Contacts of the strand formed by residues 80 - 86 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LEU* 3.8 24.2 - - + -
38K TYR* 4.3 15.9 - - + -
39K THR 5.6 0.4 - - - +
40K ILE* 4.2 11.2 - - + -
41K PRO* 3.5 12.9 - - + +
73K MET* 3.5 14.2 - - - +
78K PHE* 3.5 2.1 + - - +
79K PRO* 1.3 88.5 - - + +
81K ILE* 1.3 66.7 + - - +
118K ILE* 4.4 1.6 - - - -
119K LYS* 3.2 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LEU* 4.7 0.6 - - - +
40K ILE* 3.9 3.4 - - - +
41K PRO* 3.7 18.2 - - + +
43K ILE* 3.8 12.3 - - + +
69K VAL* 3.7 22.0 - - + -
70K MET* 4.0 28.3 - - + -
73K MET* 3.7 33.0 - - + -
80K ALA* 1.3 78.4 - - - +
82K ILE* 1.3 92.4 + - - +
83K LEU* 4.0 2.4 + - + -
118K ILE* 4.2 4.7 - - + -
119K LYS 3.1 6.1 + - - -
120K CYS* 3.0 39.4 - - + +
121K ALA 3.3 0.7 + - - -
330K SER* 5.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LEU* 3.6 30.3 - - + -
34K ILE* 4.2 11.0 - - + -
40K ILE* 3.7 13.0 - - + -
41K PRO 2.9 10.8 + - - +
42K GLU* 3.2 30.1 - - + +
43K ILE 2.9 26.2 + - - -
81K ILE* 1.3 82.6 - - - +
83K LEU* 1.3 67.6 + - - +
121K ALA* 3.3 15.9 - - + +
123K ARG* 4.5 6.5 - - + -
160K LEU* 4.6 9.4 - - + -
265K PRO* 5.3 0.2 - - + -
309K CYS* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ILE* 3.7 14.6 - - + -
45K TYR* 3.7 20.6 - - + +
66K THR* 3.8 40.8 - - + +
69K VAL* 4.1 15.9 - - + -
70K MET* 3.9 25.1 - - - -
81K ILE* 4.0 12.8 - - + +
82K ILE* 1.3 77.3 - - - +
84K GLU* 1.3 60.0 + - - +
105K GLN* 4.2 1.3 - - - +
109K MET* 4.0 15.3 - - + -
120K CYS* 5.3 0.4 - - + -
121K ALA 3.1 7.7 + - - +
122K LEU* 3.4 14.2 - - + +
123K ARG 2.8 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K GLU* 3.6 21.2 - - + +
43K ILE 2.8 11.6 + - - +
44K ASN* 2.9 44.3 + - - +
45K TYR* 3.0 25.2 + - - -
82K ILE 4.1 0.6 - - - -
83K LEU* 1.3 72.5 - - - +
85K THR* 1.3 65.7 + - - +
86K GLU* 3.8 3.9 + - - +
123K ARG* 3.4 23.7 - - + +
125K THR* 2.8 20.5 + - - +
267K LYS* 2.8 30.5 + - - +
268K ASP* 3.3 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K TYR* 2.8 18.0 + - - -
62K TYR* 4.0 17.0 - - + -
83K LEU 4.1 0.4 + - - -
84K GLU* 1.3 72.7 - - - +
86K GLU* 1.3 64.7 + - - +
87K HIS* 3.6 1.4 + - - -
91K MET* 3.8 28.7 - - + -
105K GLN* 2.6 27.5 + - - +
122K LEU* 3.9 1.6 - - - +
123K ARG 2.7 8.9 + - - -
124K HIS* 3.4 25.1 + - + +
125K THR 2.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K ASN* 3.9 13.7 + - - +
45K TYR 4.9 14.4 + - - +
47K PRO* 5.5 1.0 - - - +
62K TYR* 4.0 10.2 + - - -
84K GLU* 3.9 15.3 + - - +
85K THR* 1.3 72.5 - - - +
87K HIS* 1.3 66.4 + - - +
88K VAL* 3.3 4.5 + - - +
125K THR* 3.8 17.0 - - + +
164K GLU* 3.0 1.6 - - - +
267K LYS* 2.6 27.6 + - - +
313K GLU* 3.8 14.7 - - - +
314K SER* 4.3 10.2 + - - -
516K K 2.6 23.0 - - - -
500L B13 5.4 9.2 - - - +
----------------------------------------------------------
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