Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 1AP5
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 152 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 4.1 0.7 - - - -
128B PHE 3.2 37.9 - - - +
129B ASN* 3.5 20.2 - - + +
136B GLN* 3.8 34.5 - - + +
138B ALA* 3.9 28.7 - - + -
146B LEU* 3.7 20.9 - - + +
147B GLN* 3.3 25.3 + - - +
150B THR* 3.3 16.9 + - - +
151B GLY* 1.3 79.9 - - - +
153B ILE* 1.3 62.1 + - - +
154B PRO* 3.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 3.1 5.5 - - - -
128B PHE* 2.8 49.5 + - + +
130B LYS* 5.0 17.5 - - + -
146B LEU* 4.2 0.2 - - - -
147B GLN* 3.9 23.6 - - - +
151B GLY 3.7 10.5 - - - +
152B LEU* 1.3 75.9 - - - +
154B PRO* 1.4 76.1 - - + +
155B LEU* 4.0 14.3 - - + +
192B ARG* 4.8 2.2 - - + +
196B CYS* 3.9 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 6.3 2.2 - - + -
76B ILE* 4.7 17.5 - - + -
125B TRP* 3.5 31.4 - - + -
146B LEU* 3.8 17.7 - - + -
147B GLN* 3.9 22.0 - - + +
152B LEU 3.6 8.5 - - - +
153B ILE* 1.4 88.3 - - + +
155B LEU* 1.3 65.1 + - - +
192B ARG* 3.8 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 5.4 0.2 - - - -
80B ASN* 3.3 10.2 - - - +
93B LEU* 5.3 4.7 - - + -
125B TRP* 4.6 0.9 - - - -
126B LEU* 3.0 28.6 + - + +
127B GLY 3.9 20.2 - - - +
128B PHE* 4.1 9.9 - - + +
135B LEU* 4.6 8.1 - - + -
153B ILE* 4.0 17.5 - - + +
154B PRO* 1.3 77.9 - - - +
156B LEU* 1.3 62.1 + - - +
189B VAL* 4.0 17.8 - - + +
192B ARG* 3.2 61.2 - - + +
193B TYR* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 3.3 33.0 - - + +
107B PHE* 5.1 3.8 - - + -
111B LEU* 3.6 30.2 - - + +
124B GLY 4.2 0.2 - - - +
125B TRP* 3.3 7.3 - - - -
126B LEU* 2.9 41.0 + - + +
155B LEU* 1.3 81.1 - - - +
157B GLY* 1.3 62.8 + - - +
158B ILE* 4.6 11.2 - - + -
181B TRP* 5.2 3.8 - - + -
184B ILE* 4.1 31.4 - - + -
186B TRP* 5.2 2.0 - - + -
189B VAL* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.2 26.3 - - - -
80B ASN* 3.0 14.3 + - - +
123B TRP* 4.2 5.2 - - - -
124B GLY 3.4 7.6 - - - -
125B TRP* 3.5 22.1 - - - -
156B LEU* 1.3 79.5 - - - +
158B ILE* 1.3 64.4 + - - +
159B ASP 4.1 0.2 - - - -
180B ILE* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.2 2.5 - - - -
111B LEU* 3.8 27.1 - - + +
115B SER* 3.8 16.6 - - - +
123B TRP* 3.3 6.6 - - - -
124B GLY 2.9 30.3 + - - +
156B LEU* 4.6 10.3 - - + -
157B GLY* 1.3 74.9 - - - +
159B ASP* 1.3 73.6 + - - +
160B VAL* 3.5 5.8 + - + +
176B TYR* 4.0 7.0 - - + -
177B LEU* 3.7 34.5 - - + -
180B ILE* 3.9 31.2 - - + -
181B TRP* 4.8 9.2 - - + -
184B ILE* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS* 2.8 10.0 + - - -
74B HIS* 3.5 0.7 + - - -
77B PHE* 4.0 19.6 - - + -
122B GLY 3.7 1.2 - - - +
123B TRP* 3.4 31.8 - - + -
158B ILE* 1.3 70.5 - - - +
160B VAL* 1.3 67.5 + - - +
161B TRP* 3.1 30.4 + - - +
163B HIS* 3.6 0.9 + - - -
164B ALA* 3.9 9.6 - - + +
176B TYR* 3.1 27.5 + - - -
199B MN 2.1 35.7 + - - -
----------------------------------------------------------
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