Contacts of the strand formed by residues 31 - 34 (chain B) in PDB entry 1KJ4
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 31 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 1.3 75.0 - - - +
32B VAL* 1.3 55.2 + - - +
33B LEU* 4.1 18.4 - - + -
64B VAL* 6.3 0.2 - - + -
74B THR 3.9 9.8 + - - -
75B VAL* 4.6 12.1 - - + -
76B LEU* 2.8 37.7 + - - +
84B ILE 3.0 18.4 - - - +
85B ILE* 3.7 9.9 - - + -
86B GLY 2.9 13.5 + - - -
88B ASN* 2.7 23.8 + - - -
89B LEU* 4.0 15.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
50A ILE* 5.4 0.9 - - + -
30B ASP* 4.2 2.9 + - + -
31B THR* 1.3 78.6 - - - +
33B LEU* 1.3 64.0 + - - +
47B ILE* 3.4 35.4 - - + -
54B ILE* 4.8 0.2 - - + -
56B VAL* 4.4 10.3 - - + -
76B LEU* 3.2 16.6 - - + +
78B GLY 4.6 1.6 - - - +
80B THR* 3.8 28.5 - - + +
82B VAL 4.0 1.9 - - - +
83B ASN* 3.5 1.9 - - - -
84B ILE* 2.6 39.8 + - + +
7P ILE* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.3 15.5 - - + -
15B ILE* 3.6 34.3 - - + -
20B LYS* 5.4 3.8 - - + -
22B ALA* 5.1 2.2 - - + -
31B THR* 4.1 13.5 - - + -
32B VAL* 1.3 80.1 - - - +
34B GLU* 1.3 71.8 + - - +
36B MET* 4.1 12.3 - - - -
64B VAL* 6.0 0.7 - - + -
75B VAL* 3.5 29.6 - - + -
76B LEU 2.9 9.8 + - - +
77B VAL* 3.5 4.4 - - + -
78B GLY 3.2 20.6 + - - -
80B THR* 3.3 8.8 - - - +
83B ASN* 3.4 22.9 - - + +
84B ILE 4.2 4.0 - - - +
85B ILE* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 5.9 0.3 - - - -
33B LEU* 1.3 76.9 - - - +
35B GLU* 1.3 70.2 + - - +
36B MET* 3.1 13.0 + - - +
77B VAL* 3.7 2.8 - - - +
78B GLY 3.8 0.9 - - - -
80B THR* 3.5 29.6 - - + +
81B PRO 4.4 5.4 - - - +
82B VAL* 4.2 3.2 - - - -
83B ASN* 2.6 44.4 + - - +
44C PRO 5.7 2.9 - - - +
45C LYS* 2.9 41.8 + - - +
46C MET 5.3 0.3 + - - +
58C GLN* 5.3 0.3 - - - +
----------------------------------------------------------
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