Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 3AS2
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 GLN 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 6.0 6.2 - - + +
67A PHE 3.5 5.8 - - - +
68A ASN* 3.4 23.6 + - + +
70A TRP* 5.2 10.8 - - - +
94A GLY* 4.2 6.3 + - - +
95A SER* 1.3 85.7 + - - +
97A THR* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL 3.8 0.7 - - - +
66A LYS* 3.4 3.1 - - - +
67A PHE* 3.0 74.0 + - + +
69A GLN* 4.7 0.7 + - - -
78A TYR* 4.0 18.2 - - + -
91A ALA 4.0 9.0 - - - +
92A ILE* 3.9 21.8 - - + +
93A THR* 4.7 2.2 + - + +
94A GLY 4.0 2.9 + - - -
96A GLN* 1.3 75.3 + - - +
98A THR* 1.4 73.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 3.5 42.9 + - + +
65A VAL 3.5 6.1 - - - +
66A LYS* 3.4 29.1 - - + +
78A TYR* 4.6 2.6 + - - -
97A THR* 1.4 80.4 - - - +
99A ALA* 1.3 61.7 + - - +
100A SER* 3.6 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE 3.6 1.7 - - - +
64A LYS* 3.3 2.9 - - - -
65A VAL* 2.7 48.7 + - + +
67A PHE* 4.3 9.6 - - + -
78A TYR* 3.5 37.9 - - + -
80A VAL* 4.4 12.6 - - + -
97A THR* 4.0 2.0 - - - +
98A THR* 1.3 70.8 - - - +
100A SER* 1.3 59.8 + - - +
101A PHE* 4.2 7.9 - - + -
113A ILE* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE 3.2 7.2 - - - -
64A LYS* 4.2 12.5 - - - +
78A TYR* 4.0 8.3 + - - -
98A THR* 3.6 17.7 + - - +
99A ALA* 1.3 74.2 + - - +
101A PHE* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.6 2.1 - - - +
63A ILE* 2.6 69.1 + - + -
65A VAL* 4.9 5.4 - - + -
80A VAL* 3.8 29.6 - - + -
82A PHE* 3.6 31.0 - + - -
87A VAL* 3.9 16.4 - - + +
88A ALA* 3.4 27.8 - - + -
99A ALA* 4.2 15.5 - - + -
100A SER* 1.3 78.5 - - - +
102A GLU* 1.3 73.2 + - - +
103A TYR* 4.6 2.0 - - + -
111A MET* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.6 39.0 - - + +
61A ALA 3.1 11.2 - - - +
62A LYS* 4.5 22.1 - - + +
63A ILE* 4.6 0.7 - - - +
87A VAL 5.0 3.6 - - - +
101A PHE* 1.3 90.8 - - - +
103A TYR* 1.3 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 4.7 0.2 - - - +
60A LEU* 4.1 4.5 - - - -
61A ALA* 2.7 43.1 + - - +
63A ILE* 4.2 7.4 - - + +
82A PHE* 3.7 23.3 - + + +
87A VAL* 3.8 30.5 - - + +
101A PHE* 4.6 1.6 - - + -
102A GLU* 1.3 78.1 - - - +
104A GLY* 1.3 60.6 + - - +
105A GLN* 3.5 34.2 + - + +
109A TYR* 3.7 24.2 + + - -
131A ILE* 3.6 28.4 - - + +
----------------------------------------------------------
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