Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 1BFD
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 LEU 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 4.0 24.2 - - + -
54A ALA 4.0 4.7 - - - +
55A ASP* 3.9 23.3 - - + +
58A ALA* 3.9 22.0 - - + -
65A ALA* 3.6 8.5 - - + -
67A ILE* 4.1 13.2 - - + -
82A LEU* 4.5 5.2 - - + -
85A ALA* 3.6 28.5 - - + -
90A SER* 2.9 16.7 + - - +
91A PRO* 1.3 79.7 - - - +
93A ILE* 1.3 61.4 + - - +
94A VAL* 3.7 2.9 - - + -
146A ALA* 4.5 0.2 - - - -
152A GLY 3.7 3.5 + - - +
153A PRO* 3.3 8.1 - - + +
154A VAL* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.7 29.8 - - + -
64A PRO* 4.0 19.7 - - + -
65A ALA 2.9 15.2 + - - +
66A PHE* 3.6 23.6 - - + -
67A ILE* 2.8 31.5 + - - +
92A LEU* 1.3 73.4 - - - +
94A VAL* 1.3 61.4 + - - +
95A THR* 4.3 8.3 - - + -
139A MET* 4.5 4.9 - - - -
142A ALA* 4.1 27.4 - - + +
143A ILE* 3.9 18.8 - - + +
146A ALA* 4.0 15.7 - - + -
154A VAL* 3.9 3.4 - - + -
156A LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 5.4 1.3 - - + -
67A ILE* 3.8 24.2 - - + -
69A LEU* 4.0 27.1 - - + -
75A THR* 5.6 0.7 - - + -
82A LEU* 4.1 33.0 - - + -
92A LEU* 4.4 7.6 - - + +
93A ILE* 1.3 74.4 - - - +
95A THR* 1.3 63.8 + - - +
123A VAL* 6.0 0.7 - - + -
153A PRO* 5.0 1.8 - - + -
154A VAL 3.0 17.8 + - - +
155A TYR* 3.3 25.4 - - + -
156A LEU* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 5.0 0.7 - - - -
66A PHE* 3.6 34.6 - - + -
67A ILE 2.8 20.6 + - - +
68A ASN* 3.0 18.3 + - - -
69A LEU* 2.8 27.5 + - - +
93A ILE* 4.3 5.2 - - + -
94A VAL* 1.3 81.7 - - - +
96A ALA* 1.3 61.7 + - - +
139A MET* 4.0 20.6 - - + -
155A TYR* 5.0 0.2 - - - -
156A LEU* 3.2 16.6 - - + -
158A VAL* 5.6 4.5 - - - -
163A TRP* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 4.7 2.0 - - - -
69A LEU* 3.2 13.0 - - + +
71A SER* 4.0 10.8 - - - +
75A THR* 3.4 24.9 - - - +
95A THR* 1.3 76.0 - - - +
97A GLY* 1.3 61.6 + - - +
112A ASN* 4.8 1.8 - - - +
155A TYR* 3.4 19.5 - - + +
156A LEU 3.0 6.5 + - - +
157A SER* 3.4 4.1 - - - -
158A VAL* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.1 27.1 + - - -
28A GLU* 2.9 28.5 + - - +
69A LEU 3.3 2.0 + - - -
71A SER* 3.2 20.8 + - - -
96A ALA* 1.3 73.9 - - - +
98A GLN* 1.3 59.9 + - - -
112A ASN* 5.1 0.7 - - - +
157A SER* 5.0 0.7 - - - -
158A VAL* 3.6 7.0 - - - -
163A TRP* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.3 15.6 - - - +
71A SER* 5.1 0.4 - - - -
97A GLY* 1.3 71.4 - - - -
99A GLN* 1.3 83.4 + - - +
104A ILE* 3.7 22.8 - - + +
111A THR* 3.5 8.6 - - - +
112A ASN* 2.8 53.2 + - + +
128A GLU* 2.9 28.2 + - - +
157A SER* 3.5 16.2 - - - +
158A VAL 2.9 6.4 + - - +
159A PRO* 3.6 16.8 - - + -
160A TYR* 3.0 21.1 + - - -
----------------------------------------------------------
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