Contacts of the strand formed by residues 128 - 136 (chain C) in PDB entry 5Y7K
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 128 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 2.7 39.3 + - - -
120C TYR* 3.3 36.8 - + + +
121C VAL 3.4 15.0 - - - +
122C LYS* 3.9 3.6 - - - -
123C GLN* 4.0 5.8 - - - +
126C HIS 3.5 17.3 - - - -
127C SER* 1.3 76.0 - - - +
129C THR* 1.3 66.4 + - - +
130C ALA* 4.4 2.0 - - + -
132C TYR* 3.7 13.3 + - - -
152C THR 4.1 0.2 - - - +
153C GLN 3.3 24.1 - - - +
154C TRP* 4.6 23.4 - + - -
155C VAL* 6.1 0.2 - - - +
211C TYR* 3.9 8.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN 3.5 0.6 - - - +
120C TYR* 3.6 0.5 - - - -
121C VAL* 2.9 58.1 + - + +
123C GLN* 5.5 1.8 - - + +
128C TYR* 1.3 76.9 - - - +
130C ALA* 1.3 66.8 + - - +
151C ASN* 3.2 37.3 + - - +
152C THR 3.4 8.1 - - - -
153C GLN* 5.1 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 4.0 12.8 - - + -
118C TYR 3.4 11.2 - - - +
119C ASN* 3.4 11.4 - - - +
120C TYR* 4.1 5.8 - - - -
128C TYR* 4.4 4.9 - - + -
129C THR* 1.3 80.9 + - - +
131C SER* 1.3 66.8 + - - +
132C TYR* 4.0 18.6 - - - +
151C ASN* 3.6 4.0 + - - -
152C THR* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 3.8 0.3 - - - -
118C TYR* 2.8 54.6 + - - +
119C ASN* 3.3 20.1 + - - +
130C ALA* 1.3 76.0 - - - +
132C TYR* 1.3 68.7 + - - +
149C PRO 4.8 0.7 - - - -
150C ASN* 3.0 38.3 + - - +
151C ASN* 4.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.9 17.9 - - + -
116C LEU 3.3 16.4 - - - +
117C GLU* 3.0 39.5 + - + -
118C TYR* 3.9 5.2 + - - -
128C TYR* 3.7 15.6 + - - -
130C ALA* 3.7 13.0 - - + +
131C SER* 1.3 78.5 - - - +
133C ASP* 1.3 71.9 + - - +
147C ARG* 4.7 1.7 + - - +
148C ILE* 4.0 46.0 + - + +
149C PRO 5.0 0.4 + - - -
152C THR* 3.6 38.2 + - + -
153C GLN 5.5 0.3 - - - -
154C TRP* 5.1 4.2 - - - -
155C VAL* 3.4 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 2.9 40.5 - - + -
100C HIS* 4.9 0.2 - - - -
114C ILE 3.7 0.9 - - - +
115C LEU* 3.7 1.1 - - - -
116C LEU* 2.8 39.7 + - + +
118C TYR* 3.4 6.9 + - + -
132C TYR* 1.3 78.1 - - - +
134C ILE* 1.3 64.7 + - - +
142C LEU* 4.1 15.7 - - + +
143C ILE 4.4 2.3 - - - +
147C ARG* 2.8 49.1 + - - +
148C ILE* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C PHE* 4.0 20.9 - - + -
114C ILE 3.6 4.5 - - - +
115C LEU* 3.7 15.5 - - + -
133C ASP* 1.3 76.5 + - - +
135C TYR* 1.3 61.8 + - - +
142C LEU* 3.5 5.1 - - - +
143C ILE* 2.9 52.1 + - + +
146C GLU 6.1 0.2 - - - +
147C ARG* 6.5 0.2 - - - -
148C ILE* 4.0 15.7 - - + -
157C TRP* 4.2 6.3 - - + -
164C LEU* 3.5 30.5 - - + -
175C LYS* 5.1 1.1 - - + -
178C PRO* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 6.3 0.7 - - + -
94C THR* 3.5 29.6 - - + +
95C PHE* 3.3 31.0 - + + -
113C PHE* 3.5 3.8 - - - -
114C ILE* 3.0 52.8 + - + +
116C LEU* 4.7 2.5 - - + -
133C ASP 4.1 0.2 + - - -
134C ILE* 1.3 73.2 - - - +
136C ASP* 1.3 68.3 + - - +
137C LEU* 3.3 20.5 + - + -
140C ARG* 3.2 41.0 + - - +
141C GLN* 3.5 28.5 - - - -
142C LEU* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN 3.7 4.3 - - - +
113C PHE* 3.6 29.6 - - + -
134C ILE 4.1 2.0 + - - -
135C TYR* 1.3 71.9 - - - +
137C LEU* 1.3 55.5 + - - +
138C ASN* 3.1 23.9 + - - +
139C LYS* 3.1 43.7 + - + -
140C ARG* 2.7 33.6 + - - -
141C GLN 3.0 18.5 + - - +
143C ILE* 4.3 11.5 - - + +
179C ASN* 5.4 1.9 - - - +
----------------------------------------------------------
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