Contacts of the strand formed by residues 147 - 155 (chain C) in PDB entry 2IB8
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 VAL 147 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 4.2 14.4 - - + -
85C GLU* 3.4 22.9 - - - +
86C VAL* 4.1 11.2 - - + -
87C LYS* 2.9 31.0 + - - +
140C LEU* 4.2 0.2 - - - -
145C GLN 3.8 0.4 - - - -
146C ASP* 1.3 98.3 + - - +
148C MET* 1.3 67.6 + - - +
294C VAL* 4.3 5.8 - - + -
295C LEU 3.4 10.8 - - - +
296C MET* 3.7 23.6 - - + -
300C ALA* 4.0 11.2 - - + -
304C LEU* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 4.4 4.9 - - - -
88C GLU* 3.4 39.5 - - + +
89C ALA* 4.1 1.3 - - - +
90C TYR* 3.9 36.6 - - + +
136C ALA* 3.9 28.0 - - + +
139C SER* 3.9 22.2 - - - -
140C LEU* 4.1 10.7 - - + +
145C GLN* 4.0 18.8 - - + -
147C VAL* 1.3 81.5 - - - +
149C VAL* 1.3 62.0 + - - +
150C ALA 4.2 0.2 - - - -
294C VAL* 3.7 5.7 - - - +
295C LEU* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 4.3 31.0 - - + +
75C ALA* 5.2 1.3 - - + -
76C ILE* 5.6 1.1 - - + -
86C VAL* 3.9 21.0 - - + +
88C GLU 3.1 4.7 + - - +
89C ALA* 3.3 25.7 - - + -
90C TYR* 3.1 23.0 + - - +
91C MET* 5.5 2.0 - - - -
113C LEU* 4.6 2.9 - - + -
148C MET* 1.3 77.8 - - - +
150C ALA* 1.3 63.1 + - - +
292C ALA* 3.9 25.1 - - + -
293C LEU 3.3 17.3 - - - +
294C VAL* 4.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.2 8.7 - - + +
91C MET* 4.3 3.4 - - - -
132C ALA 3.8 4.5 - - - +
133C ILE* 3.8 32.9 - - + +
136C ALA* 3.8 17.9 - - + -
149C VAL* 1.3 76.7 - - - +
151C GLY* 1.3 58.1 + - - +
292C ALA* 4.5 0.4 - - - -
293C LEU* 2.8 37.1 + - - +
295C LEU* 4.1 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR 3.1 8.1 + - - -
91C MET* 3.5 10.3 - - - -
92C GLY* 2.8 20.6 + - - -
129C GLY* 3.7 5.1 - - - -
132C ALA* 3.4 11.8 - - - +
150C ALA* 1.3 75.7 - - - +
152C GLY* 1.3 58.5 + - - -
291C ALA 3.3 13.2 - - - -
392C ALA* 3.8 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C MET* 3.7 5.3 - - - +
92C GLY 3.3 11.7 - - - -
129C GLY* 4.4 0.4 - - - -
151C GLY* 1.3 75.6 - - - -
153C MET* 1.3 62.8 + - - +
290C ALA* 3.2 3.1 - - - +
291C ALA 2.9 33.4 + - - +
388C GLY 3.3 14.4 - - - -
389C MET* 3.5 10.8 - - - +
392C ALA* 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 3.7 27.1 - - + +
65C THR* 4.1 7.2 - - + +
68C GLY* 4.0 12.6 - - - -
91C MET* 4.1 20.2 - - + -
92C GLY 2.9 15.3 + - - +
93C ASN* 3.3 34.2 + - + +
99C GLU* 5.1 0.2 - - - +
103C PRO* 3.8 42.2 - - + +
104C THR* 4.0 4.9 - - - +
107C ALA* 4.1 11.0 - - - -
152C GLY* 1.3 75.3 - - - +
154C GLU* 1.3 65.1 + - - +
289C GLY 3.5 7.2 - - - -
290C ALA* 3.8 11.0 - - + -
388C GLY* 3.8 1.8 + - - -
389C MET* 3.8 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 3.9 8.0 - - - +
67C LEU* 3.9 2.6 - - - +
93C ASN* 3.0 10.7 + - - -
94C VAL* 2.9 22.5 + - - +
95C LEU* 2.9 35.3 + - + +
99C GLU* 4.5 0.9 - - - +
153C MET* 1.3 74.0 - - - +
155C SER* 1.3 62.6 + - - +
156C MET* 3.8 22.7 - - + +
159C VAL* 5.2 1.1 - - + +
288C ASP* 3.4 2.1 - - - -
289C GLY 3.0 32.7 + - - +
386C PRO* 3.8 23.3 - - + -
387C ILE* 3.9 12.3 - - + +
388C GLY* 2.8 24.9 + - - +
389C MET* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU 3.4 7.3 + - - -
64C ALA* 3.5 35.1 - - - +
67C LEU* 4.7 2.0 - - - -
99C GLU* 5.1 0.6 + - - +
154C GLU* 1.3 73.9 + - - +
156C MET* 1.3 64.7 + - - +
157C SER* 3.2 0.6 - - - -
158C ASN* 2.9 40.5 + - - +
159C VAL* 3.4 14.2 + - - +
288C ASP* 3.4 14.4 + - - -
----------------------------------------------------------
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