Contacts of the helix formed by residues 133 - 147 (chain B) in PDB entry 1YFL
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 ASN 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 5.7 0.3 - - - -
131B THR 4.6 4.8 - - - +
132B ILE* 1.3 78.6 - - - +
134B LYS* 1.3 71.0 + - - +
135B ASN* 3.6 8.7 - - - +
136B SER* 2.7 39.4 + - - +
137B GLU 4.0 0.3 + - - -
605G A 2.8 57.3 + - - +
606G G 3.4 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 1.3 78.2 - - - +
135B ASN* 1.3 64.1 + - - +
136B SER 2.8 4.2 + - - -
137B GLU* 3.3 13.0 + - - +
138B LYS* 3.8 29.1 + - - +
604G C 4.4 19.7 - - - +
605G A 3.6 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 5.2 9.6 - - - +
133B ASN* 3.4 5.3 - - - +
134B LYS* 1.3 76.0 - - - +
136B SER* 1.3 55.2 + - - +
138B LYS* 3.4 33.2 - - + +
139B ARG* 2.7 45.4 + - + +
605G A 3.4 26.0 - - - +
606G G 3.5 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 3.9 10.8 - - - -
104B TYR* 4.3 3.1 + - - -
108B PHE* 3.4 20.1 - - - -
132B ILE* 3.1 27.5 - - - +
133B ASN* 2.7 51.4 + - - +
135B ASN* 1.3 69.7 - - - +
137B GLU* 1.3 56.1 + - - -
139B ARG* 3.4 6.4 + - - +
140B PHE* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 2.8 58.3 + - + +
133B ASN 4.0 0.2 + - - -
134B LYS 3.3 7.9 + - - +
136B SER* 1.3 76.7 - - - +
138B LYS* 1.3 58.2 + - + +
140B PHE* 3.7 5.2 - - - -
141B ASN* 2.6 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.8 16.4 - - + -
134B LYS* 3.9 28.3 - - - +
135B ASN* 3.0 32.9 + - - +
137B GLU* 1.3 76.1 - - + +
139B ARG* 1.3 64.9 + - - +
141B ASN* 3.7 6.6 - - - +
142B HIS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.5 19.2 - - + +
3B GLY* 2.9 21.8 + - - +
4B ALA* 3.4 17.2 - - - +
5B ILE* 3.5 21.1 + - - +
6B ALA* 3.8 20.8 - - - +
7B TYR 5.0 0.2 - - - +
10B ASN* 5.1 2.2 - - - +
12B GLN* 2.3 36.3 + - - +
104B TYR* 5.4 0.4 - - - +
107B HIS* 6.0 0.4 - - - -
108B PHE* 6.2 3.6 - - + -
135B ASN* 2.7 28.5 + - + +
136B SER* 3.5 5.8 - - - +
138B LYS* 1.3 73.3 - - - +
140B PHE* 1.3 67.3 + - - +
142B HIS* 3.5 2.9 + - - +
143B PHE* 3.1 20.6 + - - +
606G G 2.5 39.5 + - - -
607G G 3.6 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA 5.0 0.2 - - - -
62B LEU* 4.1 8.5 - - + -
65B VAL* 3.8 22.7 - - + -
66B SER* 3.8 5.6 - - - -
67B TRP* 3.4 54.3 - + + -
70B VAL* 3.9 8.5 - - + -
104B TYR* 3.4 24.8 + + - +
136B SER 2.8 16.2 + - - +
137B GLU 3.1 6.9 + - - +
139B ARG* 1.3 78.9 - - - +
141B ASN* 1.3 83.3 + - - +
143B PHE* 3.2 17.6 + + - +
144B LYS* 3.3 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 5.2 1.8 - - - +
137B GLU* 2.6 47.2 + - - +
138B LYS* 3.7 6.3 - - - +
140B PHE* 1.3 88.8 - - - +
142B HIS* 1.3 68.7 + - - +
144B LYS* 2.7 21.9 + - - +
145B GLN* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.2 14.6 - - - -
2B LEU* 3.5 31.8 + - + +
3B GLY 5.7 0.2 - - - +
40B LEU* 3.7 17.9 + - + +
41B ASN* 3.0 35.1 + - - -
138B LYS 2.9 18.4 + - - +
139B ARG 3.8 3.8 - - - +
141B ASN* 1.3 75.7 - - - +
143B PHE* 1.3 64.3 + - - +
145B GLN* 4.5 11.5 + - - +
146B ASN* 3.3 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 3.7 21.8 - - + +
36B LEU* 3.6 22.0 - - + -
40B LEU* 3.5 22.5 - - + +
59B TYR* 3.8 28.9 - + + -
62B LEU* 3.6 30.7 - - + -
63B ILE* 4.1 9.0 - - + -
139B ARG 3.1 11.8 + - - +
140B PHE* 3.2 12.6 - + + +
141B ASN 2.7 4.8 + - - -
142B HIS* 1.3 73.8 - - - +
144B LYS* 1.3 67.1 + - + +
146B ASN 3.0 4.0 + - - -
147B CYS* 2.8 60.3 + - + +
152B PHE* 3.9 7.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 4.1 3.6 - - - +
63B ILE* 3.0 29.9 + - - +
64B ASN* 4.2 3.6 + - - +
65B VAL 3.1 18.7 + - - +
66B SER* 5.2 1.2 - - - +
140B PHE* 3.4 44.6 - - + +
141B ASN* 2.7 13.6 + - - +
143B PHE* 1.3 85.3 - - + +
145B GLN* 1.3 59.3 + - + +
146B ASN 3.3 0.4 + - - -
147B CYS* 4.0 16.4 - - - -
148B ASP* 4.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASN* 3.0 32.2 + - - +
142B HIS* 4.1 8.1 + - - +
143B PHE 3.2 0.4 - - - -
144B LYS* 1.3 79.5 - - + +
146B ASN* 1.3 73.8 + - - +
148B ASP* 3.8 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.2 31.4 + - + +
41B ASN* 4.7 4.2 + - - -
142B HIS* 3.3 28.7 + - - +
143B PHE 3.0 2.8 + - - +
145B GLN* 1.3 96.2 - - - +
147B CYS* 1.3 57.8 - - - +
148B ASP* 3.0 9.7 + - - -
149B LYS* 2.9 60.2 + - - +
150B ILE* 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.2 1.0 - - - +
63B ILE* 4.3 25.1 - - + +
143B PHE* 2.8 60.5 + - + +
144B LYS* 4.0 16.6 - - - -
146B ASN* 1.3 71.3 - - - +
148B ASP* 1.3 61.3 + - - +
149B LYS 3.0 1.6 - - - -
150B ILE* 3.1 40.3 + - + +
152B PHE* 4.6 6.6 - - + -
----------------------------------------------------------
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