Contacts of the strand formed by residues 119 - 126 (chain M) 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 LYS 119 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M LEU 3.5 9.0 - - - +
31M ASP* 3.5 41.2 + - + +
32M LEU* 3.7 17.3 - - + -
33M GLU* 6.3 0.4 - - - -
38M TYR* 3.9 25.1 - - + +
79M PRO* 3.0 22.4 + - + +
80M ALA* 3.3 5.5 - - + -
81M ILE 3.1 22.3 + - - -
113M HIS* 4.6 0.9 - - - +
117M GLY 4.3 7.7 + - - +
118M ILE* 1.3 73.5 - - - +
120M CYS* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 120 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M GLY 3.6 0.2 - - - -
30M LEU* 2.7 66.2 + - - +
32M LEU* 4.1 8.0 - - - +
70M MET* 4.2 14.1 - - + -
81M ILE* 3.0 25.4 - - + +
83M LEU* 5.4 0.7 - - + -
106M LYS* 6.0 0.2 - - - -
109M MET* 4.1 24.5 - - - -
113M HIS* 4.6 0.2 - - - -
118M ILE 3.9 9.9 - - - +
119M LYS* 1.3 77.6 - - - +
121M ALA* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ALA* 4.4 6.1 - - + -
29M GLY* 4.0 12.3 - - - +
32M LEU* 3.7 20.1 - - + +
34M ILE* 5.5 0.4 - - + -
81M ILE 3.3 4.9 + - - +
82M ILE* 3.4 11.4 - - + +
83M LEU* 3.1 25.3 + - - +
106M LYS* 5.4 1.1 - - - +
109M MET* 4.5 7.8 - - - +
120M CYS* 1.3 77.9 - - - +
122M LEU* 1.3 60.3 + - - +
159M ASP* 3.6 15.9 - - + +
160M LEU* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82M ILE* 5.2 0.2 - - - -
83M LEU* 3.4 17.9 - - + +
85M THR* 4.1 2.9 - - - +
102M ALA* 3.7 24.7 - - - +
105M GLN* 3.9 21.8 - - + +
106M LYS* 4.4 4.3 - - + +
109M MET* 3.5 33.4 - - + -
121M ALA* 1.3 74.7 - - - +
123M ARG* 1.3 67.2 + - - +
124M HIS* 3.9 19.3 - - + +
157M GLY 3.7 19.7 - - - +
158M ALA* 3.8 1.3 - - - -
159M ASP* 2.8 41.5 + - - +
160M LEU* 2.9 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M GLU* 2.8 54.1 + - - +
82M ILE* 4.5 1.1 - - + +
83M LEU 2.8 13.4 + - - +
84M GLU* 3.4 19.8 + - + -
85M THR* 2.9 28.1 + - - +
121M ALA 4.2 0.4 - - - -
122M LEU* 1.3 74.9 - - - +
124M HIS* 1.3 67.7 + - - +
125M THR* 4.1 6.5 - - - +
160M LEU* 3.5 26.0 - - + +
162M SER* 3.4 24.8 + - - +
215M ALA* 3.8 3.5 - - - +
265M PRO* 2.3 45.8 + - - +
266M GLY 3.1 16.6 + - - -
267M LYS* 3.6 7.3 - - - +
268M ASP 5.0 0.4 - - - +
285M THR* 3.0 15.2 + - - -
309M CYS* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M THR* 3.5 13.1 - - - +
87M HIS* 2.9 34.5 + + - +
91M MET* 4.4 0.8 - - - +
98M GLY 3.6 14.9 + - - -
101M VAL* 4.2 2.6 - - - +
102M ALA* 3.6 17.9 + - + +
105M GLN* 3.2 31.5 + - - -
122M LEU* 3.9 12.2 + - + +
123M ARG* 1.3 77.8 + - - +
125M THR* 1.3 61.2 + - - +
126M ILE* 3.8 8.0 + - + +
153M CYS* 3.6 18.6 - - + -
158M ALA* 4.0 17.5 - - + +
160M LEU 3.0 9.8 + - - +
161M LEU* 3.6 3.1 - - + -
162M SER* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M GLU* 2.6 28.6 + - - +
85M THR 3.0 10.2 + - - -
86M GLU* 3.8 8.2 - - + +
87M HIS* 3.1 25.6 + - - +
123M ARG* 4.1 1.6 - - - +
124M HIS* 1.3 73.4 - - - +
126M ILE* 1.3 64.4 + - - +
127M GLY* 4.7 0.2 - - - -
162M SER* 3.2 23.8 - - - +
163M VAL* 3.9 12.6 - - - -
164M GLU* 4.2 8.3 - - + +
267M LYS* 3.6 25.8 - - - +
500N B13 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M HIS* 3.7 24.5 - - + +
92M SER* 3.7 9.2 - - - +
124M HIS* 4.1 19.1 - - + +
125M THR* 1.3 78.5 - - - +
127M GLY* 1.3 78.9 + - - +
128M ASP 3.5 0.3 + - - -
146M PHE* 4.1 6.1 - - + -
149M ALA* 3.9 28.3 - - + +
150M PHE* 3.6 57.2 - - + +
153M CYS* 4.6 3.8 - - + -
161M LEU* 5.1 2.9 - - + -
162M SER 2.9 6.3 + - - -
163M VAL* 3.3 19.2 - - - +
164M GLU 4.4 1.2 + - - -
500N B13 5.4 0.7 - - - +
----------------------------------------------------------
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