Contacts of the strand formed by residues 999 - 1004 (chain D) in PDB entry 4OUL
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 999 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998D VAL* 1.3 79.4 - - - +
1000D PHE* 1.3 59.5 + - - +
1024D ASN* 2.8 25.5 - - - +
1025D ASN 3.4 1.2 - - - -
1026D LEU* 2.8 30.0 + - + +
1029D THR* 5.2 0.9 - - - -
1121D GLY 3.2 8.3 - - - +
1122D TYR* 3.8 12.6 - - + +
1044E THR* 4.6 2.9 - - + -
1091E ILE* 4.1 12.8 - - + -
1124E LEU* 4.0 15.9 - - + -
1125E TYR* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1000 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999D ALA* 1.3 76.7 - - - +
1001D SER* 1.3 65.0 + - - +
1002D ALA 4.5 1.1 - - - -
1022D LEU* 5.3 0.2 - - + -
1024D ASN* 3.3 11.9 - - - +
1025D ASN* 4.0 5.8 - - - +
1029D THR* 4.2 3.6 - - - +
1030D PHE* 3.5 54.3 - + + -
1037D PHE* 3.5 38.8 - + + -
1047D PHE* 3.9 6.7 - + - -
1119D PHE* 3.6 38.8 - + - -
1120D SER* 3.1 13.5 - - - -
1121D GLY* 2.9 55.3 + - - +
1091E ILE* 3.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1001 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000D PHE* 1.3 75.6 - - - +
1002D ALA* 1.3 57.4 + - - +
1022D LEU* 3.6 3.1 - - - +
1023D LEU* 2.7 43.9 + - - +
1024D ASN* 2.9 15.3 + - - +
1118D THR* 5.6 2.6 - - - +
1119D PHE 3.5 1.3 - - - -
1120D SER* 2.6 24.3 + - - -
1089E HIS* 4.7 0.5 + - - -
1090E ALA* 4.2 4.3 - - - -
1091E ILE* 3.4 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1002 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000D PHE* 4.9 0.7 - - + -
1001D SER* 1.3 75.4 + - - +
1003D ALA* 1.3 62.8 + - - +
1019D PHE* 3.7 26.0 - - + -
1021D LEU 3.4 9.9 - - - +
1022D LEU* 4.5 3.6 - - + -
1023D LEU* 3.9 2.4 - - - +
1030D PHE* 3.8 25.4 - - + -
1032D LEU* 4.7 0.4 - - + -
1118D THR* 3.2 7.4 - - - +
1119D PHE 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1003 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002D ALA* 1.3 76.4 - - - +
1004D ARG* 1.3 58.2 + - - +
1019D PHE* 3.5 8.3 - - - -
1020D ASP* 3.2 26.9 + - - +
1021D LEU* 3.0 16.4 + - + +
1023D LEU* 3.5 20.2 - - + -
1115D LYS* 3.8 29.2 - - + -
1117D SER 3.2 11.0 - - - +
1118D THR* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1004 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003D ALA* 1.3 72.5 - - - +
1005D THR* 1.3 61.6 + - - +
1006D SER* 3.1 23.2 + - - +
1007D ASN 4.2 4.2 + - - -
1008D LEU* 3.2 35.5 - - - +
1017D ILE* 5.0 3.8 - - + -
1018D VAL* 2.6 48.3 + - - +
1019D PHE* 3.7 18.0 + - + +
1020D ASP* 3.6 19.0 + - - +
1051D MET* 5.8 0.2 - - - -
1109D ILE* 4.5 13.5 - - + -
1110D TYR 4.4 1.6 - - - +
1111D GLY* 3.5 13.1 - - - -
1112D SER 3.5 9.4 + - - +
1115D LYS* 4.1 10.2 - - - -
1116D TYR 4.9 0.2 + - - -
1117D SER* 3.0 26.3 + - - +
----------------------------------------------------------
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