Contacts of the strand formed by residues 41 - 45 (chain G) in PDB entry 2ZJP
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 TRP 41 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLN* 3.0 43.4 + - - +
40G ASN* 1.3 74.4 + - - +
42G VAL* 1.3 66.4 + - - +
43G VAL* 5.0 2.9 - - + -
79G PHE* 3.2 48.2 - + + -
81G VAL* 3.6 25.9 - - + +
149G LYS* 4.4 13.5 - - + -
161G GLN* 5.1 4.1 - - + +
163G PRO* 3.4 28.7 - - + +
164G GLN* 2.7 61.4 - - + +
165G VAL* 3.0 14.9 - - + -
166G LEU 3.9 1.8 - - - -
6X A 5.7 1.1 - - - -
7X G 3.3 35.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ASN* 3.1 19.5 + - - +
41G TRP* 1.3 79.8 - - - +
43G VAL* 1.3 77.6 + - - +
44G VAL* 4.4 7.9 - - + +
61G ARG* 3.9 26.9 - - - +
78G ASP* 5.5 0.2 - - + -
79G PHE 3.6 15.2 + - - +
80G VAL* 5.1 2.7 - - + -
81G VAL* 3.7 20.6 + - - +
166G LEU* 2.6 32.1 - - + +
168G THR* 2.8 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G TRP* 3.8 1.6 - - + +
42G VAL* 1.3 87.1 - - - +
44G VAL* 1.3 66.3 + - - +
81G VAL* 3.8 14.4 - - + -
83G ILE* 4.3 7.9 - - + -
158G HIS* 4.0 16.8 - - + -
161G GLN* 3.2 31.0 - - - +
164G GLN 4.6 0.4 - - - +
165G VAL* 3.4 37.7 - - + +
166G LEU 3.0 2.8 + - - -
167G LYS* 3.0 36.1 - - + +
168G THR 3.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL* 4.6 6.1 - - + -
43G VAL* 1.3 79.6 - - - +
45G ASP* 1.3 85.6 + - - +
54G LEU* 3.4 19.5 - - + -
57G LEU* 4.5 7.9 - - + -
58G ILE* 4.0 16.6 - - + -
61G ARG* 5.8 3.4 - - - -
80G VAL* 3.8 25.6 - - + -
81G VAL 2.9 11.0 + - - +
82G VAL* 4.7 1.8 - - + -
83G ILE* 3.4 27.6 + - - +
167G LYS* 5.1 1.3 - - - -
168G THR* 4.5 10.1 - - - +
169G GLN* 4.6 5.4 - - - +
170G PRO* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G VAL* 1.3 82.3 - - - +
46G ALA* 1.3 59.2 + - - +
47G SER* 2.8 42.7 + - - +
49G VAL* 4.8 1.1 - - + +
54G LEU* 3.0 16.6 - - - +
83G ILE* 3.5 20.3 - - + +
84G ASN* 3.6 9.0 + - - -
167G LYS* 4.0 16.0 + - + -
169G GLN* 4.7 7.7 - - + +
170G PRO* 3.5 21.8 - - + +
----------------------------------------------------------
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