Contacts of the strand formed by residues 77 - 83 (chain A) in PDB entry 3SBW
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 GLU 77 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 4.2 2.2 - - - -
69A ARG* 2.9 51.1 + - - +
70A LEU 4.7 1.2 - - - +
71A SER* 4.6 9.2 - - - -
75A GLN 3.8 13.2 - - - +
76A THR* 1.3 71.2 - - - +
78A LYS* 1.3 61.6 + - - +
79A GLN* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.5 34.2 + - - +
68A ASN* 3.2 20.0 - - - +
76A THR 4.0 2.8 + - - -
77A GLU* 1.3 73.8 - - - +
79A GLN* 1.3 63.6 + - - +
80A ALA 3.9 12.8 - - - +
81A ALA* 4.3 14.5 - - - +
90A VAL* 3.3 40.3 - - + +
91A GLN* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 2.7 24.9 + - + +
68A ASN 4.2 0.2 - - - -
69A ARG* 3.4 27.3 + - + +
77A GLU* 2.8 35.5 + - - +
78A LYS* 1.3 76.3 + - - +
80A ALA* 1.3 56.3 + - - +
89A PRO* 3.6 2.4 - - - +
90A VAL* 2.8 29.1 + - - +
91A GLN 4.4 1.6 + - - -
92A ASP 4.9 1.0 + - - +
95A PHE* 3.5 48.0 - - + +
121A TYR* 4.0 22.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.6 1.6 - - - -
67A TRP* 2.8 39.5 + - + +
78A LYS* 3.8 7.0 - - - +
79A GLN* 1.3 82.0 - - - +
81A ALA* 1.3 58.6 + - - +
87A SER* 4.6 2.5 - - - +
88A GLN 3.3 14.8 - - - +
89A PRO* 3.9 1.6 - - + -
90A VAL* 4.2 3.4 - - - +
95A PHE 3.8 20.2 - - - +
97A ILE* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 6.0 2.2 - - + -
65A LEU 3.2 5.8 - - - +
66A ASN* 3.6 20.0 - - - +
78A LYS* 4.3 15.0 - - - +
80A ALA* 1.3 73.2 - - - +
82A PHE* 1.3 63.0 + - - +
83A SER* 4.0 5.4 - - - +
86A LEU 3.4 1.4 - - - +
87A SER* 3.5 1.9 - - - -
88A GLN* 2.8 38.2 + - + +
90A VAL* 5.1 0.6 - - + +
97A ILE* 3.8 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 4.6 11.7 - + - -
63A LEU 4.1 2.7 - - - +
64A MET* 3.7 2.1 - - - -
65A LEU* 2.7 39.3 + - + +
81A ALA* 1.3 74.1 - - - +
83A SER* 1.3 61.5 + - - +
85A GLY* 3.5 43.1 - - - -
86A LEU 3.2 4.7 - - - -
87A SER* 3.6 15.7 - - - -
97A ILE* 3.8 41.5 - - + +
99A GLN* 3.7 35.4 - - + -
106A PHE* 3.8 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU 4.4 5.2 - - - -
64A MET* 3.7 31.4 - - - +
81A ALA* 4.0 6.0 - - - +
82A PHE* 1.3 79.8 + - - +
84A ASN* 1.3 82.7 + - - +
85A GLY 3.2 3.6 - - - +
86A LEU* 3.0 22.8 + - - +
88A GLN* 5.3 6.1 + - - +
----------------------------------------------------------
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