Contacts of the strand formed by residues 157 - 166 (chain A) in PDB entry 3F00
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 GLN 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 3.4 9.8 + - - -
152A ASP* 2.8 56.3 + - + +
155A ASN* 3.8 21.9 - - + +
156A ASN* 1.3 78.1 - - - +
158A LEU* 1.3 59.0 + - - +
159A LEU* 4.0 14.0 - - + +
211A THR* 3.4 27.1 + - + +
212A PHE 3.3 13.7 - - - +
213A LYS* 4.2 13.4 - - + +
214A VAL 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 3.6 32.3 - - + -
150A ASP 3.9 7.0 - - - +
151A TYR* 3.7 15.3 - - + -
157A GLN* 1.3 71.6 - - - +
159A LEU* 1.3 62.8 + - - +
160A VAL* 4.2 20.0 - - + -
185A LEU* 4.4 10.5 - - + -
210A PHE 3.8 0.5 - - - +
211A THR* 3.4 4.0 - - - -
212A PHE* 2.8 57.3 + - + +
214A VAL* 5.7 0.7 - - + +
219A LEU* 4.3 24.2 - - + -
224A LEU* 5.0 2.5 - - + -
247A MET* 3.9 26.7 - - + -
252A PHE* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 3.4 6.4 - - - +
150A ASP* 2.8 54.6 + - + +
152A ASP* 4.2 17.9 - - + +
157A GLN* 4.0 26.7 - - + +
158A LEU* 1.3 77.0 - - - +
160A VAL* 1.3 62.6 + - - +
161A GLY 4.2 0.4 - - - -
209A GLN* 4.1 25.6 - - - +
210A PHE 3.5 2.0 - - - +
211A THR* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 5.1 0.7 - - + -
148A SER 3.5 9.0 - - - +
149A LEU* 5.0 1.8 - - + -
158A LEU* 4.2 10.1 - - + -
159A LEU* 1.3 78.6 - - - +
161A GLY* 1.3 62.7 + - - +
162A ILE* 3.9 25.4 + - + -
183A VAL* 4.2 8.1 - - + -
208A GLU 3.9 0.3 - - - +
209A GLN* 3.2 5.6 - - - +
210A PHE* 2.7 45.5 + - + +
212A PHE* 3.7 31.4 - - + -
224A LEU* 3.9 30.1 - - + -
226A MET* 4.5 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 3.0 11.8 - - - +
148A SER* 2.8 50.3 + - - -
159A LEU 4.2 0.2 - - - -
160A VAL* 1.3 72.0 - - - +
162A ILE* 1.3 62.9 + - - -
163A ILE* 3.6 4.3 - - - -
208A GLU 3.4 7.0 - - - -
209A GLN* 4.4 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.3 9.4 - - + -
146A GLN 4.3 1.3 - - - -
147A TYR* 4.4 1.8 - - + -
160A VAL* 3.9 10.8 - - + -
161A GLY* 1.3 71.5 - - - +
163A ILE* 1.3 60.2 + - - +
181A VAL* 3.8 29.4 - - + -
183A VAL* 3.7 19.5 - - + -
195A THR* 3.8 14.4 - - + -
206A PHE* 3.4 12.2 - - + +
207A ASN 3.2 5.4 + - - -
208A GLU 2.8 33.0 + - - +
210A PHE* 3.7 27.1 - - + -
226A MET* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLN* 3.0 45.8 + - + +
147A TYR* 3.8 24.2 - - - +
148A SER* 3.9 14.8 - - - +
161A GLY* 3.9 10.5 - - - +
162A ILE* 1.3 73.1 - - - +
164A GLN* 1.3 68.3 + - + +
205A VAL* 3.7 1.7 - - + +
206A PHE* 2.8 22.8 + - - -
207A ASN* 3.0 26.1 + - - +
257A GLU* 4.3 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.4 7.4 - - - +
146A GLN* 2.8 54.3 + - + +
162A ILE 4.0 0.2 - - - -
163A ILE* 1.3 87.0 - - + +
165A ALA* 1.3 63.0 + - - +
204A PRO 3.2 14.6 - - - +
205A VAL* 3.9 19.5 - - + +
206A PHE* 4.0 5.0 - - - -
259A TRP* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS 3.1 13.2 - - - +
145A LEU* 3.9 14.4 - - + -
164A GLN* 1.3 79.5 - - - +
166A ALA* 1.3 62.8 + - - +
168A LEU* 4.2 17.5 - - + -
203A ASN* 3.4 19.9 - - - +
204A PRO* 2.9 31.6 + - + +
206A PHE* 4.1 4.1 - - + -
228A VAL* 5.3 4.3 - - + -
259A TRP* 4.3 2.0 - - - -
262A LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY* 3.2 0.3 - - - -
144A LYS* 2.9 54.3 + - - +
164A GLN* 5.9 0.4 - - - +
165A ALA* 1.3 76.2 - - - +
167A GLU* 1.3 74.1 + - + +
168A LEU* 3.2 4.9 + - - +
202A LEU 3.8 1.1 - - - -
203A ASN* 3.2 11.4 - - + +
259A TRP* 3.9 11.4 - - + -
----------------------------------------------------------
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