Contacts of the strand formed by residues 135 - 140 (chain U) in PDB entry 1W13
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 SER 135 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133U GLY 3.7 1.1 + - - -
134U THR* 1.3 82.3 - - - +
136U CYS* 1.3 64.2 + - - +
159U VAL* 3.9 20.0 - - - +
160U VAL 3.4 5.4 - - - -
161U LYS* 3.7 25.1 - - - +
201U CYS* 4.6 4.3 - - - -
202U SER* 4.8 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134U THR* 3.9 4.0 - - - -
135U SER* 1.3 78.8 - - - +
137U GLU* 1.3 61.9 + - - +
159U VAL* 3.3 7.0 - - - -
160U VAL* 2.7 34.9 + - - +
162U LEU* 3.5 25.1 - - + -
199U LEU* 3.7 16.4 - - + -
200U VAL 3.2 6.1 - - - +
201U CYS* 2.0 50.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U ASN 4.9 1.2 - - - +
27U GLN* 2.8 39.6 + - - +
29U TRP* 3.8 7.6 - - - -
136U CYS* 1.3 74.7 - - - +
138U ILE* 1.3 65.2 + - - +
139U THR* 5.2 0.7 - - - +
157U MET* 4.3 10.6 - - + +
158U THR 3.2 12.1 - - - +
159U VAL* 4.7 7.6 - - + -
198U PRO 3.5 0.7 - - - +
199U LEU* 3.3 4.0 - - - -
200U VAL* 2.7 55.4 + - + +
207U MET* 3.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U ILE* 3.8 19.4 - - + +
137U GLU* 1.3 71.6 - - - +
139U THR* 1.3 66.3 + - - +
157U MET* 3.3 5.5 - - - +
158U THR* 3.0 56.5 + - + +
160U VAL* 4.3 12.6 - - + -
189U ASP 4.1 0.7 - - - -
190U SER* 3.8 17.9 - - - +
198U PRO 3.3 11.9 - - - +
199U LEU* 3.6 28.9 - - + -
213U VAL* 4.7 4.9 - - + -
228U TYR* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U ILE* 4.4 5.5 - - - +
22U THR* 4.7 0.2 - - + -
27U GLN* 2.8 47.7 + - + -
30U PHE* 3.8 23.9 - - + -
137U GLU* 4.8 1.4 + - - +
138U ILE* 1.3 79.8 + - - +
140U GLY* 1.3 58.8 + - - +
155U LEU* 3.6 24.9 - - + -
156U LYS 3.2 18.2 - - - +
157U MET* 4.4 1.1 - - + +
194U ASP* 4.5 4.7 - - - +
197U GLY* 4.3 6.2 - - - -
198U PRO* 3.7 20.3 + - - +
200U VAL* 6.1 0.2 - - - +
213U VAL* 5.4 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U ILE* 4.0 5.1 + - - +
30U PHE* 4.2 8.1 - - - -
40U TYR* 5.4 0.4 - - - -
139U THR* 1.3 77.9 - - - +
141U PHE* 1.3 58.3 + - - -
142U GLY 3.3 5.5 + - - -
155U LEU* 3.7 11.2 - - - -
156U LYS* 3.1 37.6 + - - +
194U ASP* 3.2 16.6 - - - -
----------------------------------------------------------
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