Contacts of the strand formed by residues 154 - 160 (chain A) in PDB entry 2Z9I
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 VAL 154 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR 4.7 5.7 + - - +
142A VAL 3.2 12.3 - - - +
143A SER* 3.8 13.5 - - - -
152A ASN 3.8 11.2 - - - +
153A THR* 1.3 76.8 + - - +
155A LEU* 1.3 75.4 + - - +
156A ASP 4.2 0.2 + - - -
278A ASP* 3.8 42.6 - - + +
281A VAL* 3.8 20.0 - - + -
282A ALA* 4.0 10.9 - - + +
285A ARG* 4.5 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR 5.8 0.2 - - - +
87A SER 4.1 14.6 - - - +
88A ASP* 4.6 7.4 - - + +
140A ARG 3.4 1.4 - - - +
141A PRO* 3.4 5.7 - - - +
142A VAL* 2.7 48.5 + - + +
153A THR* 4.6 11.9 - - - +
154A VAL* 1.3 78.8 - - - +
156A ASP* 1.3 60.5 + - - +
157A ALA* 3.7 9.6 - - + +
185A SER* 4.0 23.6 - - - -
186A ALA* 4.2 18.8 - - + -
206A PHE* 4.6 9.4 - - + +
208A ILE* 4.0 25.1 - - + +
282A ALA* 3.5 6.8 - - - +
410D GLN* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASN* 3.3 23.3 + - - -
140A ARG 3.7 1.6 - - - -
154A VAL 4.2 0.6 + - - -
155A LEU* 1.3 71.8 - - - +
157A ALA* 1.3 58.7 + - - +
208A ILE* 6.0 1.0 - - - +
209A PRO* 3.0 28.4 - - - +
212A GLN* 3.1 33.9 + - - +
272A ARG* 2.2 46.9 + - - +
282A ALA* 3.7 19.1 - - + +
285A ARG* 5.7 0.9 - - + -
286A SER* 3.5 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 3.8 1.2 - - - -
139A ASN 3.2 9.7 + - - -
140A ARG* 2.8 45.9 + - + +
142A VAL* 4.0 6.1 - - + -
155A LEU* 4.3 11.0 - - + -
156A ASP* 1.3 73.5 - - - +
158A ILE* 1.3 62.9 + - - +
159A GLN 3.8 0.3 + - - -
206A PHE* 3.8 33.9 - - + -
207A ALA 3.4 12.6 - - - +
209A PRO* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 5.6 0.2 - - - -
111A LEU* 3.5 20.6 - - + -
135A VAL* 4.3 14.1 - - + -
137A ALA 3.8 8.1 - - - +
138A LEU* 4.1 15.7 - - + -
156A ASP 4.0 0.4 + - - -
157A ALA* 1.3 73.3 - - - +
159A GLN* 1.3 72.6 + - - +
160A THR* 5.1 0.5 - - - +
173A LEU* 3.9 19.1 - - + -
181A VAL 3.4 26.5 - - - +
182A GLY* 4.1 9.0 - - - -
205A GLY 3.7 0.2 - - - +
206A PHE* 3.1 5.5 - - - -
207A ALA* 2.7 42.4 + - + +
209A PRO* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.6 5.5 - - - -
136A SER* 2.8 31.2 + - - -
137A ALA* 3.0 22.2 + - + +
140A ARG* 2.9 43.7 - - + +
157A ALA 3.8 1.2 + - - -
158A ILE* 1.3 75.8 - - - +
160A THR* 1.3 67.1 + - - +
203A GLY 5.1 0.2 - - - +
204A LEU* 3.5 15.6 - - - +
205A GLY 3.1 14.8 - - - +
206A PHE* 3.6 22.4 - - + -
126B LEU* 4.1 7.1 - - - +
129B THR* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 3.4 14.8 - - - +
134A ILE 2.7 20.9 + - - -
135A VAL* 4.9 0.7 - - - -
136A SER* 3.8 4.5 - - - -
158A ILE 5.1 1.8 - - - +
159A GLN* 1.3 77.8 - - - +
161A ASP* 1.3 59.1 + - - +
162A ALA* 3.2 14.1 + - + +
164A ILE* 3.4 31.0 - - + -
173A LEU* 3.9 25.6 - - + -
184A ASN* 4.6 0.9 - - - +
203A GLY 3.5 6.3 - - - +
205A GLY* 2.7 40.0 + - - +
206A PHE* 4.9 0.4 - - - +
207A ALA 5.5 0.9 - - - +
----------------------------------------------------------
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