Contacts of the strand formed by residues 1099 - 1106 (chain F) 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 GLN1099 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036F ARG* 2.8 51.7 + - - +
1037F PHE 3.3 3.8 - - - +
1038F ASN* 3.8 17.2 + - + +
1065F MET 3.6 0.3 - - - +
1066F LYS* 3.4 3.3 - - - +
1067F ASN* 2.6 51.8 + - - +
1097F GLY 3.8 9.6 + - - +
1098F ASP* 1.3 79.4 - - - +
1100F ILE* 1.3 62.3 + - - +
1101F TRP* 3.8 8.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035F GLY 4.0 0.5 - - - +
1036F ARG 3.7 0.2 - - - -
1037F PHE* 2.7 64.3 + - + +
1047F PHE* 3.5 31.2 - - + -
1064F LEU* 3.5 27.8 - - + -
1065F MET 3.3 9.4 - - - +
1066F LYS* 4.0 13.5 - - + -
1071F LEU* 4.4 6.5 - - + -
1092F LEU* 5.0 0.2 - - + -
1094F LEU* 3.8 29.6 - - + -
1098F ASP 5.2 0.2 - - - +
1099F GLN* 1.3 80.1 - - - +
1101F TRP* 1.3 66.4 + - - +
1119F PHE* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095C PHE* 3.8 29.8 - + - -
1016F PRO* 4.0 29.4 - - + -
1034F LEU 5.2 0.4 - - - +
1035F GLY 3.2 19.3 - - - +
1036F ARG* 4.2 19.0 - - + +
1064F LEU* 3.7 4.6 - - - +
1065F MET* 2.7 59.2 + - + +
1067F ASN* 2.7 32.6 + - - +
1068F GLU* 4.9 2.0 - - - -
1099F GLN* 3.8 19.8 + - + +
1100F ILE* 1.3 82.1 - - - +
1102F LEU* 1.3 80.1 + - - +
1103F ARG* 3.6 31.0 - - + -
1119F PHE* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016F PRO* 3.5 4.7 - - - +
1017F ILE* 2.7 52.5 + - + +
1019F PHE* 4.2 4.7 - - + -
1035F GLY 4.3 2.8 + - - -
1049F PHE* 3.7 39.0 - - + -
1051F MET* 3.7 30.3 - - + -
1062F VAL* 4.2 5.4 - - + -
1063F ASN 3.4 9.4 - - - +
1064F LEU* 3.6 29.6 - - + +
1101F TRP* 1.3 77.1 - - - +
1103F ARG* 1.3 55.4 + - - +
1119F PHE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095C PHE* 5.8 2.7 - - - -
1114E TRP* 3.7 15.2 - - - -
1014F ASP* 3.5 50.9 + - - +
1015F GLN 3.4 11.2 - - - +
1017F ILE* 4.1 2.9 - - - -
1062F VAL* 3.3 5.0 - - - +
1063F ASN* 2.8 57.2 + - + +
1065F MET* 3.7 27.5 - - + +
1068F GLU 5.7 0.4 + - - -
1070F VAL* 3.7 16.8 - - - +
1101F TRP* 3.6 26.4 + - + -
1102F LEU* 1.3 73.0 - - - +
1104F LEU* 1.3 61.3 + - - +
1105F HIS* 3.2 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008F LEU* 4.3 5.6 - - + +
1010F PRO* 3.6 34.5 - - + -
1012F THR 4.9 1.7 - - - +
1013F LEU* 4.1 1.0 - - - -
1014F ASP 3.1 15.9 + - - -
1015F GLN* 2.7 20.4 + - - +
1017F ILE* 3.7 19.6 - - + +
1060F LEU* 3.4 21.8 - - + -
1061F TYR 3.7 3.1 - - - +
1062F VAL* 4.6 0.9 - - + -
1103F ARG* 1.3 68.9 - - - +
1105F HIS* 1.3 65.2 - - - +
1106F ARG 3.1 29.4 - - - +
1107F GLY 3.3 22.0 - - - +
1108F ALA* 4.2 6.3 - - - -
1109F ILE* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114E TRP* 3.7 32.4 - + + -
1013F LEU* 3.5 17.5 - - + +
1014F ASP* 2.4 57.2 + - - +
1061F TYR* 2.8 33.5 + + + +
1063F ASN* 3.7 17.9 - - - +
1103F ARG* 3.2 4.7 + - - -
1104F LEU* 1.3 73.5 - - - +
1106F ARG* 1.3 85.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013F LEU* 4.2 22.9 - - + +
1058F VAL* 4.5 8.9 - - + +
1059F PRO* 3.5 40.7 - - - +
1060F LEU* 3.3 0.9 - - - -
1061F TYR* 2.8 50.4 + - + +
1104F LEU* 3.1 13.4 - - - +
1105F HIS* 1.3 104.5 - - + +
1107F GLY* 1.3 62.2 + - - +
----------------------------------------------------------
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