Contacts of the strand formed by residues 71 - 76 (chain C) in PDB entry 2I3T
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 71 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.3 4.0 - - - -
65C ILE* 3.0 55.9 + - + +
67C ASN* 3.6 18.2 + - - +
68C THR* 5.4 0.2 + - - -
69C ASP* 3.0 25.0 + - + +
70C LEU* 1.3 74.8 - - - +
72C ILE* 1.3 63.4 + - - +
73C TYR* 3.9 17.5 + - + +
83C LYS* 5.8 6.1 - - + +
84C VAL 5.3 3.4 - - - +
129C PRO* 3.9 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 5.0 0.2 - - + -
25C LEU* 6.3 0.2 - - + -
27C LEU* 3.7 41.7 - - + -
35C LEU* 3.9 24.0 - - + -
37C VAL* 4.8 1.6 - - + -
62C CYS* 5.0 0.9 - - + -
63C ASN 3.6 8.3 - - - +
64C PHE* 4.2 6.3 - - + -
70C LEU* 4.5 17.5 - - + -
71C GLN* 1.3 75.9 - - - +
73C TYR* 1.3 76.3 + - - +
74C VAL* 4.7 1.3 - - + -
83C LYS* 3.8 1.8 - - - +
84C VAL* 2.8 47.1 + - + +
86C LEU* 4.2 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C CYS* 3.1 7.5 - - - +
63C ASN 3.0 31.7 + - - +
65C ILE* 4.3 10.8 - - + -
71C GLN* 3.9 23.8 + - + +
72C ILE* 1.3 77.6 - - - +
74C VAL* 1.3 64.0 + - - +
81C ILE* 4.5 3.4 - - + -
82C LEU 3.3 15.7 - - - +
83C LYS* 3.9 32.6 - - + +
84C VAL* 4.5 0.2 - - - -
95C LEU* 3.7 32.5 - - + -
107C ILE* 4.3 12.1 - - + -
115C LEU* 3.6 27.6 - - + -
127C ILE* 3.8 18.5 - - + +
129C PRO* 3.2 25.1 - - - +
133C GLY 4.7 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 4.1 8.1 - - + -
35C LEU* 4.1 14.6 - - + -
59C LEU* 4.1 20.4 - - + -
61C CYS 3.3 8.5 - - - +
62C CYS* 3.7 15.7 - - + -
73C TYR* 1.3 80.1 - - - +
75C GLY* 1.3 59.4 + - - +
80C GLU 3.7 0.2 - - - +
81C ILE* 3.3 7.8 - - - +
82C LEU* 3.0 60.4 + - + +
84C VAL* 4.1 12.3 - - + -
92C PHE* 4.2 10.1 - - + -
107C ILE* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.3 6.4 - - - +
60C LEU 2.7 31.3 + - - -
61C CYS* 3.1 17.2 + - - -
74C VAL* 1.3 75.1 - - - +
76C THR* 1.3 59.0 + - - -
80C GLU 3.3 7.4 - - - -
81C ILE* 4.7 0.2 - - - -
104C ILE* 3.8 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.7 27.6 - - + -
57C HIS* 4.2 6.7 - - - -
58C PRO 3.3 9.4 - - - -
59C LEU* 3.8 14.6 - - + -
60C LEU* 4.3 3.4 - - - -
75C GLY* 1.3 77.7 - - - -
77C VAL* 1.3 58.5 + - - +
78C GLN 3.4 4.2 + - - -
79C GLY* 3.0 19.1 + - - -
80C GLU* 3.0 43.3 + - + +
82C LEU* 3.8 12.3 - - + -
104C ILE 3.2 17.1 + - - -
----------------------------------------------------------
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