Contacts of the strand formed by residues 1114 - 1118 (chain Q) in PDB entry 1YYL
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 SER1114 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112Q ALA 4.9 1.9 + - - -
1113Q PRO* 1.3 71.8 - - - +
1115Q VAL* 1.3 61.5 + - - +
1116Q PHE* 3.5 18.5 - - - -
1135Q LEU 3.1 4.7 - - - +
1136Q LEU* 3.5 0.6 - - - -
1137Q ASN* 2.7 57.1 + - - +
1138Q ASN* 5.3 0.7 + - - +
1130R SER* 5.4 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1115 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113Q PRO* 3.7 23.5 + - + +
1114Q SER* 1.3 76.5 - - - +
1116Q PHE* 1.3 72.3 + - - +
1134Q CYS* 4.0 20.0 - - - -
1135Q LEU 3.2 7.4 - - - +
1136Q LEU* 4.6 3.1 - - + -
1194Q CYS* 4.8 1.8 - - - +
1196Q VAL* 4.1 24.5 - - + -
1205Q VAL* 4.2 22.7 - - + +
1207Q LYS* 3.2 42.6 - - + +
1129R LYS 5.2 0.5 - - - +
1130R SER* 5.3 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1116 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114Q SER* 3.5 33.2 - - - -
1115Q VAL* 1.3 81.6 - - - +
1117Q ILE* 1.3 60.2 + - - +
1118Q PHE* 4.2 12.6 - - + -
1133Q VAL 4.2 0.2 - - - +
1134Q CYS* 3.5 6.5 - - - -
1135Q LEU* 2.8 47.5 + - + +
1137Q ASN* 3.9 15.0 - - + -
1207Q LYS* 4.5 6.1 - - - +
1129R LYS* 3.4 44.9 - - + +
1130R SER* 3.4 36.1 - - - -
1135R THR* 4.7 15.0 - - + -
1137R ALA* 3.8 13.2 - - + -
1183R THR* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1117 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116Q PHE* 1.3 74.5 - - - +
1118Q PHE* 1.3 68.9 + - - +
1119Q PRO* 4.1 0.8 - - + +
1132Q VAL* 4.5 3.1 - - + -
1133Q VAL 3.6 8.5 - - - +
1134Q CYS* 4.5 0.2 - - - +
1148Q TRP* 4.2 19.5 - - + -
1192Q TYR 3.6 23.3 - - - +
1194Q CYS* 4.3 7.4 - - + +
1207Q LYS* 3.6 38.2 - - + +
1208Q SER* 3.8 14.6 - - - +
1209Q PHE* 3.7 25.1 - - + -
1127R SER* 3.9 17.6 - - - +
1128R SER* 6.1 0.2 - - - +
1129R LYS* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1118 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116Q PHE* 4.2 6.1 - - + -
1117Q ILE* 1.3 80.0 - - - +
1119Q PRO* 1.3 68.8 - - + +
1131Q SER 4.5 0.5 - - - +
1132Q VAL* 3.3 9.2 - - - +
1133Q VAL* 2.8 54.5 + - + +
1135Q LEU* 3.9 29.4 - - + -
1124R LEU* 3.7 40.2 - - + -
1125R ALA 3.5 17.5 - - - +
1129R LYS* 3.6 15.3 - - - -
1137R ALA* 3.2 45.3 - - + -
1138R LEU 4.7 4.5 - - - -
1181R VAL* 4.8 4.3 - - + -
----------------------------------------------------------
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