Contacts of the strand formed by residues 112 - 130 (chain 1) in PDB entry 1D3E
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 MET 112 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111 GLU* 3.8 28.5 - - - +
1131 PHE* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121 MET* 3.8 29.2 - - - +
1141 THR* 3.8 28.9 - - - +
2481 PRO* 4.3 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 PHE* 3.8 29.4 - - - +
1151 TYR* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141 THR* 3.8 29.2 - - - +
1161 ALA* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151 TYR* 3.8 28.7 - - - +
1171 ARG* 3.8 28.9 - - - +
2451 ALA* 4.3 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 ALA* 3.8 28.9 - - - +
1181 PHE* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 ARG* 3.8 28.9 - - - +
1191 ASP* 3.8 28.7 - - - +
2431 THR* 4.4 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181 PHE* 3.8 29.4 - - - +
1201 SER* 3.8 28.5 - - - +
1821 PRO* 4.7 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191 ASP* 3.8 29.4 - - - +
1211 GLU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201 SER* 3.8 29.4 - - - +
1221 ILE* 3.8 28.5 - - - +
1801 SER* 4.4 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211 GLU* 3.8 28.9 - - - +
1231 THR* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221 ILE* 3.8 28.7 - - - +
1241 MET* 3.8 28.9 - - - +
1781 ARG* 4.3 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231 THR* 3.8 28.9 - - - +
1251 VAL* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 MET* 3.8 29.4 - - - +
1261 PRO* 3.8 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 126 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251 VAL* 3.8 29.2 - - - -
1271 SER* 3.8 29.2 - - - -
2341 THR* 4.1 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 PRO* 3.8 30.1 - - - -
1281 VAL* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271 SER* 3.8 29.2 - - - +
1291 ALA* 3.8 29.2 - - - +
2321 VAL* 4.5 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281 VAL* 3.8 29.6 - - - +
1301 ALA* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291 ALA* 3.8 28.9 - - - +
1311 LYS* 3.8 27.4 - - - +
----------------------------------------------------------
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