Contacts of the strand formed by residues 165 - 174 (chain A) in PDB entry 5JJ2
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 165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A HIS* 3.7 14.7 + - - +
164A LEU* 1.3 74.3 - - - +
166A LEU* 1.3 62.8 + - - +
167A PRO* 3.3 11.9 - - + +
188A HIS* 3.5 16.8 + - - +
254A GLU* 3.4 42.2 - - + +
255A GLU 3.8 2.2 - - - -
256A ILE* 3.9 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.5 25.6 - - + -
128A ILE* 5.5 2.7 - - + -
164A LEU* 4.0 28.7 - - + +
165A THR* 1.3 75.3 - - - +
167A PRO* 1.3 65.3 - - - +
168A PHE* 3.4 18.2 - - + -
183A LEU* 3.7 21.3 - - + -
188A HIS* 4.3 9.9 - - + -
192A LEU* 4.3 29.8 - - + -
254A GLU* 3.3 2.7 - - - -
255A GLU* 2.8 45.1 + - + +
257A LEU* 5.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 3.3 13.0 - - + +
166A LEU* 1.3 85.1 - - - +
168A PHE* 1.3 61.2 + - - +
169A GLN* 6.3 0.2 - - + -
183A LEU* 3.4 7.8 - - - +
184A ALA* 2.8 34.8 + - + -
185A GLU 5.3 0.2 - - - +
188A HIS* 3.3 33.2 - - + +
253A GLY 3.7 6.3 - - - +
254A GLU* 3.9 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.3 7.2 - - + -
98A ILE* 3.8 20.0 - - + -
128A ILE* 3.5 39.5 - - + -
166A LEU* 3.4 31.0 - - + -
167A PRO* 1.3 73.3 - - - +
169A GLN* 1.3 63.9 + - - +
181A VAL* 3.9 22.9 - - + -
182A LYS 3.3 18.4 - - - +
183A LEU* 4.3 13.5 - - + -
218A PRO 6.1 0.2 - - - -
219A HIS* 5.0 1.6 - - - -
220A LEU* 4.1 15.3 - - + -
251A ARG* 3.7 2.9 - - - +
252A PHE* 3.0 36.5 + - + -
253A GLY 3.0 18.6 + - - +
255A GLU* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 1.3 75.3 - - - +
170A GLY* 1.3 65.2 + - - +
181A VAL* 4.1 2.8 - - - +
182A LYS* 2.9 23.0 + - - +
183A LEU 4.3 0.2 - - - +
184A ALA* 4.1 29.4 + - + +
248A ILE 5.1 0.2 - - - +
249A SER* 2.9 38.0 + - - +
250A HIS 3.6 11.9 - - - +
251A ARG* 3.3 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 1.3 78.4 - - - +
171A ILE* 1.3 62.8 + - - +
181A VAL* 3.3 8.3 - - - +
182A LYS* 2.7 41.0 + - - -
247A PHE 5.3 0.4 + - - -
248A ILE 3.8 17.2 + - - -
250A HIS 4.4 3.0 + - - -
252A PHE* 5.5 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.2 15.3 - - + -
170A GLY* 1.3 78.4 - - - +
172A GLY* 1.3 63.6 + - - +
180A PHE 3.3 13.7 - - - +
181A VAL* 4.4 9.2 - - + -
182A LYS* 4.2 6.7 - - - +
222A PHE* 4.0 10.8 - - + -
244A TYR* 3.6 58.1 + - + -
247A PHE* 3.7 42.0 - - + +
248A ILE* 4.4 9.8 + - + +
252A PHE* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 1.3 77.9 - - - +
173A THR* 1.3 68.9 + - - +
179A GLY* 3.6 0.3 - - - -
180A PHE* 3.0 50.4 + - - +
182A LYS* 4.3 3.6 - - - +
217A LYS* 5.9 0.7 - - - -
244A TYR* 4.6 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY* 1.3 79.5 - - - +
174A PHE* 1.3 62.8 + - - +
175A GLY 4.1 0.9 + - - -
176A ASN* 3.5 38.1 + - - +
178A VAL 3.0 13.9 - - - +
179A GLY* 4.2 7.2 - - - -
180A PHE* 3.5 12.4 - - - -
217A LYS* 5.5 1.2 + - - -
239A ILE* 4.5 13.2 - - + +
244A TYR* 3.6 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A THR* 1.3 73.5 - - - +
175A GLY* 1.3 60.3 + - - +
176A ASN 3.1 0.4 - - - -
177A GLN* 2.9 21.5 + - - +
178A VAL* 3.0 28.6 + - + +
180A PHE* 3.5 32.8 - + - -
214A ARG* 3.3 61.2 - - + +
215A SER 5.2 0.9 - - - -
217A LYS* 3.9 30.5 - - + -
219A HIS* 3.5 28.0 - + - -
----------------------------------------------------------
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