Contacts of the helix formed by residues 118 - 129 (chain 2) in PDB entry 5IY6
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 LEU 118 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN* 1.3 80.8 + - - +
1192 ARG* 1.3 79.8 + - - +
1212 ALA* 2.9 12.8 + - + +
1222 LEU* 2.8 36.3 + - + +
393 ASP* 1.7 85.9 - - - +
423 MET* 3.0 20.2 - - + -
433 VAL* 2.9 25.8 - - + +
1083 ASN* 3.4 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002 LEU* 3.0 53.6 + - + +
1012 LEU* 3.4 46.0 + - - +
1172 ASN 2.9 8.4 - - - +
1182 LEU* 1.3 93.8 - - + +
1202 ILE* 1.3 64.3 + - + +
1222 LEU* 3.0 15.3 + - - +
1232 LEU* 3.0 13.0 + - - +
433 VAL* 4.7 16.1 - - + +
463 ASN* 5.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN* 2.8 29.3 + - - +
1192 ARG* 1.3 78.2 - - + +
1212 ALA* 1.3 65.2 + - - +
1232 LEU* 3.2 16.3 + - + +
1242 GLY* 3.2 11.4 + - - -
463 ASN* 5.0 4.5 - - - +
1043 LEU* 4.8 6.7 - - + -
1053 THR* 6.1 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN 3.3 2.9 + - - +
1182 LEU* 2.9 16.9 + - + +
1202 ILE* 1.3 81.9 - - - +
1222 LEU* 1.3 65.7 + - + +
1242 GLY* 3.3 2.1 + - - -
1252 GLY* 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962 TRP* 5.5 3.3 - - - -
1002 LEU* 3.5 27.4 - - + -
1182 LEU* 2.8 37.2 + - + +
1192 ARG 3.0 5.8 + - - +
1212 ALA* 1.3 80.3 - - + +
1232 LEU* 1.3 63.5 + - - +
1252 GLY* 3.0 3.6 + - - -
1262 GLY* 2.9 20.3 + - - -
393 ASP* 4.1 18.2 - - - +
433 VAL* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962 TRP* 6.4 0.9 - - - -
1002 LEU* 4.0 20.8 - - + +
1192 ARG* 3.0 11.8 + - + +
1202 ILE* 3.2 10.5 + - + +
1222 LEU* 1.3 75.2 - - - +
1242 GLY* 1.3 60.8 + - - +
1262 GLY 3.0 1.7 + - - -
1272 LYS* 2.9 27.8 + - + -
1762 ALA* 4.1 13.0 - - + +
1772 GLN* 5.3 2.9 - - + +
1782 LEU* 3.0 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202 ILE 3.2 11.2 + - - -
1212 ALA* 3.8 2.5 - - - -
1232 LEU* 1.3 80.9 - - - +
1252 GLY* 1.3 63.9 + - - +
1272 LYS* 3.0 19.4 + - - +
1282 ALA* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 ALA 2.9 14.3 + - - -
1222 LEU* 3.0 4.2 + - - -
1242 GLY* 1.3 74.6 - - - +
1262 GLY* 1.3 60.2 + - - +
1282 ALA* 3.2 6.7 + - - -
1292 TRP* 2.8 39.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 GLU* 3.2 23.4 - - - +
962 TRP* 3.8 12.0 - - - -
972 HIS* 5.1 0.3 - - - -
1222 LEU 2.9 13.4 + - - -
1232 LEU 3.0 0.4 + - - -
1252 GLY* 1.3 73.6 - - - +
1272 LYS* 1.3 64.5 + - - +
1292 TRP* 3.1 11.1 + - - -
1302 SER* 3.3 8.1 + - - -
1782 LEU* 3.0 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232 LEU* 2.9 13.5 + - + +
1242 GLY* 3.0 14.5 + - - +
1262 GLY* 1.3 76.1 - - - +
1282 ALA* 1.3 64.3 + - - +
1302 SER* 3.2 18.4 + - - -
1772 GLN 4.5 5.3 + - - +
1782 LEU* 2.9 54.8 + - + +
1792 LEU 4.5 4.6 + - - -
1802 SER* 4.6 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242 GLY 3.1 10.5 + - - +
1252 GLY* 3.3 13.9 - - - +
1262 GLY 3.1 0.4 - - - -
1272 LYS* 1.3 80.0 - - - +
1292 TRP* 1.3 83.2 + - + +
1302 SER* 3.5 1.2 + - - -
1312 ASP* 4.5 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 LYS* 3.6 46.8 - - + +
782 GLU* 2.7 50.9 - - + +
792 PHE* 4.7 19.2 - + + +
1252 GLY* 2.8 37.7 - - - -
1262 GLY 3.1 5.7 + - - -
1282 ALA* 1.3 92.3 - - + +
1302 SER* 1.3 62.3 + - - +
1312 ASP* 3.1 3.6 - - - +
1322 ASP* 3.2 25.5 + - + +
1332 THR 3.4 4.0 + - - -
----------------------------------------------------------
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