Contacts of the strand formed by residues 182 - 187 (chain H) in PDB entry 1A4J
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 182 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H THR* 6.0 0.9 - - - +
116H THR* 4.4 17.2 - - - +
150H ASP* 2.9 23.4 + - - -
151H TYR* 2.9 49.9 + + + +
152H PHE* 3.8 27.2 - + - -
153H PRO* 5.1 0.4 - - + -
154H GLU* 3.7 41.3 - - + +
174H ALA* 4.0 12.8 - - + -
175H VAL 3.3 17.3 - - - -
176H LEU* 3.6 32.9 - - + +
177H GLN* 3.8 0.2 - - - -
181H LEU* 1.3 73.0 - - - +
183H SER* 1.3 60.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H LEU* 3.8 8.8 - - - +
148H VAL 3.5 6.5 - - - -
149H LYS* 2.9 28.0 - - - +
151H TYR* 4.1 2.5 - - - -
173H PRO 4.7 0.3 - - - +
174H ALA* 3.5 0.6 - - - -
175H VAL* 3.1 34.6 + - - +
177H GLN* 3.5 27.5 + - - -
182H TYR* 1.3 77.1 - - - +
184H LEU* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H LEU* 3.5 7.0 - - - +
148H VAL* 2.6 68.0 + - + +
151H TYR* 3.3 22.0 - - - +
154H GLU* 5.2 1.6 - - - +
156H VAL* 4.1 15.7 - - + +
158H VAL* 4.7 5.6 - - + -
171H THR* 4.2 16.4 - - + -
172H PHE* 3.7 23.1 - - - +
173H PRO 4.4 2.0 - - - +
174H ALA* 3.9 12.6 - - + +
183H SER* 1.3 77.4 + - - +
185H SER* 1.3 73.4 + - - +
186H SER 4.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU* 4.2 17.3 - - - -
146H CYS 3.2 11.7 - - - -
147H LEU* 4.4 9.9 - - - -
172H PHE* 3.1 36.3 + - - +
184H LEU* 1.3 81.2 - - - +
186H SER* 1.3 59.6 + - - +
187H VAL* 4.1 4.0 - - - -
138L VAL* 4.7 8.3 - - - +
181L SER* 3.7 26.9 + - - -
183L THR* 5.0 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H GLY* 3.3 2.1 - - - -
146H CYS* 2.9 33.9 + - - -
148H VAL* 5.5 0.7 - - - -
158H VAL* 3.9 21.4 - - - +
160H TRP* 2.9 32.6 + - - -
169H VAL* 4.1 1.9 - - - +
170H HIS 3.4 5.8 + - - -
171H THR* 2.7 28.0 + - - +
184H LEU* 4.1 1.7 - - - +
185H SER* 1.3 71.9 - - - +
187H VAL* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU* 4.0 21.1 - - + -
144H LEU 3.5 9.4 - - - +
145H GLY* 4.0 0.2 - - - -
168H GLY 5.1 0.2 - - - +
169H VAL* 3.3 3.6 - - - +
170H HIS* 2.8 53.1 + - + +
172H PHE* 4.0 11.9 - - + -
185H SER* 4.8 3.8 - - - +
186H SER* 1.3 78.9 - - - +
188H VAL* 1.3 71.2 + - - +
123L PHE* 5.1 3.4 - - + -
138L VAL* 5.7 2.7 - - + -
140L LEU* 3.9 43.1 - - + -
142L ASN* 4.7 3.8 - - - +
181L SER* 5.9 0.4 - - - -
----------------------------------------------------------
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