Contacts of the strand formed by residues 108 - 118 (chain C) in PDB entry 2BBV
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 108 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA* 1.3 78.7 - - + +
109C ARG* 1.3 67.9 + - - +
129C PRO* 4.5 1.6 - - - +
130C ALA* 3.8 23.1 + - - +
303C ALA 2.6 18.7 + - - -
304C PRO* 3.6 2.8 + - - +
305C THR* 2.7 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C THR* 3.3 30.3 - - - +
107C ALA 3.6 5.4 - - - +
108C ASN* 1.3 84.7 + - - +
110C ASP* 1.3 69.5 + - - +
111C THR* 4.0 2.4 + - - +
127C ASP* 2.6 49.4 + - + -
128C VAL* 3.1 38.5 - - - +
129C PRO* 3.5 24.6 - - - +
130C ALA* 3.6 5.8 - - - +
301C VAL 4.0 0.7 - - - +
303C ALA* 3.4 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG* 1.3 78.9 - - - +
111C THR* 1.3 62.2 - - - +
112C PHE* 3.9 13.9 + - + -
127C ASP* 3.2 2.5 - - - -
128C VAL* 2.8 33.5 + - + +
129C PRO 4.6 0.2 - - - -
130C ALA* 3.0 14.9 - - - +
131C GLY* 3.2 25.0 + - - -
132C THR 3.9 6.0 - - - +
300C ARG* 3.8 28.1 + - + -
301C VAL 3.1 7.4 - - - +
302C SER* 2.6 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 5.4 1.3 - - + -
104C ASN 6.0 0.4 - - - +
105C PHE* 3.7 45.8 - - + +
106C THR* 4.5 8.2 + - + +
109C ARG 4.0 1.9 + - - -
110C ASP* 1.3 74.2 + - - +
112C PHE* 1.3 59.3 + - - +
113C ILE* 4.1 3.7 + - + +
125C VAL* 3.4 31.9 - - + -
126C ALA 3.4 4.9 - - - +
127C ASP* 3.8 15.6 + - + +
299C ILE 3.6 0.9 - - - +
300C ARG* 3.1 5.7 - - - -
301C VAL* 2.6 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP* 3.9 12.6 - - + -
111C THR* 1.3 72.4 - - - -
113C ILE* 1.3 62.2 + - - +
124C TRP 3.6 0.7 - - - +
125C VAL* 3.3 6.8 - - - +
126C ALA 2.4 48.8 + - - +
128C VAL* 4.1 6.7 - - + -
132C THR 3.8 16.6 - - - -
133C PHE* 3.2 42.2 - + - -
134C PRO* 4.0 16.8 - - + -
140C PHE* 3.6 21.5 - - + -
191C TRP* 3.8 6.7 - + - -
223C VAL* 3.8 22.9 - - + -
298C VAL* 4.1 9.0 - - + -
299C ILE 3.5 0.7 - - - -
300C ARG* 3.5 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 3.7 29.4 - - + -
105C PHE* 3.8 18.8 - - + -
111C THR* 4.5 2.7 - - + -
112C PHE* 1.3 80.5 - - - +
114C LEU* 1.3 67.6 + - - +
115C ILE* 3.4 25.4 - - + +
123C TYR* 3.6 24.0 - - + -
124C TRP 3.4 1.3 - - - -
125C VAL* 4.0 14.1 - - + -
175C ILE* 4.8 7.4 - - + -
297C ILE 3.5 1.2 - - - +
298C VAL* 3.3 6.1 - - - +
299C ILE* 2.7 44.9 + - + +
301C VAL* 5.0 4.0 - - + -
313C LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 5.6 0.2 - - + -
113C ILE* 1.3 78.0 - - - +
115C ILE* 1.3 62.8 - - - +
116C ALA* 3.6 7.7 + - + +
123C TYR* 3.2 6.1 - - - -
124C TRP* 2.7 50.4 + - + +
140C PHE* 3.8 34.1 - - + -
220C LEU* 5.0 5.2 - - + -
223C VAL* 3.9 25.4 - - + -
276C PHE* 4.4 7.2 - - + -
278C LEU* 4.4 17.5 - - + -
291C TRP* 6.5 0.7 - - + -
296C THR* 4.6 8.1 - - - +
297C ILE 3.4 2.0 - - - +
298C VAL* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ILE* 3.4 29.8 - - + +
114C LEU* 1.3 70.5 - - - +
116C ALA* 1.3 59.4 + - - +
122C ALA 4.1 10.5 - - - +
123C TYR* 4.1 11.0 - - + -
171C MET* 3.6 31.9 - - + +
172C ASN 5.1 2.7 - - - +
173C VAL* 2.9 39.5 - - + -
296C THR* 3.0 5.9 - - - -
297C ILE* 2.7 55.7 + - + +
299C ILE* 3.8 15.5 - - + -
313C LEU* 5.9 1.6 - - + -
315C THR* 5.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 3.6 8.6 + - + -
115C ILE* 1.3 76.7 - - - +
117C PRO* 1.3 61.6 - - + +
118C THR* 2.7 29.2 + - + +
121C VAL 4.5 4.9 - - - +
122C ALA 4.9 3.1 + - - +
124C TRP* 4.3 15.1 + - + -
168C TYR* 4.2 1.4 + - - -
171C MET* 3.8 6.1 - - - +
278C LEU* 5.7 0.2 - - + -
291C TRP* 3.6 28.0 - - + -
296C THR* 3.7 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE 4.5 0.2 - - - +
116C ALA* 1.3 82.8 - - + +
118C THR* 1.3 57.5 + - - +
119C PRO* 3.4 1.4 - - - +
168C TYR* 2.9 22.8 - - + +
171C MET* 3.1 27.1 - - + -
291C TRP* 3.3 20.1 - - - +
292C GLY* 2.8 47.8 + - - +
294C MET* 3.6 23.8 - - + +
296C THR* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 2.7 14.3 + - + +
117C PRO* 1.3 70.1 - - - +
119C PRO* 1.3 74.1 - - - +
120C GLY 3.4 0.2 + - - -
121C VAL* 3.1 27.8 + - - +
124C TRP* 3.2 37.5 + - + +
168C TYR* 2.9 5.7 + - - -
288C ILE* 4.6 9.4 - - + -
290C GLY 3.6 6.5 - - - +
291C TRP* 3.1 44.0 - - + -
----------------------------------------------------------
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