Contacts of the strand formed by residues 61 - 66 (chain B) in PDB entry 3KJR
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 ASN 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR 3.1 34.6 + - - +
46B THR* 3.5 7.4 - - - +
47B TYR 3.0 24.0 + - - -
48B ILE* 3.6 6.4 - - - +
60B GLN* 1.3 75.0 - - - +
62B VAL* 1.3 58.5 + - - +
82B ASN 4.7 3.4 + - - -
83B ARG* 3.6 6.9 - - + +
84B ILE* 2.8 30.5 + - - -
118B ASN* 3.1 25.1 + - - +
119B LYS* 3.1 18.3 + - - +
121B PHE* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN 4.1 0.2 + - - -
61B ASN* 1.3 74.3 - - - +
63B VAL* 1.3 64.7 + - - +
64B ILE* 3.7 25.6 - - + -
84B ILE* 3.5 20.4 - - + +
86B VAL* 3.7 17.9 - - + -
111B LEU* 3.9 18.8 - - + -
117B HIS* 3.6 36.3 - - + +
119B LYS 2.8 14.5 + - - +
120B ILE* 3.9 9.2 - - + -
121B PHE* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 4.1 14.1 - - - +
62B VAL* 1.3 78.0 - - - +
64B ILE* 1.3 56.5 + - - +
65B PHE* 3.2 32.5 - - + -
80B LEU* 3.9 7.9 - - + -
83B ARG* 4.0 29.2 - - + -
84B ILE 2.7 15.2 + - - +
85B ASN* 3.6 2.6 - - - +
86B VAL* 2.8 32.1 + - - +
121B PHE* 3.6 6.1 - - + -
123B LEU* 3.4 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.7 13.5 - - + -
63B VAL* 1.3 77.5 - - - +
65B PHE* 1.3 64.5 + - - +
86B VAL* 3.3 15.3 - - + +
88B LEU* 4.0 23.6 - - + -
104B LEU* 4.7 2.5 - - + -
107B ALA* 5.2 3.1 - - + -
108B ILE* 3.7 20.2 - - + -
111B LEU* 4.2 12.3 - - + -
120B ILE* 3.6 24.5 - - + -
121B PHE 2.9 13.9 + - - +
122B ILE* 4.2 9.9 - - + -
123B LEU* 2.9 31.5 + - - +
124B GLY 3.9 1.0 + - - -
128B LEU* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.2 37.0 - - + -
64B ILE* 1.3 73.0 - - - +
66B GLY* 1.3 69.8 + - - +
69B THR* 3.8 23.1 - - + -
70B TYR* 4.3 17.9 - - + +
78B LEU* 5.4 9.9 - - + -
80B LEU* 3.6 21.8 - - + -
85B ASN* 4.0 17.3 - - + -
86B VAL 2.9 18.8 + - - -
87B ILE* 3.5 8.8 - - + -
88B LEU* 2.9 30.8 + - - +
123B LEU* 4.0 21.8 - - + -
124B GLY 3.9 4.5 - - - -
128B LEU* 3.7 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 1.3 80.1 - - - +
67B ARG* 1.3 66.1 + - - -
68B LYS 3.4 2.5 - - - -
69B THR 3.4 2.1 + - - -
70B TYR* 3.3 17.2 + - - +
87B ILE* 4.8 0.7 - - - -
88B LEU* 3.8 5.2 - - - -
124B GLY 3.0 16.7 + - - -
128B LEU* 3.8 4.4 - - - +
512B NAP 3.6 32.3 + - - -
----------------------------------------------------------
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