Contacts of the strand formed by residues 147 - 158 (chain C) in PDB entry 5UH8
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 ILE 147 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLU* 4.0 35.2 - - + +
139C PHE 3.7 5.4 - - - +
140C ILE* 4.1 34.8 - - + -
145C GLY 4.0 6.3 + - - +
146C GLU* 1.3 81.0 - - - +
148C LYS* 1.3 66.9 + - - +
149C SER* 3.9 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ALA 4.0 1.0 - - - +
138C GLU* 3.3 1.8 - - - -
139C PHE* 2.9 41.8 + - + +
146C GLU* 4.3 25.7 + - + +
147C ILE* 1.3 78.4 - - - +
149C SER* 1.3 60.8 + - - +
150C GLN* 5.7 1.3 - - - -
409C VAL 6.0 0.4 - - - -
410C GLU* 3.0 30.3 + - - -
411C ALA* 4.9 1.6 - - - +
412C ILE 3.9 21.4 + - - +
413C THR* 4.6 14.6 - - + +
414C PRO* 4.0 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C THR* 3.9 16.3 - - - +
137C ALA 3.5 5.0 + - - -
138C GLU* 3.5 28.7 + - - +
147C ILE* 3.9 7.6 + - - -
148C LYS* 1.3 72.8 - - - +
150C GLN* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C THR* 3.6 5.7 - - - -
137C ALA* 2.7 43.4 + - - +
148C LYS* 6.1 1.3 - - - -
149C SER* 1.3 76.2 + - - +
151C THR* 1.3 60.5 + - - +
152C VAL* 4.8 0.7 - - + -
413C THR* 3.4 11.0 - - - +
414C PRO* 3.2 34.5 - - + +
415C GLN* 3.1 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 2.5 32.9 + - - +
134C PHE* 4.2 24.2 - - + -
135C VAL 3.2 12.1 - - - +
136C THR* 3.8 6.6 + - - +
150C GLN* 1.3 75.2 + - - +
152C VAL* 1.3 66.5 + - - +
153C PHE 4.3 0.5 + - - -
415C GLN* 3.0 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.8 2.1 - - - -
135C VAL* 2.8 43.0 + - + +
137C ALA* 3.8 20.6 - - + -
150C GLN* 4.1 2.9 - - + +
151C THR* 1.3 82.0 - - - +
153C PHE* 1.3 74.5 + - - +
154C MET* 3.7 2.3 + - - -
414C PRO* 4.4 7.0 - - + -
415C GLN* 3.8 21.1 - - - +
418C ILE* 3.6 46.2 - - + -
388F GLN* 4.0 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C PRO* 3.6 13.7 - - + -
133C LEU 3.3 8.7 - - - -
134C PHE* 3.3 26.7 - + + -
151C THR 4.3 0.6 + - - -
152C VAL* 1.3 75.6 - - - +
154C MET* 1.3 60.4 + - - +
155C GLY* 3.3 42.0 - - - -
156C ASP* 3.5 11.9 - - - -
415C GLN* 5.0 0.4 - - - +
420C ILE* 3.2 31.4 - - + +
387F LEU* 3.5 29.6 - - + +
388F GLN* 3.4 19.3 + - - +
391F GLY* 3.3 32.8 - - - -
392F ARG* 3.8 11.4 - - - -
393F GLU* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 6.0 2.9 - - + -
133C LEU* 3.1 35.7 + - + +
135C VAL* 3.6 40.2 - - + -
152C VAL* 4.0 8.1 - - - +
153C PHE* 1.3 81.8 - - - +
155C GLY* 1.3 60.7 + - - +
393C MET* 4.7 12.1 - - + -
396C MET* 4.5 11.2 - - - -
418C ILE* 4.9 5.6 - - + -
420C ILE* 3.8 25.0 - - + +
423C VAL* 3.8 46.2 - - + +
424C VAL* 3.9 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.0 26.5 + - - +
153C PHE* 3.3 28.8 - - - -
154C MET* 1.3 81.6 - - - +
156C ASP* 1.3 63.9 + - - -
157C PHE* 3.6 0.5 + - - +
420C ILE* 3.8 2.8 - - - +
424C VAL* 4.1 15.3 - - - -
393F GLU* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LYS* 2.8 45.6 + - + +
130C ALA* 4.1 15.1 - - + +
132C PRO* 3.6 11.5 - - + +
153C PHE* 3.5 17.1 - - - -
155C GLY* 1.3 69.8 - - - -
157C PHE* 1.3 59.8 + - - +
158C PRO* 3.6 8.7 - - - +
424C VAL* 5.0 6.0 - - + +
427C ILE* 4.1 13.2 - - - +
391F GLY 4.5 0.3 - - - +
393F GLU* 4.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 4.0 17.7 - + - -
64C LEU* 3.8 23.1 - - + -
65C ILE* 4.6 0.9 - - + -
86C LEU* 4.7 9.0 - - + -
112C PHE* 3.8 28.9 - + + -
130C ALA* 3.4 3.8 - - - +
131C ALA 2.9 42.9 + - - +
133C LEU* 4.3 22.9 - - + -
155C GLY 3.6 0.8 + - - +
156C ASP* 1.3 71.1 - - - +
158C PRO* 1.3 89.1 - - + +
159C MET* 3.3 5.6 + - - +
385C ILE* 4.4 7.9 - - + -
389C ILE* 3.8 27.6 - - + -
427C ILE* 5.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 3.7 4.7 - - - -
128C THR* 4.7 14.4 - - + -
129C TYR 3.4 11.9 - - - +
130C ALA* 3.7 2.6 - - + -
156C ASP 3.6 7.6 - - - +
157C PHE* 1.3 110.0 - - + +
159C MET* 1.3 60.6 + - - +
166C PHE* 3.8 9.3 - - + -
168C ILE* 4.8 5.8 - - + -
385C ILE* 5.9 0.2 - - - +
427C ILE* 4.2 18.6 - - + -
431C PHE* 3.6 41.1 - - + -
----------------------------------------------------------
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