Contacts of the strand formed by residues 137 - 147 (chain C) in PDB entry 3IU3
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 THR 137 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C THR* 3.3 5.5 - - - +
134C SER* 2.7 44.0 + - - -
136C GLY* 1.3 79.0 - - - +
138C ALA* 1.3 73.2 + - - +
185C THR* 3.7 26.0 - - + -
186C VAL 3.4 8.9 - - - +
188C SER* 3.5 2.9 - - - -
111D SER* 6.2 0.7 - - - +
113D PHE* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PRO* 5.0 3.6 - - + -
132C SER 3.6 8.5 - - - +
133C THR* 4.3 7.4 - - - +
137C THR* 1.3 77.3 - - - +
139C ALA* 1.3 62.4 + - - +
140C LEU* 5.7 0.2 - - + -
185C THR* 3.3 5.0 - - - -
186C VAL* 2.8 39.4 + - + +
188C SER* 3.6 9.9 + - - +
191C LEU* 3.7 35.7 - - + -
113D PHE* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PRO* 4.1 2.5 - - - +
132C SER* 2.9 29.7 + - - -
138C ALA* 1.3 75.6 - - - +
140C LEU* 1.3 62.7 + - - +
184C VAL 3.5 4.9 - - - +
185C THR* 4.1 9.2 - - + -
113D PHE* 3.6 41.7 - - + -
115D PHE* 3.2 10.2 - - + -
132D LEU* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU 3.4 16.6 - - - +
128C PRO* 3.6 26.2 - - + -
139C ALA* 1.3 75.7 - - - +
141C GLY* 1.3 57.4 + - - +
156C TRP* 3.6 28.3 - - + -
183C VAL* 3.5 4.1 - - - +
184C VAL* 2.7 56.4 + - + +
186C VAL* 3.9 27.8 - - + -
191C LEU* 4.7 4.3 - - + -
196C TYR* 4.1 16.4 - - + -
213C VAL* 3.8 15.0 - - + +
115D PHE* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PRO 3.7 0.2 - - - -
126C LEU* 2.7 44.8 + - - +
140C LEU* 1.3 79.3 - - - +
142C CYS* 1.3 57.3 + - - -
156C TRP* 3.6 16.2 - - - -
182C SER 3.0 12.6 - - - -
183C VAL* 4.0 0.7 - - - -
213C VAL* 3.6 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C VAL* 4.0 15.3 - - + -
124C PHE 3.6 4.5 - - - -
125C PRO* 4.9 1.1 - - - -
126C LEU* 4.0 3.4 - - - -
141C GLY* 1.3 77.9 - - - -
143C LEU* 1.3 60.9 + - - +
144C VAL* 3.7 8.3 + - + +
156C TRP* 3.8 2.4 - - + -
181C SER* 3.4 3.5 - - - -
182C SER* 2.6 42.8 + - - +
198C CYS* 2.0 53.2 - - + -
200C VAL* 5.0 0.4 - - + -
211C LYS* 4.5 5.6 - - - -
213C VAL* 4.0 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C SER 3.5 2.8 - - - +
123C VAL* 3.4 4.7 - - - -
124C PHE* 2.7 52.3 + - + +
126C LEU* 4.2 15.3 - - + +
142C CYS* 1.3 71.8 - - - +
144C VAL* 1.3 57.9 + - - +
145C LYS* 3.7 10.7 + - + -
179C SER* 4.4 11.0 - - - +
180C LEU 3.7 11.7 - - - +
181C SER* 3.4 21.3 - - - +
121D GLN* 4.2 17.0 - - - +
128D SER* 3.7 30.3 - - - +
130D VAL* 4.4 14.6 - - + -
175D THR* 5.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PRO* 3.6 25.8 - - + -
122C SER 3.8 2.9 - - - -
123C VAL* 4.4 5.6 - - + +
142C CYS* 4.3 10.5 - - + +
143C LEU* 1.3 72.1 - - - +
145C LYS* 1.3 59.0 + - - +
147C TYR* 3.9 6.0 - - + -
152C VAL* 4.2 15.5 - - + -
154C VAL* 4.2 14.6 - - + -
179C SER* 3.4 2.8 - - - -
180C LEU* 2.9 49.1 + - + +
182C SER 5.2 0.4 - - - +
200C VAL* 3.7 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PRO* 3.5 2.4 - - - +
122C SER* 3.0 37.9 + - - +
124C PHE* 4.3 12.8 - - + -
143C LEU* 4.4 14.4 - - + +
144C VAL* 1.3 75.0 - - - +
146C ASP* 1.3 92.9 + - - +
147C TYR* 3.7 1.8 - - - -
173C GLN* 3.3 22.8 + - - +
179C SER* 3.4 17.0 - - - +
121D GLN* 3.8 26.9 - - - +
126D THR* 4.1 21.1 - - - +
128D SER* 4.3 7.7 + - - +
177D THR* 4.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 3.7 18.3 - - - +
120C GLY 3.5 15.4 - - - +
122C SER* 4.7 4.7 + - - +
145C LYS* 1.3 100.3 + - + +
147C TYR* 1.3 56.0 + - - +
173C GLN* 3.3 24.8 + - - -
175C SER* 4.4 1.0 + - - -
177C LEU* 3.8 27.4 - - + +
178C TYR 3.0 14.3 + - - -
126D THR* 5.4 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 3.5 11.2 - - - +
121C PRO* 3.6 28.5 - - + -
144C VAL* 3.9 22.9 - - + -
146C ASP* 1.3 75.0 - - - +
148C PHE* 1.3 61.8 + - - +
149C PRO 3.3 26.5 - - - -
150C GLU* 4.1 12.8 + - + +
152C VAL* 3.7 29.9 + - + +
170C ALA* 3.2 24.9 - - - +
177C LEU* 3.6 3.8 - - - +
178C TYR* 2.7 70.4 + - + +
179C SER* 3.9 5.8 - - - -
180C LEU* 3.4 13.7 - - + +
202C HIS* 3.8 7.2 - - - +
----------------------------------------------------------
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