Contacts of the strand formed by residues 100 - 106 (chain A) in PDB entry 1BWN
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 TYR 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.2 34.0 - - + +
80A PRO* 3.9 13.6 - - + +
98A PHE 3.5 1.4 - - - -
99A PRO* 1.3 85.6 - - + +
101A PRO* 1.3 67.4 - - + +
102A PHE* 3.9 0.5 + - - -
113A VAL 3.9 0.5 - - - +
114A PHE* 4.1 0.7 - - - -
115A SER* 2.8 36.8 + - - +
116A PRO 3.6 13.7 - - - -
117A THR* 3.2 29.4 - - - +
118A GLU* 3.7 46.1 + - - -
121A ARG* 3.5 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.7 0.2 - - - -
67A VAL* 3.4 30.3 + - + +
69A PRO* 4.6 15.5 - - + -
70A GLU 5.6 0.2 - - - +
99A PRO 3.4 11.4 - - - +
100A TYR* 1.3 86.2 - - + +
102A PHE* 1.3 61.3 + - - +
112A TYR* 5.9 0.2 - - + -
113A VAL 3.2 8.7 - - - +
114A PHE* 3.6 27.4 - - + -
121A ARG* 3.0 27.0 + - - +
146A PHE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.9 28.3 - + - -
30A PHE* 6.4 0.2 - + - -
37A LEU* 6.1 0.9 - - + -
64A VAL* 4.7 0.7 - - + -
65A GLU 3.2 15.0 - - - +
67A VAL* 3.8 6.4 - - - +
100A TYR 4.3 2.2 - - - -
101A PRO* 1.3 74.0 - - - +
103A GLN* 1.3 64.8 + - - +
104A VAL* 4.2 16.4 - - + -
111A LEU 3.8 0.2 - - - +
112A TYR* 3.6 4.0 - - - +
113A VAL* 2.8 67.1 + - + -
115A SER* 4.7 2.7 - - - -
121A ARG* 3.7 22.9 - - + -
124A TRP* 4.1 16.8 - + + -
125A ILE* 3.9 23.8 - - + -
128A LEU* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A CYS* 5.8 0.2 - - - -
64A VAL* 3.4 8.0 - - - +
65A GLU 2.9 35.8 + - - +
66A THR 3.0 17.5 - - - +
67A VAL* 3.6 18.8 - - + +
102A PHE* 1.3 76.2 - - - +
104A VAL* 1.3 63.6 + - - +
105A VAL* 3.9 20.3 - - + +
110A PRO* 4.4 9.8 - - + +
111A LEU 3.3 4.7 - - - +
112A TYR* 3.8 22.6 + - + -
142A TYR* 3.3 14.9 - - + +
143A HIS* 2.9 34.8 + - - +
152A TYR* 5.6 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.2 13.9 - - + -
56A ILE* 4.3 14.1 - - + -
61A ILE* 3.7 40.2 - - + -
63A CYS 3.6 2.2 - - - -
64A VAL* 4.2 3.8 - - + -
102A PHE* 4.2 13.2 - - + -
103A GLN* 1.3 76.7 - - - +
105A VAL* 1.3 62.3 + - - +
106A TYR* 3.9 2.6 + - - -
109A GLY 3.8 1.2 - - - +
110A PRO* 3.5 0.5 - - - +
111A LEU* 2.8 42.5 + - + +
113A VAL* 4.9 4.5 - - + -
128A LEU* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.4 4.3 - - - +
62A THR* 2.7 37.5 + - - +
63A CYS* 2.5 35.4 + - + +
103A GLN* 4.0 29.6 - - + +
104A VAL* 1.3 73.0 - - - +
106A TYR* 1.3 70.5 + - - +
109A GLY* 3.7 13.0 - - - +
110A PRO* 4.5 7.6 - - + -
139A VAL* 5.8 2.0 - - + -
142A TYR* 5.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.1 22.6 + - - -
17A LYS* 2.9 28.7 + - - -
56A ILE* 3.7 48.2 - - + +
60A LYS* 3.1 28.0 - - + +
61A ILE* 3.8 3.1 - - + -
62A THR* 4.0 6.3 - - - -
104A VAL 3.9 6.3 - - - -
105A VAL* 1.3 82.9 - - - +
107A ASP* 1.3 76.3 + - - +
108A GLU* 2.7 47.4 + - + -
109A GLY* 3.1 29.5 + - - +
111A LEU 4.6 1.3 - - - -
161A ASN* 5.4 1.7 - - - +
----------------------------------------------------------
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