Contacts of the strand formed by residues 152 - 161 (chain A) in PDB entry 1A8H
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 GLU 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.4 3.4 - - - -
126A TYR* 2.8 36.0 + - - +
128A VAL* 3.8 25.0 + - - +
149A ARG* 4.8 3.8 + - - -
150A PRO* 4.2 13.0 - - + +
151A VAL* 1.3 78.6 - - - +
153A ARG* 1.3 70.1 + - - +
154A ARG* 3.3 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 3.5 43.8 + - - +
124A GLY* 3.4 26.0 - - - +
125A LEU* 4.6 18.3 - - + +
136A GLU* 5.6 3.6 + - - -
152A GLU* 1.3 75.6 - - - +
154A ARG* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 3.2 8.9 - - - +
124A GLY 2.9 29.7 + - - +
126A TYR* 3.7 44.0 - - + -
128A VAL* 3.8 21.2 - - - +
133A PHE* 3.4 7.9 - - + -
152A GLU* 3.3 32.1 + - - +
153A ARG* 1.3 79.2 - - - +
155A LYS* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.1 31.2 - - + +
122A TYR 3.0 11.4 - - - +
123A GLU* 4.8 9.9 - - + -
133A PHE* 4.5 0.9 - - - -
154A ARG* 1.3 82.6 - - - +
156A GLU* 1.3 66.4 + - - +
157A GLY 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.6 4.7 - - - -
122A TYR* 2.9 32.9 + - - +
126A TYR* 4.1 2.5 + - + -
133A PHE* 3.8 19.5 - - + -
155A LYS* 1.3 80.6 - - - +
157A GLY* 1.3 69.5 + - - +
158A ASN* 2.9 25.0 + - - +
205A ARG* 2.9 41.5 + - - -
206A PRO* 3.5 20.0 - - + +
209A ARG* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 3.1 29.6 - - - -
120A GLY 3.5 9.0 - - - -
121A GLU* 4.6 6.0 + - - -
156A GLU* 1.3 72.3 - - - +
158A ASN* 1.3 69.7 + - - +
206A PRO* 3.7 7.3 - - - +
222A HIS* 3.2 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 3.7 6.0 - - - -
120A GLY 2.8 32.1 + - - +
122A TYR* 3.7 18.8 - - + +
133A PHE* 5.2 1.4 - - - -
156A GLU* 2.9 30.8 + - - +
157A GLY* 1.3 90.9 - - - +
159A TYR* 1.3 60.6 + - - +
160A PHE* 3.2 18.4 - - + -
202A SER* 2.7 27.1 + - - +
204A SER* 3.1 18.3 + - - +
205A ARG* 3.9 6.6 - - - +
222A HIS* 4.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 5.1 3.8 - + - -
117A ILE* 4.1 13.7 - - + -
118A TYR* 3.4 13.5 - - - -
119A TYR* 3.7 34.8 - + + +
158A ASN* 1.3 74.7 - - - +
160A PHE* 1.3 61.1 + - - +
202A SER* 3.6 3.6 - - - -
203A ILE* 2.9 33.4 + - + +
204A SER* 3.2 21.9 + - - +
216A LEU* 3.4 24.9 - - + -
218A TRP* 3.1 28.8 - + - -
219A ASP* 2.5 34.1 + - - +
222A HIS* 3.6 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP 3.6 0.3 - - - +
117A ILE* 3.1 11.4 - - - +
118A TYR* 2.7 65.9 + + + +
120A GLY* 3.6 25.6 - - - -
121A GLU 3.6 21.8 - - - -
122A TYR* 4.0 21.3 - + + -
158A ASN* 3.2 30.5 - - + -
159A TYR* 1.3 75.4 - - - +
161A PHE* 1.3 61.8 + - - +
200A ASP* 4.3 13.0 - - + -
201A LEU 3.1 6.3 - - - -
202A SER* 3.6 28.3 - - - -
203A ILE* 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 4.0 12.8 - - + -
116A ASP* 3.3 21.8 - - + -
117A ILE* 4.6 4.0 - - + -
160A PHE* 1.3 74.7 - - - +
162A ARG* 1.3 56.7 + - - +
163A MET* 2.7 29.6 + - + -
166A TYR* 4.0 13.5 - + - -
200A ASP* 3.6 4.0 - - - -
201A LEU* 2.7 42.6 + - + +
203A ILE* 3.9 14.6 - - + -
228A PHE* 4.0 16.6 - + + -
271A THR* 3.6 42.0 - - - -
272A MET* 3.9 16.2 - - + -
275A ALA* 3.6 22.7 - - + -
----------------------------------------------------------
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