
58B LYS* 3.7 17.6 + - + +
129B THR 5.1 2.7 - - - +
131B PRO* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR 3.9 4.7 - - - +
44B VAL* 4.1 8.7 - - + -
55B PHE 3.5 7.8 - - - +
56B THR* 1.3 89.0 - - + +
58B LYS* 1.3 65.0 - - - +
59B LEU* 4.0 11.7 - - + -
69B PHE* 5.9 1.8 - - + -
120B LEU* 3.8 27.6 - - + -
128B ALA 3.3 20.5 - - - +
129B THR* 3.4 13.2 - - - +
130B THR 3.4 42.2 - - - +
131B PRO* 3.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 4.7 3.2 - - - +
42B GLY* 3.5 6.4 - - - -
43B THR* 2.8 44.2 + - - +
45B GLU* 2.8 43.5 + - + +
56B THR* 4.2 14.8 - - + +
57B PRO* 1.3 78.4 - - - +
59B LEU* 1.3 57.5 + - - +
60B HIS* 4.8 2.5 - - - -
128B ALA 3.8 1.3 - - - -
129B THR* 5.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.8 24.9 - - + -
41B VAL* 3.1 19.3 - - + +
43B THR 3.4 29.2 - - - +
44B VAL* 3.9 13.0 - - + -
57B PRO* 4.0 10.8 - - + -
58B LYS* 1.3 77.9 - - - +
60B HIS* 1.3 64.0 + - - +
62B LEU* 3.9 17.7 - - + -
120B LEU* 4.1 9.4 - - + -
126B GLY 4.4 0.4 - - - -
127B SER* 3.3 7.3 - - - -
128B ALA* 3.0 33.9 + - + +
129B THR* 4.9 1.7 - - - +
150B ILE* 3.7 28.3 - - + -
----------------------------------------------------------
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