Contacts of the helix formed by residues 40 - 53 (chain B) in PDB entry 5IY8
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 VAL 40 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.5 0.4 - - - -
39B LEU* 1.3 88.1 - - + +
41B ARG* 1.3 66.2 + - - +
42B GLN* 3.5 15.5 - - - +
43B GLN* 3.8 7.9 + - + +
44B LEU* 3.4 27.0 + - + +
181B PRO* 3.6 35.0 - - + +
182B GLY 4.2 3.4 - - - +
479B LEU* 5.1 8.1 - - + +
482B LEU* 3.7 41.5 - - + -
483B ARG 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU 4.8 4.2 + - - -
37B LYS* 3.2 52.5 + - + +
38B GLY* 4.4 4.6 + - - +
39B LEU 4.0 0.4 - - - -
40B VAL* 1.3 79.1 - - - +
42B GLN* 1.3 62.5 + - - +
43B GLN 3.2 0.2 - - - -
44B LEU* 4.3 20.0 - - - +
45B ASP* 2.7 65.0 + - - +
48B ASP* 5.8 1.4 + - - -
159B THR* 6.2 2.6 - - - +
483B ARG* 5.8 0.2 - - - +
531B TYR* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 5.0 0.2 + - - -
40B VAL* 4.2 13.4 - - - +
41B ARG* 1.3 80.1 + - - +
43B GLN* 1.3 80.0 + - + +
45B ASP* 3.9 3.2 - - - +
46B SER* 2.9 27.0 + - - -
395B LEU* 3.4 24.9 - - + +
482B LEU 3.8 22.0 + - - -
483B ARG* 4.1 22.1 + - - +
526B LEU* 3.9 20.3 - - - +
530B ALA 5.3 2.3 - - - +
531B TYR* 4.7 11.8 - - + -
532B ILE* 4.0 29.6 - - + +
534B VAL* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.8 8.3 + - + +
41B ARG 3.2 1.0 - - - -
42B GLN* 1.3 99.1 - - + +
44B LEU* 1.3 62.1 + - + +
46B SER* 2.8 19.1 + - - -
47B PHE* 3.1 15.6 + - - +
155B MET* 3.8 13.5 - - - +
183B GLY* 3.4 28.8 + - - +
185B PHE* 6.2 0.2 - - - -
193B VAL* 3.8 14.6 - - - +
194B LEU* 3.6 27.1 + - - +
395B LEU* 4.3 8.0 - - - +
396B ALA* 3.8 21.3 + - - +
482B LEU* 4.0 17.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.4 32.5 + - + +
41B ARG* 3.3 26.6 + - - +
43B GLN* 1.3 78.8 - - - +
45B ASP* 1.3 61.6 + - - +
47B PHE* 4.1 0.7 - - - +
48B ASP* 3.0 31.0 + - - +
155B MET* 4.1 4.9 - - - -
156B LEU 3.7 22.7 - - - +
157B ARG* 4.2 5.8 - - + +
158B SER* 3.8 26.7 - - - +
181B PRO 4.5 7.0 - - - +
183B GLY* 3.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 5.1 1.7 + - - -
41B ARG* 2.7 51.7 + - - +
42B GLN* 4.0 2.7 - - - +
44B LEU* 1.3 70.6 - - - +
46B SER* 1.3 58.8 + - - +
48B ASP* 3.8 9.5 - - - +
49B GLU* 2.9 32.6 + - - +
531B TYR* 2.6 28.9 + - + +
532B ILE 6.0 0.4 - - - +
534B VAL* 3.9 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN 2.9 16.6 + - - -
43B GLN* 2.8 16.8 + - - -
45B ASP* 1.3 77.2 - - - +
47B PHE* 1.3 55.0 + - - +
49B GLU* 3.9 4.9 - - - +
50B PHE* 3.0 25.8 + - - +
395B LEU* 3.8 17.4 - - - +
396B ALA* 3.5 11.3 + - - +
