Contacts of the strand formed by residues 168 - 175 (chain A) in PDB entry 5AJO
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 ILE 168 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 3.8 2.2 - - + -
140A VAL* 4.0 13.0 - - + -
159A VAL* 3.8 17.3 - - + +
160A LEU* 4.5 9.9 - - + -
163A SER* 3.5 37.7 - - - +
164A PRO 4.1 3.6 - - - +
165A PRO* 3.0 11.0 + - + +
166A HIS 4.6 2.2 - - - -
167A LEU* 1.3 76.6 - - - +
169A LYS* 1.3 62.5 + - - +
170A GLU 3.9 20.0 - - - +
171A ILE* 4.0 18.2 - - + -
192A LYS* 2.8 39.8 + - + +
233A TRP* 5.0 0.9 - - + -
234A LEU* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 4.3 12.5 - - + +
138A THR 2.9 17.3 + - - +
139A SER* 4.3 0.7 - - - +
166A HIS 5.4 0.4 - - - -
167A LEU 3.6 2.4 + - - -
168A ILE* 1.3 75.2 - - - +
170A GLU* 1.3 66.5 + - + +
192A LYS* 4.1 8.7 - - - +
216A GLN* 4.0 45.6 - - + +
217A ALA* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR 3.9 0.5 - - - +
139A SER* 2.6 31.1 + - - +
140A VAL 3.0 23.7 + - - -
168A ILE* 3.2 9.7 - - - +
169A LYS* 1.3 79.2 - - - +
171A ILE* 1.3 67.4 + - - +
172A ILE* 3.8 16.6 - - + +
192A LYS* 3.5 14.6 - - - +
194A ARG* 3.9 23.8 + - + -
214A ALA 4.7 1.6 - - - +
215A ALA* 3.4 5.0 - - - -
216A GLN* 2.8 46.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
140A VAL* 3.4 11.4 - - + +
142A ILE* 4.0 16.2 - - + -
156A VAL* 4.0 16.6 - - + +
159A VAL* 3.8 24.9 - - + -
160A LEU* 3.7 35.4 - - + -
168A ILE* 4.0 11.2 - - + -
170A GLU* 1.3 76.7 - - - +
172A ILE* 1.3 62.6 + - - +
173A LEU* 3.8 26.1 + - + -
192A LYS* 2.9 11.8 + - + +
193A VAL* 3.4 9.5 - - + -
194A ARG* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 4.7 1.1 - - - -
140A VAL 2.7 13.4 + - - +
141A VAL* 3.4 10.1 - - + +
142A ILE 2.9 26.7 + - - +
170A GLU* 3.7 36.3 - - + +
171A ILE* 1.3 71.7 - - - +
173A LEU* 1.3 63.8 + - - +
174A VAL* 3.7 12.4 + - + -
194A ARG* 3.4 16.6 - - + +
196A LEU* 3.8 32.3 - - + -
211A GLY* 3.6 23.8 - - - +
214A ALA* 4.1 7.6 - - + -
215A ALA* 3.9 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 3.3 28.7 - - + +
144A PHE* 3.9 18.4 - - + -
152A LEU* 4.7 5.4 - - + -
156A VAL* 3.9 14.6 - - + -
171A ILE* 3.9 16.6 - - + -
172A ILE* 1.3 72.7 - - - +
174A VAL* 1.3 59.6 + - - +
175A ASP 3.7 0.7 + - - -
184A GLY* 4.6 2.7 - - - +
187A LEU* 3.9 31.2 - - + -
193A VAL* 3.8 27.1 - - + -
194A ARG 2.8 10.1 + - - +
195A VAL* 3.4 12.5 - - + +
196A LEU* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 4.3 4.7 - - + -
142A ILE 2.9 8.9 + - - -
143A THR* 3.3 17.9 - - + -
144A PHE* 3.0 29.6 + - - -
172A ILE* 4.1 9.4 - - + -
173A LEU* 1.3 73.6 - - - +
175A ASP* 1.3 58.4 + - - +
176A ASP* 3.2 4.0 + - - -
196A LEU* 3.3 13.2 - - + +
198A ASN* 3.9 20.6 - - - +
207A SER* 3.8 38.4 - - - +
210A ARG* 4.6 7.0 - - - -
211A GLY* 4.0 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.5 26.2 - - + -
173A LEU 3.7 1.4 + - - -
174A VAL* 1.3 70.6 - - - +
176A ASP* 1.3 57.7 + - - +
177A TYR 2.9 4.3 + - - -
178A SER* 2.8 35.5 + - - -
180A ASP 4.6 0.5 - - - +
181A PRO* 4.0 12.8 - - - +
184A GLY* 4.9 1.8 + - - -
195A VAL* 4.6 7.7 - - + +
196A LEU 2.8 13.9 + - - +
197A ARG* 2.9 37.9 + - + +
198A ASN 2.8 28.1 + - - -
----------------------------------------------------------
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