Contacts of the strand formed by residues 176 - 181 (chain B) in PDB entry 1A4K
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 TYR 176 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASP* 2.9 24.6 + - - -
145B TYR* 2.9 47.9 + - + +
146B PHE* 4.0 25.5 - + - -
147B PRO* 4.7 0.7 - - + -
148B GLU* 3.6 52.1 + - + -
168B ALA* 4.1 7.0 - - + -
169B VAL 3.5 6.3 - - - -
170B LEU* 3.5 48.2 - - + +
171B GLN* 3.9 0.2 - - - -
175B LEU* 1.3 73.4 - - - +
177B SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 5.9 2.4 - - - +
141B LEU* 4.2 9.7 - - - +
142B VAL 3.7 5.1 + - - -
143B LYS* 3.0 23.2 + - - +
145B TYR* 4.2 0.7 - - - -
167B PRO 4.4 0.3 - - - +
168B ALA* 4.3 1.3 - - - -
169B VAL* 2.8 44.0 + - - +
171B GLN* 3.5 27.2 + - - -
176B TYR* 1.3 78.4 - - - +
178B LEU* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.8 5.9 - - - +
142B VAL* 2.9 58.1 + - + +
145B TYR* 3.4 21.5 - - + +
148B GLU* 5.6 0.4 - - - +
150B VAL* 3.7 24.9 - - + +
152B VAL* 4.3 5.6 - - + -
165B THR* 3.9 21.5 - - + -
166B PHE 3.8 13.5 - - - +
167B PRO 4.1 2.7 - - - +
168B ALA* 3.7 16.4 - - + +
177B SER* 1.3 75.6 - - - +
179B SER* 1.3 79.5 + - - +
180B SER 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 4.7 6.9 - - - +
176A SER* 3.0 27.7 + - - -
178A THR* 4.8 2.6 + - - -
124B LEU* 4.6 9.6 - - - -
140B CYS 3.4 12.1 - - - -
141B LEU* 4.5 11.0 - - - +
166B PHE* 2.9 39.0 + - - +
178B LEU* 1.3 82.8 - - - +
180B SER* 1.3 62.1 + - - +
181B VAL* 5.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLY* 3.4 1.2 - - - -
140B CYS* 2.9 33.6 + - - -
142B VAL* 5.7 0.9 - - - -
152B VAL* 3.5 23.5 - - - +
154B TRP* 2.9 32.3 + - - -
163B VAL* 4.5 0.5 - - - +
164B HIS 3.3 7.0 + - - -
165B THR* 3.1 27.3 + - - +
178B LEU* 4.3 0.8 - - - +
179B SER* 1.3 74.9 - - - +
181B VAL* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 4.9 7.9 - - + -
133A VAL* 5.9 3.1 - - + -
135A LEU* 3.6 45.3 - - + -
137A ASN* 4.9 4.7 - - - +
176A SER* 6.1 0.9 - - - -
124B LEU* 4.7 10.5 - - + -
137B ALA 5.4 0.4 - - - +
138B LEU 3.7 9.2 - - - +
139B GLY* 3.9 9.6 - - - -
162B GLY 3.7 1.4 - - - +
163B VAL* 4.4 0.2 - - - +
164B HIS* 2.7 48.8 + - + +
166B PHE* 3.8 17.0 - - + -
179B SER* 5.0 3.6 - - - -
180B SER* 1.3 79.3 - - - +
182B VAL* 1.3 66.2 + - - +
183B THR 5.7 0.2 - - - +
----------------------------------------------------------
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