Contacts of the helix formed by residues 141 - 151 (chain 2) in PDB entry 1AFB
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 141 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402 ASN* 1.3 73.7 - - - +
1422 GLU* 1.3 75.8 + - - +
1442 ASN* 3.2 3.2 + - - +
1452 LYS* 3.0 24.1 + - - +
1782 TYR* 3.6 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092 LYS* 5.7 10.8 - - - +
1402 ASN* 2.9 21.0 + - - +
1412 ALA* 1.3 88.7 + - - +
1432 GLU* 1.3 59.4 + - + +
1452 LYS* 3.3 16.3 + - - +
1462 ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092 LYS* 6.5 1.6 - - + -
1102 LYS* 2.9 45.5 + - + +
1122 PHE* 4.3 9.6 - - + -
1372 ILE 3.3 0.9 - - - +
1382 PRO* 4.0 5.2 - - + -
1392 ARG* 3.0 29.6 + - - +
1402 ASN* 2.9 30.9 + - - +
1422 GLU* 1.3 73.7 - - + +
1442 ASN* 1.3 60.5 + - - +
1462 ALA* 3.5 7.3 + - - +
1472 ILE* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382 PRO* 3.5 18.7 - - + +
1402 ASN 3.0 8.4 + - - +
1412 ALA* 3.4 9.0 - - - +
1432 GLU* 1.3 78.0 - - - +
1452 LYS* 1.3 57.4 + - - +
1472 ILE* 3.5 0.6 + - - +
1482 GLN* 3.0 30.2 + - - +
1782 TYR* 3.4 22.6 + - - +
1802 ASN* 3.4 9.5 - - - +
2032 ILE* 3.4 14.7 - - - +
2072 GLY* 2.8 31.1 + - - -
2092 TRP* 2.8 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412 ALA 3.0 15.6 + - - +
1422 GLU* 3.7 12.4 + - - +
1442 ASN* 1.3 77.1 - - - +
1462 ALA* 1.3 58.3 + - - +
1482 GLN* 3.3 16.5 + - - +
1492 GLU* 2.9 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122 PHE* 4.0 19.1 - - + -
1422 GLU 3.0 17.3 + - - +
1432 GLU* 3.6 7.2 - - - +
1452 LYS* 1.3 80.7 - - - +
1472 ILE* 1.3 61.1 + - - +
1492 GLU* 3.5 8.9 + - - +
1502 VAL* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122 PHE* 3.6 35.9 - - + -
1362 ALA* 3.9 20.9 - - + -
1382 PRO* 3.6 40.8 - - + -
1432 GLU 3.0 18.0 + - - +
1442 ASN 3.8 3.8 - - - +
1462 ALA* 1.3 72.1 - - - +
1482 GLN* 1.3 67.9 + - - +
1502 VAL* 3.1 7.7 + - - +
1512 ALA* 2.8 23.4 + - + +
1552 ALA* 5.5 0.7 - - + -
1572 LEU* 4.2 3.8 - - + -
2032 ILE* 4.2 21.8 - - + -
2212 VAL* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1442 ASN* 3.0 17.3 + - - +
1452 LYS* 3.4 19.7 - - - +
1472 ILE* 1.3 76.4 - - - +
1492 GLU* 1.3 62.4 + - + +
1512 ALA* 3.9 3.4 - - - +
1522 LYS* 2.8 31.2 + - - -
1532 THR 4.7 0.2 + - - -
2032 ILE* 3.8 15.9 - - + +
2042 VAL 4.5 2.9 - - - +
2052 ASP* 2.7 30.0 + - - +
2062 ASN* 3.5 11.5 + - - +
2072 GLY* 3.7 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1452 LYS* 2.9 51.7 + - + +
1462 ALA* 3.8 8.0 - - - +
1482 GLN* 1.3 81.9 - - + +
1502 VAL* 1.3 58.9 + - + +
1522 LYS* 3.0 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032 MET 5.7 2.7 - - - +
1122 PHE* 3.6 34.5 - - + +
1132 VAL* 4.0 4.7 - - - +
1142 THR* 3.6 37.8 - - + +
1162 HIS* 3.7 8.7 - - - -
1462 ALA* 3.1 15.8 + - + +
1472 ILE* 3.1 10.1 + - - +
1492 GLU* 1.3 80.5 - - + +
1512 ALA* 1.3 64.0 + - - +
1522 LYS* 3.8 3.8 - - - -
2212 VAL* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142 THR* 4.6 3.4 - - - -
1162 HIS* 4.1 10.6 + - - -
1472 ILE* 2.8 18.6 + - + +
1482 GLN* 4.0 3.6 - - - +
1502 VAL* 1.3 77.2 - - - +
1522 LYS* 1.3 64.7 + - - +
1532 THR* 2.9 38.2 + - - +
1552 ALA* 3.6 21.5 - - + -
2032 ILE* 5.1 1.6 - - + -
2192 THR* 4.6 3.5 - - + +
2212 VAL* 3.8 14.4 - - + -
----------------------------------------------------------
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