Contacts of the helix formed by residues 114 - 122 (chain A) in PDB entry 1BO1
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 ASP 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.9 20.2 - - + +
57A LEU* 4.3 10.4 - - - +
104A ARG* 4.2 18.0 + - - +
107A ARG* 2.6 47.9 + - - +
112A ILE 3.6 2.1 + - - +
113A ASP* 1.3 74.1 + - - +
115A GLN* 1.3 56.7 + - - +
117A TYR* 3.1 8.0 + - - +
118A GLN* 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 5.2 0.7 - - - -
113A ASP* 3.1 13.0 + - - +
114A ASP* 1.3 76.4 - - - +
116A ASP* 1.3 65.2 + - - +
118A GLN* 4.0 19.5 - - - +
119A ASN* 2.8 55.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 5.0 3.6 - - + -
113A ASP* 2.8 33.0 + - + +
115A GLN* 1.3 80.0 - - - +
117A TYR* 1.3 63.9 + - - +
119A ASN* 4.0 7.5 + - - +
120A SER* 2.8 31.1 + - - +
147A PHE* 4.7 3.1 - - + -
349A TYR* 5.7 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.8 9.9 - - + +
54A ILE* 3.3 29.4 - - + -
107A ARG* 3.9 20.2 - - - -
112A ILE* 4.0 9.8 - - + +
113A ASP 2.8 11.7 + - - +
114A ASP* 3.2 9.9 - - - +
116A ASP* 1.3 79.6 - - - +
118A GLN* 1.3 61.3 + - - +
120A SER* 3.4 8.5 + - - -
121A VAL* 3.4 20.4 + - + +
147A PHE* 3.9 25.6 - + - -
184A LEU* 4.0 25.8 - - + -
185A GLY* 4.3 2.9 - - - -
187A TYR* 3.0 28.6 + - - -
200A VAL* 3.1 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 4.2 15.9 - - - +
51A ASN* 3.0 46.1 + - - +
54A ILE* 3.1 22.1 - - + +
55A ASN* 3.0 29.6 + - - +
114A ASP 2.8 15.5 + - - +
115A GLN* 3.7 20.2 - - - +
116A ASP 3.3 0.2 - - - -
117A TYR* 1.3 77.9 - - - +
119A ASN* 1.3 62.1 + - - +
121A VAL* 3.1 4.0 + - - +
122A THR* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 5.8 2.4 - - - +
115A GLN* 2.8 49.1 + - - +
116A ASP* 4.1 7.9 + - - +
118A GLN* 1.3 75.5 - - - +
120A SER* 1.3 62.1 + - - +
121A VAL 3.0 1.8 - - - -
122A THR* 3.8 9.2 + - - -
123A ARG* 2.9 48.8 + - + +
143A TYR* 3.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 2.8 23.1 + - - +
117A TYR 3.6 2.2 - - - -
118A GLN 3.3 0.2 - - - -
119A ASN* 1.3 78.2 - - - +
121A VAL* 1.3 58.8 + - - +
124A SER 4.3 1.4 - - - +
126A PRO* 5.8 0.3 - - - +
142A THR* 3.2 21.0 - - - +
143A TYR* 3.5 16.4 + - - -
144A ASP* 2.8 30.3 + - - -
146A ARG* 5.0 2.4 + - - +
147A PHE* 3.3 33.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 20.9 - - + -
47A MET* 3.2 25.8 - - + +
50A VAL* 3.8 39.0 - - + -
117A TYR* 3.4 26.9 - - + +
118A GLN 3.1 6.8 + - - +
120A SER* 1.3 80.7 - - - +
122A THR* 1.3 59.4 + - - +
123A ARG 3.7 0.2 - - - -
124A SER 4.2 5.1 - - - +
126A PRO* 4.3 5.9 - - + +
142A THR* 3.7 20.0 - - + -
147A PHE* 5.1 0.4 - - + -
149A ILE* 4.8 9.6 - - + -
200A VAL* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.8 30.5 - - - +
36A PHE 4.5 5.4 - - - +
37A ARG* 4.4 2.9 + - - +
47A MET* 3.1 49.0 - - - +
50A VAL 4.7 1.6 - - - -
51A ASN* 3.5 26.8 + - + +
118A GLN* 2.8 26.0 + - - +
119A ASN* 3.8 5.9 + - - -
121A VAL* 1.3 80.5 - - + +
123A ARG* 1.3 68.9 + - - +
124A SER 3.4 1.8 - - - -
----------------------------------------------------------
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