397B GLY* 3.5 25.1 + - - -
398B PRO* 4.8 4.7 - - - +
534B VAL* 4.1 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN 3.1 4.3 + - - +
44B LEU* 4.2 2.9 - - - +
46B SER* 1.3 77.8 + - - +
48B ASP* 1.3 66.2 + - - +
50B PHE* 3.1 22.8 + + - +
51B ILE* 3.2 31.3 + - + +
152B ILE* 4.8 3.1 - - + -
153B PRO 3.2 22.9 - - - -
154B ILE* 3.9 11.9 - - + -
155B MET* 3.5 43.1 - - + -
158B SER* 3.8 22.0 - - - -
160B TYR* 4.9 4.9 - + - -
185B PHE* 3.5 23.8 - + - -
396B ALA* 4.9 0.9 - - + -
397B GLY 4.8 1.6 - - - +
400B LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 5.8 1.2 + - - -
44B LEU 3.0 19.1 + - - +
45B ASP* 3.8 11.6 - - - +
47B PHE* 1.3 78.1 - - - +
49B GLU* 1.3 62.1 + - - +
51B ILE 3.6 0.2 + - - -
52B GLN* 3.1 40.0 + - - +
158B SER* 5.5 0.9 - - - -
159B THR* 2.5 48.3 + - + +
160B TYR* 3.4 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP 2.9 18.4 + - - +
46B SER* 3.9 5.7 - - - +
48B ASP* 1.3 78.3 - - - +
50B PHE* 1.3 59.3 + - - +
52B GLN* 4.6 4.7 - - - +
53B MET* 2.9 60.5 + - + +
54B SER* 3.6 12.3 + - - -
397B GLY* 5.3 3.1 - - - -
398B PRO* 5.6 3.3 - - - +
534B VAL* 4.1 36.1 - - + +
535B GLY 4.3 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER 3.0 16.7 + - - +
47B PHE* 3.1 25.5 + + - +
49B GLU* 1.3 77.1 + - - +
51B ILE* 1.3 80.7 + - + +
54B SER* 3.0 39.9 + - - -
55B VAL* 3.2 27.9 + - + +
58B ILE* 5.7 0.7 - - + -
152B ILE* 4.7 9.9 - - + -
397B GLY* 3.7 26.9 - - - -
400B LEU* 3.9 21.1 - - + -
401B ALA* 3.8 22.2 - - - -
404B PHE* 4.2 18.4 - + + -
444B LEU* 5.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.2 19.1 + - + +
50B PHE* 1.3 99.5 - - + +
52B GLN* 1.3 67.2 + - - +
53B MET 3.2 2.1 - - - +
55B VAL* 3.1 32.1 - - + +
56B GLN* 4.6 1.4 + - - +
91B ILE* 5.1 5.7 - - + +
93B LEU* 3.5 34.1 - - + -
124B LEU* 5.5 2.2 - - + -
152B ILE* 4.3 18.4 - - + -
154B ILE* 5.7 0.4 - - + -
160B TYR* 3.4 32.3 - - + +
140T ARG 5.5 0.3 - - - +
141T LEU* 6.0 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.1 32.8 + - - +
49B GLU* 4.5 2.7 - - - +
51B ILE* 1.3 80.1 - - - +
53B MET* 1.3 61.9 + - + +
56B GLN* 4.8 1.4 - - - +
160B TYR* 3.1 18.3 + - - +
140T ARG* 3.1 42.0 - - + +
142T SER* 5.2 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.9 36.2 + - + +
52B GLN* 1.3 84.0 - - + +
54B SER* 1.3 66.0 + - - +
55B VAL 3.4 1.6 - - - -
56B GLN* 3.1 17.3 + - - +
57B ARG* 3.2 34.9 + - + +
537B GLN* 6.2 2.5 - - + -
140T ARG* 3.8 37.9 - - + +
----------------------------------------------------------
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