Contacts of the strand formed by residues 140 - 150 (chain C) in PDB entry 4IJ3
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 140 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASN* 3.2 27.6 + - - +
139C SER* 1.3 88.3 + - - +
141C VAL* 1.3 61.2 + - - +
187C THR* 3.5 35.9 - - + +
188C VAL* 3.4 15.3 - - - +
189C PRO* 3.6 22.2 - - + -
190C SER* 3.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PRO* 4.5 10.5 - - + -
140C MET* 1.3 76.0 - - - +
142C THR* 1.3 67.5 + - - +
143C LEU* 3.8 23.4 + - + +
186C VAL 4.1 0.3 - - - +
187C THR* 3.4 3.2 - - - +
188C VAL* 2.7 60.5 + - + +
189C PRO 4.1 0.7 - - - +
190C SER* 4.0 22.0 - - - +
193C TRP* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 5.0 8.8 - - - +
116B SER* 3.9 24.9 + - - +
118B PHE* 3.1 28.7 - - + -
135B PHE* 4.3 11.9 - - + -
137B ASN* 4.6 7.3 + - - +
131C PRO* 4.3 3.1 - - - +
140C MET 5.6 0.2 - - - -
141C VAL* 1.3 78.2 - - - +
143C LEU* 1.3 74.6 + - - +
185C SER* 4.3 6.7 - - - -
186C VAL 3.5 11.0 - - - +
187C THR* 3.0 20.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
118B PHE* 4.2 4.5 - - - -
129C LEU 3.5 7.6 - - - +
131C PRO* 3.4 29.6 - - + -
141C VAL* 3.8 17.3 - - + +
142C THR* 1.3 81.5 - - - +
144C GLY* 1.3 59.3 + - - +
185C SER* 3.4 4.3 - - - -
186C VAL* 3.0 39.1 + - + +
188C VAL* 4.9 5.6 - - + -
193C TRP* 3.6 49.8 - - + +
198C VAL* 3.8 20.6 - - + -
215C ILE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 4.4 1.3 - - - -
129C LEU* 2.7 51.1 + - - +
143C LEU* 1.3 78.2 - - - +
145C CYS* 1.3 55.9 + - - -
159C TRP* 3.4 12.7 - - - -
184C SER 3.1 13.0 - - - -
185C SER* 4.1 0.7 - - - -
215C ILE* 3.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C VAL* 4.0 14.1 - - + -
127C TYR 3.5 5.6 - - - -
129C LEU* 3.8 4.2 - - - +
144C GLY* 1.3 78.4 - - - -
146C LEU* 1.3 60.2 + - - +
147C VAL* 4.0 7.0 + - + +
157C VAL* 5.3 0.9 - - + -
159C TRP* 3.7 6.5 - - + -
183C SER* 3.2 7.6 - - - -
184C SER* 2.9 35.2 + - - +
200C CYS* 2.0 52.0 - - + -
202C VAL* 5.2 0.4 - - + -
213C LYS* 4.4 3.4 - - - -
215C ILE* 4.0 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLN* 4.4 3.4 - - - +
131B SER* 3.7 31.2 - - - +
133B VAL* 4.2 16.6 - - + -
178B THR* 4.9 9.4 - - + +
125C SER 3.2 6.2 - - - +
126C VAL* 3.3 0.9 - - - -
127C TYR* 2.9 63.0 + - + +
129C LEU* 4.1 13.2 - - + +
145C CYS* 1.3 74.0 - - - +
147C VAL* 1.3 59.3 + - - +
148C LYS* 4.5 11.7 - - + -
181C THR* 4.1 14.6 - - + -
182C LEU 3.5 17.3 - - - +
183C SER* 4.0 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PRO* 3.4 29.6 - - + -
125C SER 3.5 4.3 - - - +
126C VAL* 4.5 4.5 - - + -
145C CYS* 4.9 5.2 - - + +
146C LEU* 1.3 75.3 - - - +
148C LYS* 1.3 59.5 + - - +
150C TYR* 3.5 16.9 - - + -
155C VAL* 4.3 4.5 - - + -
157C VAL* 4.3 5.8 - - + -
181C THR* 3.3 3.7 - - - +
182C LEU* 2.9 58.3 + - + +
184C SER 6.0 0.2 - - - +
202C VAL* 3.7 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLN* 3.8 27.6 - - - +
129B GLY* 6.4 0.7 - - - -
131B SER* 4.3 7.9 - - - +
180B THR* 4.3 11.0 + - - +
124C PRO* 3.7 0.3 - - - +
125C SER* 2.9 44.6 + - - +
127C TYR* 4.6 9.6 - - + -
146C LEU* 4.5 11.4 - - + -
147C VAL* 1.3 76.7 - - - +
149C GLY* 1.3 68.8 + - - +
150C TYR* 3.5 3.5 + - - -
176C GLU* 2.8 36.3 + - - +
181C THR* 3.5 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C THR* 3.2 16.6 - - - +
123C PRO 3.6 3.5 - - - +
148C LYS* 1.3 83.0 - - - +
150C TYR* 1.3 57.5 + - - +
176C GLU 5.6 0.4 - - - -
179C LEU* 3.2 37.1 - - - +
180C TYR 3.0 11.1 + - - -
181C THR* 3.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C THR 3.1 13.5 - - - +
123C PRO 4.2 0.2 - - - -
124C PRO* 3.4 22.7 - - + -
147C VAL* 3.5 40.4 - - + -
149C GLY* 1.3 78.9 - - - +
151C PHE* 1.3 64.4 - - - +
152C PRO 3.7 11.2 - - - -
153C GLU* 4.0 20.1 + - + +
155C VAL* 3.3 29.6 + - + +
173C ALA* 3.3 23.7 - - - +
179C LEU* 3.7 1.5 - - - -
180C TYR* 2.8 65.2 + - + +
181C THR* 4.2 2.2 - - - -
182C LEU* 3.4 15.6 - - + +
204C HIS* 4.1 2.0 - - + -
----------------------------------------------------------
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