Contacts of the strand formed by residues 129 - 134 (chain G) in PDB entry 2J28
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 GLU 129 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LYS* 5.1 13.9 - - + +
86G LEU 4.3 9.0 - - - +
87G GLN* 4.8 15.3 - - + +
124G CYS* 2.9 31.0 - - - +
125G PRO* 3.1 30.3 - - + +
126G THR* 3.2 14.7 + - + +
128G THR* 1.3 81.1 - - + +
130G ILE* 1.3 68.2 + - - +
131G VAL* 5.7 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LYS* 3.3 3.4 - - - +
86G LEU* 2.9 55.7 + - + +
87G GLN* 5.1 0.2 - - - +
88G LEU* 4.4 15.5 - - + -
95G ALA* 3.4 26.0 - - + -
96G ALA 4.2 1.1 - - - +
97G VAL* 4.4 1.8 - - + -
102G ILE* 3.4 39.3 - - + -
104G LEU* 5.4 3.1 - - + -
122G ALA* 4.4 11.7 - - + -
123G GLU 3.5 1.6 - - - +
124G CYS* 3.4 14.6 - - + -
125G PRO* 4.8 0.4 - - - -
129G GLU* 1.3 83.6 - - - +
131G VAL* 1.3 65.1 + - - +
132G LEU 4.6 0.7 - - - +
147G LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G THR* 3.6 24.0 - - - +
85G LYS* 3.5 23.6 - - + -
122G ALA* 3.4 3.0 - - - -
123G GLU* 2.8 58.5 + - + +
125G PRO* 4.2 11.9 - - + -
129G GLU* 5.7 2.2 - - - +
130G ILE* 1.3 72.9 - - - +
132G LEU* 1.3 62.6 + - - +
133G LYS* 4.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G THR* 3.6 1.9 + - - -
84G LYS* 2.7 57.2 + - + +
86G LEU* 4.2 23.3 - - + -
116G LEU* 6.1 0.7 - - + -
120G ILE* 4.1 3.4 - - + -
121G THR 3.4 11.9 - - - +
122G ALA* 4.0 8.9 - - + +
130G ILE* 4.0 1.7 - - + +
131G VAL* 1.3 75.0 - - - +
133G LYS* 1.3 64.1 + - - +
140G ILE* 3.7 37.7 - - + +
143G VAL* 3.5 30.5 - - + -
144G ALA* 4.3 15.3 - - - -
147G LEU* 4.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G PHE 2.9 16.6 - - - +
83G THR* 3.8 14.1 - - - +
120G ILE* 3.4 5.5 - - - +
121G THR* 3.1 27.9 + - - +
123G GLU* 3.3 39.8 + - + +
131G VAL* 4.4 5.8 - - + +
132G LEU* 1.3 79.3 - - - +
134G GLY* 1.3 57.1 + - - +
140G ILE* 4.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASN* 4.5 5.6 - - - -
81G GLY* 4.8 0.9 - - - -
82G PHE* 2.7 43.0 + - - +
119G GLY 3.1 16.4 - - - -
120G ILE* 3.4 9.4 - - - -
133G LYS* 1.3 74.8 - - - +
135G ALA* 1.3 56.9 + - - -
140G ILE* 3.4 7.9 - - - +
----------------------------------------------------------
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