Contacts of the strand formed by residues 179 - 183 (chain C) in PDB entry 6AHU
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 ALA 179 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A A 3.6 2.8 + - - -
114C ALA 3.7 2.1 - - - +
116C GLY 3.2 30.1 + - - +
117C VAL* 4.0 16.8 - - + -
120C VAL* 3.8 17.3 - - + -
132C VAL* 6.2 0.2 - - + -
133C LEU 3.7 4.7 - - - +
134C VAL* 5.0 12.8 - - + +
148C ILE* 5.6 2.0 - - + -
177C VAL* 3.4 15.5 - - - +
178C LEU* 1.3 76.6 - - + +
180C LEU* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 6.3 0.2 - - + -
52C LEU* 5.8 8.1 - - + -
113C LEU* 3.9 31.6 - - + -
114C ALA 3.9 4.0 - - - +
115C ILE* 5.0 5.2 - - + -
120C VAL* 4.6 0.7 - - - -
132C VAL* 4.8 0.7 - - - +
133C LEU* 2.8 72.3 + - + +
164C LEU* 5.0 12.8 - - + -
168C ILE* 4.7 20.4 - - + -
177C VAL* 5.0 11.2 - - + +
178C LEU 3.9 1.7 + - - +
179C ALA* 1.3 73.7 - - - +
181C ALA* 1.3 65.8 + - - +
182C PHE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.3 10.4 - - - +
114C ALA* 2.6 41.0 + - + +
120C VAL* 3.8 25.8 - - + -
123C ALA* 5.8 0.2 - - + -
130C LEU* 3.9 15.9 - - + -
131C LEU 3.4 17.5 - - - +
132C VAL* 4.5 1.8 - - - -
133C LEU* 5.8 0.4 - - - -
180C LEU* 1.3 77.9 - - - +
182C PHE* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 6.2 2.5 - - + -
111C LYS* 6.2 1.6 - - + -
112C GLN 3.4 9.4 - - - +
113C LEU* 3.7 20.2 - - + +
114C ALA* 5.0 0.7 - - - -
130C LEU* 3.3 22.1 - - - +
131C LEU* 3.9 35.8 + - + -
133C LEU* 5.6 9.0 - - + -
180C LEU* 6.1 1.6 - - + -
181C ALA* 1.3 82.8 - - - +
183C LYS* 1.3 60.8 + - - +
184C LYS* 3.7 39.5 + - + +
189C PHE* 5.6 7.9 - + + -
193C VAL* 4.4 21.5 - - + -
197C ILE* 5.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 2.9 49.7 + - + +
114C ALA* 5.7 0.4 - - - +
126C ARG* 5.6 4.2 - - - +
127C ARG 5.4 0.8 + - - -
128C GLU* 3.1 42.6 + - + +
129C LEU 5.3 0.7 - - - +
130C LEU* 4.5 7.6 - - + +
182C PHE* 1.3 70.7 - - - +
184C LYS* 1.3 71.4 + - - +
185C ASN* 3.5 32.8 - - - +
----------------------------------------------------------
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