Contacts of the strand formed by residues 145 - 150 (chain C) in PDB entry 2VUU
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 SER 145 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C HIS* 4.4 2.7 - - - -
108C TYR* 3.0 19.1 - - - +
138C VAL* 3.6 14.4 + - - +
139C ARG* 4.9 3.3 + - - +
143C LEU 2.7 17.9 + - - -
144C PRO* 1.3 71.7 - - - +
146C THR* 1.3 62.1 + - - +
147C PHE* 3.3 29.9 - - - -
212C ASN* 3.2 10.7 + - - -
213C GLY* 2.6 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C HIS* 3.0 25.2 + - - -
108C TYR 3.3 3.9 + - - +
109C ILE* 3.2 13.7 - - + +
110C TYR 3.1 23.4 + - - -
145C SER* 1.3 70.7 + - - +
147C PHE* 1.3 69.2 + - - +
148C VAL* 4.8 1.6 - - + -
203C ILE* 4.2 12.3 - - + -
211C TRP* 2.6 29.2 + - + +
214C HIS* 3.5 13.9 - - + +
216C ILE* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.3 31.0 - + + -
112C SER* 3.7 13.0 - - - +
135C GLU* 3.3 47.8 - - + +
138C VAL* 3.7 14.8 - - + -
139C ARG* 3.6 37.7 - - + -
145C SER* 3.3 37.2 - - - -
146C THR* 1.3 74.8 - - - +
148C VAL* 1.3 58.9 + - - +
149C TYR* 3.8 5.5 - - + -
213C GLY* 4.8 1.3 - - - -
214C HIS 2.8 16.5 + - - +
215C ARG* 3.2 3.7 - - - -
216C ILE* 2.7 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 4.4 8.1 - - + -
109C ILE* 4.0 17.5 - - + -
110C TYR 3.1 4.6 + - - +
111C SER* 3.5 27.9 + - - +
112C SER 2.8 27.9 + - - +
146C THR* 4.1 2.0 + - + -
147C PHE* 1.3 76.6 - - - +
149C TYR* 1.3 61.7 + - - +
150C ALA 4.0 0.2 - - - -
200C LEU* 4.2 8.7 - - + -
203C ILE* 3.7 29.2 - - + -
216C ILE* 3.1 13.9 - - + +
218C LEU* 4.4 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C SER* 3.2 27.1 - - - +
113C MET* 3.7 27.1 - - - -
114C PRO* 3.9 17.0 - - + -
132C PHE* 3.8 10.2 - - - -
135C GLU* 2.7 20.1 + - - -
147C PHE* 3.8 11.0 - - + -
148C VAL* 1.3 77.2 - - - +
150C ALA* 1.3 62.1 + - - +
215C ARG* 3.0 35.9 + - + -
216C ILE 2.7 14.9 + - - +
217C ALA* 3.4 5.2 - - - -
218C LEU* 2.5 29.5 + - - -
277C PHE* 3.5 22.5 - + + -
279C LEU* 4.5 13.6 - - + +
282C PHE* 4.1 13.0 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
17C GLN* 3.6 23.8 - - - +
111C SER* 4.9 3.6 + - - +
112C SER 4.4 1.0 + - - -
113C MET* 4.0 6.2 - - - +
148C VAL 4.0 2.4 + - - -
149C TYR* 1.3 73.2 - - - +
151C GLY* 1.3 64.0 + - - +
153C TYR* 4.5 0.9 - - + -
190C LEU* 4.0 11.7 - - + -
218C LEU* 3.8 14.1 - - + +
276C TYR* 3.4 10.4 - - - -
277C PHE* 3.0 17.7 - - - -
1353C NAP 3.5 25.7 - - + -
----------------------------------------------------------
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