Contacts of the strand formed by residues 82 - 88 (chain G) in PDB entry 3BBX
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 PHE 82 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G SER* 3.6 17.7 - - - -
76G ILE* 3.6 27.6 - - + -
77G GLY* 3.6 11.7 - - - -
81G GLY* 1.3 75.3 - - - -
83G THR* 1.3 68.7 + - - +
132G LEU* 3.3 7.9 - - - +
133G LYS* 3.4 1.9 - - - -
134G GLY 2.7 40.9 + - - +
135G ALA 3.0 31.4 - - - -
137G LYS* 3.9 42.8 - - + -
140G ILE* 4.7 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLY 4.3 3.5 + - - +
82G PHE* 1.3 85.4 - - - +
84G LYS* 1.3 71.5 + - - +
85G LYS* 6.3 0.9 - - - -
131G VAL* 4.6 11.9 - - + -
132G LEU* 3.2 16.6 - - - +
133G LYS* 5.0 5.6 - - + -
140G ILE* 5.2 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2746B U 4.8 14.1 - - - +
83G THR* 1.3 82.9 + - - +
85G LYS* 1.3 101.3 + - - +
86G LEU* 4.2 1.6 - - - +
130G ILE 3.5 1.7 - - - +
131G VAL* 4.8 0.2 - - - +
132G LEU* 3.1 49.5 + - + +
140G ILE* 4.6 6.1 - - + -
144G ALA* 4.6 2.9 - - + -
163G TYR* 4.0 36.6 - - + -
164G ALA* 4.4 9.2 - - - +
165G ASP* 5.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G THR* 6.3 0.7 - - - -
84G LYS* 1.3 80.2 + - - +
86G LEU* 1.3 73.6 + - - +
87G GLN* 5.0 10.2 - - - +
125G PRO* 5.5 2.7 - - + -
129G GLU* 2.8 33.2 + - + +
130G ILE 2.9 12.3 - - - +
131G VAL* 4.2 20.0 - - + -
163G TYR* 3.4 7.6 - - - -
164G ALA* 3.4 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LYS 4.2 7.6 - - - +
85G LYS* 1.3 87.7 - - - +
87G GLN* 1.3 63.1 + - - +
129G GLU* 3.4 8.2 - - - +
130G ILE* 2.7 48.1 + - + +
132G LEU* 5.2 0.2 - - + -
144G ALA* 4.3 4.9 - - + +
147G LEU* 4.2 26.9 - - + -
148G ARG* 4.3 4.5 - - + -
161G VAL* 3.5 26.7 - - + +
162G ARG 3.3 27.6 - - - +
163G TYR* 3.3 32.8 - - + +
164G ALA 4.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LYS* 5.0 12.0 - - - +
86G LEU* 1.3 73.9 - - - +
88G LEU* 1.3 62.3 + - - +
89G VAL* 3.4 9.1 + - + -
128G THR* 4.1 6.5 - - - +
129G GLU* 4.9 7.9 - - + +
161G VAL* 3.8 0.9 - - - -
162G ARG* 2.8 49.1 + - + +
163G TYR 3.4 4.3 - - - +
164G ALA* 2.6 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G GLN* 1.3 70.7 - - - +
89G VAL* 1.3 62.2 + - - +
90G GLY 3.8 5.7 + - - +
93G TYR* 4.0 20.9 - - + +
94G ARG* 3.5 13.2 - - - +
95G ALA* 3.0 43.3 - - + +
104G LEU* 5.3 4.3 - - + -
106G LEU* 5.2 6.7 - - + -
128G THR* 3.0 30.6 + - - +
130G ILE* 3.4 20.9 - - + -
160G GLY 4.0 1.6 - - - -
161G VAL* 3.5 35.7 - - + -
----------------------------------------------------------
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