Contacts of the strand formed by residues 90 - 98 (chain I) in PDB entry 3T30
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 MET 90 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I THR* 3.7 19.5 - - + -
49I ILE 3.2 13.2 - - - +
50I CYS* 3.7 16.8 - - + -
83I LEU* 3.7 7.0 - - - -
88I LEU* 3.3 26.0 - - - +
89I PRO* 1.3 80.2 - - - +
91I VAL* 1.3 65.5 + - - +
80J ILE 3.4 24.0 - - - +
81J ALA* 3.6 6.7 - - + -
82J SER 3.4 32.8 - - - +
83J LEU* 4.1 1.6 - - - -
88J LEU* 3.7 13.4 - - + +
91J VAL* 3.6 36.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H MET* 3.7 41.3 - - + -
91H VAL* 5.6 0.7 - - - -
92H SER* 4.5 11.4 - - - +
48I THR* 3.3 6.1 - - - -
49I ILE* 3.0 44.8 + - + +
81I ALA* 4.2 1.3 - - + -
83I LEU* 4.1 4.9 - - + -
88I LEU* 4.9 3.4 - - + -
90I MET* 1.3 84.1 - - - +
92I SER* 1.3 72.2 + - - +
93I MET* 3.6 23.8 - - + -
91J VAL* 5.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H SER* 3.5 20.8 + - - -
47I HIS 3.5 5.3 + - - -
48I THR* 4.2 7.4 - - - -
91I VAL* 1.3 78.8 - - - +
93I MET* 1.3 61.3 + - - +
94I VAL* 3.3 24.8 + - - +
91J VAL* 4.3 11.7 - - - +
92J SER 3.4 25.7 + - - -
93J MET* 4.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H HIS* 6.1 0.2 - - - -
48H THR* 3.9 18.4 - - + -
90H MET* 4.2 1.6 - - + -
92H SER* 4.0 8.7 - - - +
94H VAL* 4.0 14.4 - - + -
46I LEU* 2.9 50.3 - - + +
47I HIS 2.7 14.0 + - - +
48I THR* 5.4 0.2 - - - -
49I ILE* 4.0 15.7 - - + -
80I ILE* 3.7 26.0 - - - +
91I VAL* 3.6 33.0 - - + -
92I SER* 1.3 72.1 - - - +
94I VAL* 1.3 66.6 + - - +
96I VAL* 3.2 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H VAL* 3.6 12.5 - - - +
46I LEU 3.9 5.8 - - - -
47I HIS* 3.5 22.6 + - + +
92I SER* 3.3 18.9 + - - +
93I MET* 1.3 78.0 - - - +
95I GLY* 1.3 61.3 + - - +
93J MET* 4.0 12.3 - - + +
94J VAL 3.7 11.9 - - - +
95J GLY* 3.6 32.5 - - - +
96J VAL* 3.6 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H HIS* 5.4 1.0 + - - -
94H VAL* 3.5 15.1 - - - +
45I LEU* 6.2 1.0 - - - +
46I LEU 4.5 0.6 + - - -
47I HIS* 5.2 2.0 - - - -
94I VAL* 1.3 79.6 - - - +
96I VAL* 1.3 66.4 + - - +
97I GLN* 3.3 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H HIS* 3.7 43.7 - - + +
94H VAL* 3.6 13.4 - - + +
45I LEU* 3.4 5.2 - - - +
46I LEU* 3.0 46.0 + - + -
64I ILE* 6.1 0.4 - - + -
93I MET* 3.2 27.1 + - + +
95I GLY* 1.3 78.0 + - - +
97I GLN* 1.3 62.2 - - - +
98I LEU* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H GLN* 2.8 27.5 + - - +
43I ARG* 4.2 28.7 + - - +
44I LEU 3.4 4.7 - - - -
45I LEU* 3.4 25.0 - - + +
95I GLY* 3.3 13.9 + - - +
96I VAL* 1.3 77.0 - - - +
98I LEU* 1.3 62.6 + - - +
99I SER* 4.2 0.7 + - - -
120I ARG* 3.2 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 4.2 17.3 - - + -
47H HIS* 5.6 0.4 - - + +
118H GLN* 3.8 14.8 - - - +
43I ARG* 3.4 9.0 - - - -
44I LEU* 2.8 45.2 + - + +
46I LEU* 4.0 17.9 - - + -
64I ILE* 4.0 21.8 - - + -
96I VAL* 3.8 19.7 - - + -
97I GLN* 1.3 73.3 - - - +
99I SER* 1.3 61.1 + - - +
100I PRO* 3.6 0.7 - - - +
102I VAL* 4.1 15.3 - - + -
104I PHE* 3.7 35.4 - - + -
----------------------------------------------------------
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