Contacts of the strand formed by residues 126 - 131 (chain C) in PDB entry 3SAJ
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 THR 126 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C TRP 3.8 0.2 - - - -
125C GLN* 1.3 91.3 - - + +
127C PHE* 1.3 68.6 + - - +
151C ASN 5.5 1.3 - - - +
153C GLN* 3.6 29.8 - - + +
181C LEU* 4.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ILE* 4.3 16.8 - - + -
124C TRP* 3.8 24.7 - + + -
126C THR* 1.3 85.3 - - - +
128C VAL* 1.3 72.7 + - - +
129C TYR* 4.4 4.5 - + - -
143C VAL* 4.1 14.6 - - + -
152C TRP* 3.9 33.7 - + + -
153C GLN 3.3 5.1 + - - +
154C VAL* 3.4 38.7 - - + -
155C THR* 2.9 25.3 + - - -
181C LEU 3.0 21.5 - - - +
183C VAL* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PHE* 1.3 81.6 - - - +
129C TYR* 1.3 62.8 - - - +
130C ILE* 3.9 25.8 - - + -
155C THR* 3.2 24.9 - - - +
157C VAL* 4.4 12.1 - - + -
167C TYR* 4.9 6.3 - - + -
170C LEU* 3.6 13.9 - - + -
171C PHE* 3.7 28.0 - - + -
174C LEU* 5.9 1.8 - - + -
181C LEU 3.1 5.1 + - - +
182C VAL* 3.5 12.4 - - + -
183C VAL 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.5 2.5 - - + -
127C PHE* 4.0 4.2 + + + -
128C VAL* 1.3 73.0 - - - +
130C ILE* 1.3 58.5 + - - +
131C TYR* 3.6 26.7 - + + -
139C VAL* 3.1 20.3 - - - +
140C LEU* 3.4 34.1 + - + -
143C VAL* 3.9 37.0 - - + -
154C VAL* 3.8 19.7 - - + -
155C THR 2.8 9.0 + - - +
156C ALA* 3.2 4.0 - - + -
157C VAL* 2.7 32.7 + - - +
183C VAL* 3.6 29.4 - - + -
185C ASP* 2.7 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C VAL* 3.9 15.5 - - + -
129C TYR* 1.3 76.2 - - - +
131C TYR* 1.3 58.0 + - - +
157C VAL* 3.3 13.7 - - + +
159C ILE* 3.1 33.2 - - + -
167C TYR* 3.2 36.6 - - + +
182C VAL* 4.1 6.5 - - + -
183C VAL 3.0 10.0 + - - +
184C VAL* 4.6 13.0 - - + -
185C ASP* 2.8 32.6 + - - +
186C CYS* 6.2 0.7 - - + -
194C ILE* 5.0 2.9 - - + -
198C ILE* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 3.7 27.4 + - + +
144A LEU* 5.5 3.6 - - + +
145A ASP* 4.1 6.8 + - - -
129C TYR* 3.6 24.9 - + + -
130C ILE* 1.3 73.3 - - - +
132C ASP* 1.3 62.3 + - - +
133C ALA* 4.4 3.6 - - + -
136C GLY 5.7 0.9 - - - +
137C LEU* 3.8 27.4 - - + -
140C LEU* 3.7 26.2 - - + +
156C ALA* 4.1 7.6 - - + -
157C VAL 2.9 24.4 + - - -
158C ASN* 3.1 51.7 + - + +
159C ILE* 2.8 33.5 + - - +
185C ASP* 3.2 14.6 - - - +
----------------------------------------------------------
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