Contacts of the strand formed by residues 80 - 86 (chain A) in PDB entry 2I2X
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 ALA 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.8 19.5 - - + -
38A TYR* 4.4 14.1 - - + -
39A THR 5.7 0.9 - - - +
40A ILE* 4.4 8.5 - - + -
41A PRO* 3.4 15.1 - - + +
73A MET* 3.2 15.1 - - - +
78A PHE* 3.4 3.2 + - - +
79A PRO* 1.3 87.5 - - + +
81A ILE* 1.3 68.7 + - - +
118A ILE* 4.2 1.7 - - - +
119A LYS* 3.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.7 0.4 - - - +
40A ILE* 4.0 2.6 - - - +
41A PRO* 3.7 15.3 - - + +
43A ILE* 3.6 10.3 - - + -
69A VAL* 3.6 24.0 - - + -
70A MET* 4.1 12.6 - - - -
73A MET* 3.5 38.1 - - + -
80A ALA* 1.3 80.0 - - - +
82A ILE* 1.3 93.6 + - - +
83A LEU* 3.8 4.0 - - + -
118A ILE* 4.0 12.8 - - + -
119A LYS 3.0 6.3 + - - -
120A CYS* 3.0 41.4 - - + +
121A ALA 3.4 0.5 + - - -
330A SER* 5.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.5 32.1 - - + -
34A ILE* 4.4 9.6 - - + -
40A ILE* 3.8 11.7 - - + -
41A PRO 2.9 10.9 + - - +
42A GLU* 3.2 30.7 - - + +
43A ILE 2.9 25.1 + - - -
81A ILE* 1.3 80.7 - - - +
83A LEU* 1.3 68.3 + - - +
121A ALA* 3.4 15.7 - - + +
123A ARG* 4.5 6.3 - - + -
160A LEU* 4.5 8.7 - - + -
265A PRO* 5.5 0.9 - - + -
309A CYS* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.8 13.2 - - + -
45A TYR* 3.5 20.9 - - + +
66A THR* 3.8 31.2 - - + +
69A VAL* 4.2 15.5 - - + -
70A MET* 3.8 22.9 - - - -
81A ILE* 3.8 19.1 - - + +
82A ILE* 1.3 75.0 - - - +
84A GLU* 1.3 61.2 + - - +
85A THR 4.1 0.2 - - - -
109A MET* 3.7 37.2 - - + -
120A CYS* 5.1 1.1 - - + -
121A ALA 3.1 7.4 + - - +
122A LEU* 3.4 4.0 - - + +
123A ARG* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.6 22.2 - - + +
43A ILE 2.9 11.0 + - - +
44A ASN* 2.9 49.1 + - - +
45A TYR* 3.2 22.5 + - - -
82A ILE 4.1 0.6 + - - -
83A LEU* 1.3 73.0 - - - +
85A THR* 1.3 62.5 + - - +
86A GLU* 3.6 2.8 + - + +
123A ARG* 3.3 21.7 + - + +
125A THR* 2.6 22.5 + - - +
267A LYS* 2.6 29.1 + - - +
268A ASP* 3.5 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 2.8 17.9 + - - -
62A TYR* 3.5 35.9 - - + +
83A LEU 4.1 0.2 - - - -
84A GLU* 1.3 70.3 - - - +
86A GLU* 1.3 61.8 + - - +
87A HIS* 3.4 3.5 + - - -
91A MET* 3.8 19.5 - - + -
101A VAL* 4.4 0.2 - - + -
105A GLN* 2.5 29.2 + - - +
122A LEU* 4.1 1.7 - - - +
123A ARG 2.8 8.5 + - - -
124A HIS* 3.5 18.9 + - + +
125A THR 2.9 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 3.7 12.9 - - - +
45A TYR 5.0 12.6 + - - +
47A PRO* 5.9 0.7 - - - +
62A TYR* 4.2 7.4 + - - -
84A GLU* 3.6 19.0 + - - +
85A THR* 1.3 70.7 - - - +
87A HIS* 1.3 67.9 + - - +
88A VAL* 3.2 4.3 + - - +
125A THR* 3.8 12.5 - - + +
164A GLU* 2.8 4.0 - - - +
267A LYS* 2.8 19.1 + - - +
313A GLU* 3.7 15.7 - - - +
314A SER* 4.3 10.7 + - - -
511A K 2.3 30.0 - - - -
500B B13 5.1 9.9 - - - +
----------------------------------------------------------
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