Contacts of the strand formed by residues 74 - 80 (chain B) in PDB entry 4NZD
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 ILE 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TRP* 3.4 4.1 - - - -
33B GLN* 2.5 60.2 + - + +
34B ASP 4.0 14.8 - - - +
35B GLN* 4.6 7.9 - - - +
37B GLU* 5.2 10.1 - - + -
72B ASP 3.7 10.1 - - - +
73B ASP* 1.3 81.4 - - - +
75B PHE* 1.3 61.2 + - - +
92B SER* 3.9 25.8 - - - +
93B PHE 3.5 12.1 - - - +
94B LEU* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS* 3.6 37.7 - - + -
7B TYR 4.6 2.7 - - - -
8B THR* 4.9 9.4 - - + -
14B VAL* 4.3 10.8 - - + -
30B LEU* 3.5 35.4 - - + -
31B THR 3.5 3.1 - - - +
32B TRP* 3.5 46.2 - + + -
74B ILE* 1.3 73.7 - - - +
76B SER* 1.3 59.9 + - - +
77B VAL* 4.5 2.2 - - + -
93B PHE* 2.9 69.8 + + + -
95B LEU* 5.0 4.3 - - - -
98B SER* 4.4 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.3 5.4 - - - +
31B THR 3.0 30.3 + - - -
33B GLN* 2.8 27.9 + - - -
74B ILE* 4.2 0.3 - - - +
75B PHE* 1.3 73.4 - - - +
77B VAL* 1.3 65.8 + - - +
78B GLN* 3.5 17.4 + - - -
89B GLU* 4.0 11.2 + - - -
91B GLY 3.4 10.8 - - - -
92B SER* 3.1 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.7 22.9 - - + -
6B CYS* 4.0 15.5 - - - -
16B CYS* 4.3 5.4 - - - -
28B LEU* 3.6 33.0 - - + -
29B THR 3.4 10.3 - - - +
30B LEU* 4.5 13.7 - - + -
48B LEU* 5.0 2.5 - - + -
75B PHE* 4.5 0.7 - - + -
76B SER* 1.3 79.9 - - - +
78B GLN* 1.3 64.6 + - - +
89B GLU* 2.7 21.8 - - - +
90B CYS* 3.1 15.7 + - + +
91B GLY 3.2 6.0 + - - +
93B PHE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR 3.3 3.8 - - - +
28B LEU* 3.5 5.7 - - - +
29B THR* 2.9 63.5 + - - +
31B THR* 3.2 34.0 + - - +
33B GLN* 4.9 0.4 - - - +
76B SER* 3.5 24.3 + - - +
77B VAL* 1.3 77.4 - - - +
79B ILE* 1.3 64.4 + - - +
80B THR* 4.2 2.7 - - - +
87B SER* 4.6 10.8 - - - +
88B GLN 3.3 13.5 - - - +
89B GLU* 4.0 13.9 + - - +
90B CYS* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CYS* 4.0 6.3 - - - -
2B PRO* 4.1 10.5 - - + -
18B LEU* 4.7 7.2 - - + -
23B LEU* 4.1 13.7 - - + -
26B SER* 4.2 18.2 - - - -
27B THR 3.3 5.8 - - - +
28B LEU* 3.7 19.1 - - + -
78B GLN* 1.3 74.3 - - - +
80B THR* 1.3 67.4 + - - +
86B TYR 3.9 0.5 - - - +
87B SER* 3.4 4.2 + - - -
88B GLN* 2.8 48.9 + - + +
90B CYS* 3.4 24.8 - - - -
159C VAL* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 4.8 4.7 - - - +
26B SER* 3.2 5.4 - - - -
27B THR* 2.6 48.4 + - - -
29B THR* 5.0 9.0 + - - +
78B GLN* 5.2 1.9 - - - +
79B ILE* 1.3 77.5 + - - +
81B ASP* 1.3 72.8 + - - +
84B GLY* 3.5 22.2 - - - +
86B TYR 3.3 15.8 + - - +
87B SER* 4.1 10.7 + - - -
----------------------------------------------------------
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