Contacts of the strand formed by residues 1013 - 1018 (chain C) in PDB entry 3DLS
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 VAL1013 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ADP 3.3 74.5 - - + +
1004C PRO* 3.7 3.1 - - - +
1005C LEU* 3.1 28.1 + - + +
1010C PHE 5.0 2.2 + - - +
1011C GLY* 4.7 1.2 - - - -
1012C PHE* 1.3 82.7 + - + +
1014C TRP* 1.3 72.8 + - - +
1026C VAL* 3.7 15.3 - - + -
1027C VAL 3.4 5.2 - - - +
1028C LYS* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1014 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174A LEU 5.1 0.2 - - - -
1175A MET* 3.3 54.5 - - + -
1001C THR* 3.5 30.3 - - + -
1002C MET 4.4 0.9 - - - -
1003C SER* 3.2 29.8 - - - +
1004C PRO* 3.2 11.2 - - + -
1005C LEU* 4.1 7.2 - - - +
1010C PHE* 3.9 31.0 - + + -
1011C GLY 2.9 26.6 + - - -
1012C PHE* 3.6 5.5 - - - +
1013C VAL* 1.3 99.6 + - - +
1015C THR* 1.3 60.7 + - - +
1026C VAL* 3.4 5.4 - - - +
1027C VAL* 2.9 37.2 + - + +
1029C PHE* 3.7 17.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1015 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001C THR 3.8 0.2 - - - -
1002C MET* 2.8 37.9 + - + -
1003C SER* 2.7 31.2 + - - +
1005C LEU* 3.4 18.6 - - - +
1014C TRP* 1.3 74.2 - - - +
1016C ALA* 1.3 64.2 + - - +
1024C GLU* 3.6 33.2 - - + +
1025C VAL 3.5 7.9 - - - +
1026C VAL* 4.7 0.9 - - - +
1083C LYS* 2.8 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1016 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995C TYR* 3.5 26.0 - - - +
999C TYR* 4.3 5.8 - - + -
1000C SER 3.3 9.2 - - - +
1001C THR* 4.2 0.9 - - - +
1002C MET 4.2 0.7 - - - +
1014C TRP 3.6 0.6 + - - -
1015C THR* 1.3 76.0 - - - +
1017C VAL* 1.3 66.6 + - - +
1024C GLU* 3.4 6.9 - - - -
1025C VAL* 2.9 46.5 + - + +
1027C VAL* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1017 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999C TYR* 3.2 7.1 - - - -
1000C SER* 2.8 37.8 + - - +
1002C MET* 3.6 28.5 - - + -
1015C THR* 5.3 0.2 - - + -
1016C ALA* 1.3 79.1 - - - +
1018C ASP* 1.3 72.8 + - - +
1019C LYS* 3.2 9.9 + - + +
1022C ASN* 3.9 29.2 - - - +
1023C LYS 3.5 6.5 - - - +
1024C GLU* 4.5 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1018 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998C LYS* 3.1 32.2 + - - +
999C TYR* 3.7 21.8 + - + -
1016C ALA 4.3 0.4 - - - -
1017C VAL* 1.3 68.6 - - - +
1019C LYS* 1.3 54.3 + - - +
1020C GLU* 3.2 11.1 + - - +
1021C LYS* 2.9 27.5 + - + +
1022C ASN* 2.6 36.4 + - - -
1023C LYS* 2.9 41.4 + - + +
1025C VAL* 4.6 1.9 - - + +
----------------------------------------------------------
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