Contacts of the strand formed by residues 75 - 81 (chain X) in PDB entry 1T6B
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 ASP 75 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73X LYS* 3.6 7.9 + - + +
74X SER* 1.3 78.0 - - - +
76X GLU* 1.3 72.9 + - - +
77X TYR* 3.6 24.2 + - + +
106X ILE 3.7 0.2 - - - +
107X ARG* 3.5 21.1 - - - +
108X LEU 3.0 29.5 + - - +
138X ASP* 3.3 24.9 - - - +
139X SER* 2.7 26.5 + - - -
140X GLN* 5.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75X ASP* 1.3 85.8 + - - +
77X TYR* 1.3 62.8 + - - +
105X LYS* 4.2 40.9 + - + +
106X ILE* 3.4 14.8 - - - +
107X ARG* 2.9 34.2 + - + +
137X THR 3.8 0.5 - - - +
138X ASP* 3.8 3.5 - - - -
139X SER* 3.7 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71X VAL* 3.0 27.1 - - + +
73X LYS* 2.7 28.0 + - - +
75X ASP* 3.6 30.4 + - + +
76X GLU* 1.3 78.0 - - - +
78X THR* 1.3 64.3 + - - +
79X PHE* 4.4 11.9 - - + -
104X ASN 3.5 0.2 - - - +
105X LYS* 3.4 3.7 - - - -
106X ILE* 3.0 38.6 + - - +
108X LEU* 3.8 22.9 - - + -
136X TRP* 3.6 38.4 - + + -
137X THR 3.2 15.7 - - - +
138X ASP* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X TYR* 1.3 73.5 + - - +
79X PHE* 1.3 76.1 + - - +
80X ALA* 5.1 2.9 - - + +
103X SER* 3.9 17.6 + - - +
104X ASN 3.9 23.3 - - - +
105X LYS* 4.0 20.1 + - - +
136X TRP* 3.0 7.6 - - - -
137X THR* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69X ILE* 4.5 14.1 - - + -
77X TYR* 4.0 5.6 + - + -
78X THR* 1.3 86.6 - - - +
80X ALA* 1.3 64.3 + - - +
84X ASP* 4.7 0.9 - - - +
89X MET* 3.8 19.5 - - + -
91X VAL* 4.1 16.2 - - + -
96X VAL* 3.8 32.2 - - + +
97X ILE* 3.6 18.6 - - + +
102X ASN 4.8 3.3 - - - +
103X SER* 5.0 1.6 + - - -
104X ASN 4.9 3.1 + - - +
106X ILE* 4.1 18.2 - - + -
108X LEU* 3.8 29.6 - - + -
116X ILE* 5.3 0.2 - - + -
134X LEU* 4.1 1.8 - - + -
135X TYR 3.5 13.0 - - - +
136X TRP* 3.6 30.1 - + + -
146X ILE* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X THR* 5.1 3.4 - - + +
79X PHE* 1.3 78.9 - - - +
81X THR* 1.3 64.5 + - - +
84X ASP* 3.9 16.6 - - - +
97X ILE* 3.9 2.9 - - - +
103X SER* 5.7 2.2 - - - +
134X LEU* 3.6 4.7 - - - +
135X TYR* 2.6 50.2 + - + +
143X LYS* 4.4 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80X ALA* 1.3 81.8 - - - +
82X SER* 1.3 62.6 + - - +
83X ALA 3.3 13.5 + - - -
84X ASP* 2.8 35.5 + - - +
87X VAL* 3.7 18.3 - - + +
89X MET* 5.2 1.3 - - - -
97X ILE* 4.6 5.8 - - + -
118X ILE* 4.8 4.5 - - + -
132X PHE* 3.4 30.5 - - + -
133X LYS 3.2 9.4 - - - +
134X LEU* 4.4 12.8 - - + -
135X TYR* 4.1 8.6 - - - -
143X LYS* 5.8 0.9 + - - -
----------------------------------------------------------
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