Contacts of the strand formed by residues 140 - 148 (chain D) in PDB entry 1I3R
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 LEU 140 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A NAG 6.5 1.1 - - + -
129D PRO* 3.3 7.0 - - - +
130D THR* 3.1 42.4 + - - +
131D LYS* 6.4 0.2 - - + -
138D HIS* 3.6 2.2 - - - +
139D ASN* 1.3 87.6 + - - +
141D LEU* 1.3 60.2 + - - +
142D VAL* 4.5 0.9 - - + -
169D VAL* 5.6 2.9 - - + -
186D MET* 3.3 55.4 - - + -
187D LEU 3.4 21.5 - - - +
188D GLU* 3.9 17.3 - - + -
189D THR 4.0 1.1 + - - -
191D PRO* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D VAL* 4.4 1.6 - - + -
128D TYR 3.8 2.7 - - - -
129D PRO* 4.1 15.5 - - + -
140D LEU* 1.3 74.2 - - - +
142D VAL* 1.3 60.6 + - - +
157D TRP* 3.4 31.2 - - + -
186D MET* 3.5 1.3 - - - -
187D LEU* 2.9 40.4 + - + +
189D THR* 4.6 6.9 + - - +
191D PRO* 5.1 4.9 - - + -
197D TYR* 3.3 51.4 - - + -
214D TRP* 3.5 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D VAL* 3.2 4.3 - - - +
128D TYR* 2.6 70.0 + - + +
130D THR* 4.1 25.6 - - + +
140D LEU* 4.5 1.3 - - + -
141D LEU* 1.3 73.5 - - - +
143D CYS* 1.3 72.5 + - - +
144D SER 3.7 0.9 + - - -
157D TRP* 4.0 2.7 - - - -
184D LEU* 4.1 18.4 - - + -
186D MET* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D VAL* 3.9 17.5 - - - -
126D THR 3.4 5.4 - - - -
127D VAL* 4.2 1.3 - - - -
142D VAL* 1.3 74.1 - - - +
144D SER* 1.3 60.2 + - - +
145D VAL* 3.8 14.1 + - - +
155D VAL* 4.2 1.1 - - - -
157D TRP* 3.5 16.0 - - + +
183D THR 4.0 0.3 - - - +
184D LEU* 3.8 1.0 - - - -
185D VAL* 3.1 42.3 + - + +
199D CYS* 2.0 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PRO* 3.3 24.7 - - - +
124D THR 3.3 4.9 - - - +
125D VAL* 3.4 2.1 - - - +
126D THR* 2.6 46.9 + - - -
128D TYR* 4.0 21.8 - - - -
142D VAL 3.7 1.0 + - - -
143D CYS* 1.3 72.3 - - - +
145D VAL* 1.3 61.6 + - - +
146D SER* 4.2 4.0 + - - -
183D THR 4.6 0.2 + - - -
184D LEU* 3.7 25.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PRO* 3.7 12.6 - - + -
124D THR 3.8 2.7 - - - -
125D VAL* 4.5 3.4 - - + -
143D CYS* 4.1 12.3 - - - +
144D SER* 1.3 77.8 + - - +
146D SER* 1.3 60.6 + - - +
148D PHE* 3.4 12.4 - - + -
153D ILE* 3.2 33.7 - - + -
155D VAL* 4.0 15.3 - - + -
182D GLN* 3.3 2.1 - - - -
183D THR* 2.9 47.5 + - + +
185D VAL* 5.6 0.2 - - + -
201D VAL* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG 4.8 0.2 - - - -
95C SER* 4.4 3.8 - - - -
96C PRO* 3.3 33.5 - - - +
123D PRO* 3.2 4.3 - - - +
124D THR* 2.9 40.6 + - - -
144D SER* 4.2 1.9 + - - -
145D VAL* 1.3 76.2 - - - +
147D ASP* 1.3 82.1 + - - +
148D PHE* 3.5 4.0 - - - -
181D PHE 3.6 4.9 - - - -
182D GLN* 4.1 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG* 2.8 37.0 + - - +
95C SER* 3.7 15.5 - - - -
96C PRO* 5.0 0.2 - - - +
121D VAL* 3.2 14.8 - - + +
122D GLU 3.2 18.4 - - - +
124D THR* 4.1 14.4 + - - +
146D SER* 1.3 87.4 + - - +
148D PHE* 1.3 55.6 + - - +
176D ASN* 5.1 1.6 + - - +
180D THR* 4.1 16.2 + - + -
181D PHE 3.0 12.1 + - - -
182D GLN* 4.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 3.7 10.1 - - - +
123D PRO* 3.7 22.4 - - + -
145D VAL* 3.4 43.1 - - + -
146D SER 3.7 7.6 - - - -
147D ASP* 1.3 76.0 - - - +
149D TYR* 1.3 65.0 + - - +
150D PRO 3.4 13.2 - - - -
151D GLY 3.6 22.4 - - - -
153D ILE* 3.6 24.2 - - + -
173D LEU* 4.0 7.6 - - + -
180D THR* 3.5 4.0 - - - -
181D PHE* 3.0 56.5 + - + +
182D GLN* 3.9 1.1 - - - -
183D THR* 4.2 6.3 - - + -
203D HIS* 3.7 8.7 - + - +
----------------------------------------------------------
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