Contacts of the strand formed by residues 128 - 136 (chain C) in PDB entry 3EHW
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 ARG 128 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B THR* 2.7 49.3 + - - -
162B GLY* 3.2 25.1 + - - -
163B LYS 2.8 11.9 + - - +
164B ASN* 2.8 29.6 + - - +
39C THR* 4.0 2.7 - - - -
41C GLY* 5.2 2.0 - - - -
49C ASP* 3.0 40.7 + - + -
50C LEU 3.2 7.4 - - - +
51C TYR* 3.4 37.1 + - + -
85C ARG* 3.0 35.9 + - - +
88C LEU* 3.9 5.7 - - - +
126C GLY 3.8 0.4 + - - -
127C ASP* 1.3 68.7 - - - +
129C ILE* 1.3 61.7 + - - +
130C ALA 3.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU 3.0 11.5 + - - +
51C TYR 4.8 0.4 - - - -
52C SER* 4.1 15.7 - - - +
66C VAL* 4.0 15.9 - - + -
68C THR* 5.8 0.4 - - + -
85C ARG* 4.5 3.1 + - - +
88C LEU* 3.7 26.3 - - + +
94C ILE* 5.1 0.7 - - - +
96C VAL* 4.6 2.1 - - - +
111C VAL* 3.9 32.3 - - + -
113C LEU* 3.7 24.8 - - + +
121C PHE* 4.4 8.5 - - + -
123C VAL* 4.1 19.5 - - + -
127C ASP* 3.8 29.2 - - + +
128C ARG* 1.3 77.0 - - - +
130C ALA* 1.3 68.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
49C ASP* 3.5 6.6 - - - +
50C LEU* 2.8 24.5 + - + +
82C VAL* 3.8 13.0 - - + -
83C ALA 3.5 13.7 - - - +
85C ARG* 4.0 15.9 - - - +
96C VAL* 4.1 5.4 - - + -
111C VAL* 3.7 29.2 - - + -
128C ARG 3.6 0.8 - - - -
129C ILE* 1.3 83.3 + - + +
131C GLN* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL* 3.6 20.6 - - - +
102A ASP* 4.9 1.4 - - - +
777B DUP 2.8 37.5 + - - -
45C ALA* 5.8 1.0 - - - +
47C GLY* 3.7 24.9 + - - +
48C TYR 3.3 7.4 - - - +
49C ASP* 3.7 18.8 - - - +
50C LEU* 4.2 5.2 - - - +
81C ARG 3.3 1.0 - - - +
82C VAL* 3.3 2.8 - - - -
83C ALA* 2.7 48.6 + - + +
84C PRO 2.9 22.8 + - - -
85C ARG* 3.9 7.0 - - + +
130C ALA* 1.3 78.4 - - - +
132C LEU* 1.3 58.8 + - - +
133C ILE* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.4 20.4 - - + -
38C PRO* 6.3 1.1 - - + -
46C ALA 4.1 0.9 - - - +
47C GLY* 3.3 1.2 - - - -
48C TYR* 2.7 47.1 + - + +
50C LEU* 4.0 21.1 - - + +
72C ILE* 3.6 30.3 - - + -
74C LEU* 4.4 7.6 - - + -
80C GLY* 3.6 32.5 - - - +
81C ARG 3.3 5.8 - - - +
82C VAL* 4.1 7.9 - - + +
101C ILE* 4.0 14.8 - - + -
109C VAL* 5.3 2.2 - - + -
131C GLN* 1.3 73.1 - - - +
133C ILE* 1.3 63.2 + - - +
134C CYS* 4.1 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.7 13.5 - - + +
100A VAL* 3.7 25.4 - - + -
137A ILE* 3.4 28.9 - - + -
46C ALA 3.9 18.4 - - - +
47C GLY* 4.1 8.1 - - - +
79C TYR 3.3 1.4 - - - +
80C GLY* 3.4 1.5 - - - -
81C ARG* 2.8 67.2 + - - +
83C ALA* 3.8 10.3 - - + -
131C GLN* 4.6 1.8 - - + -
132C LEU* 1.3 76.1 - - - +
134C CYS* 1.3 64.4 + - - +
135C GLU* 3.1 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 3.2 8.9 - - - +
138A PHE* 3.0 46.1 + - + +
140A PRO* 3.7 26.5 - - + -
26C LEU* 4.5 11.7 - - - -
46C ALA 4.5 3.2 + - - -
48C TYR* 5.6 1.8 - - - -
74C LEU* 3.9 23.6 - - - -
75C PRO* 4.4 3.6 - - - -
78C CYS* 3.9 16.2 - - - +
79C TYR 3.6 5.4 - - - -
132C LEU* 4.1 5.5 + - - -
133C ILE* 1.3 72.3 - - - +
135C GLU* 1.3 61.9 + - - +
136C ARG 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 2.5 40.2 + - - -
135A GLU* 3.6 14.9 - - - +
136A ARG 3.9 3.5 - - - +
137A ILE* 3.9 2.1 - - - +
135B GLU* 3.6 15.0 - - - +
78C CYS* 2.9 20.8 - - - +
79C TYR* 3.1 33.8 + - + +
81C ARG* 2.8 41.2 + - + -
133C ILE* 3.1 16.6 + - - +
134C CYS* 1.3 69.6 - - - +
136C ARG* 1.3 62.9 + - - +
137C ILE 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY 5.6 0.8 + - - -
136A ARG* 2.9 55.0 + - - +
137A ILE 3.7 30.0 + - - +
138A PHE* 3.4 47.2 - - + +
135B GLU* 3.9 2.6 - - - +
136B ARG* 2.9 60.2 + - + +
77C GLY 3.4 7.6 + - - +
78C CYS* 4.1 0.2 - - - -
135C GLU* 1.3 72.7 - - - +
137C ILE* 1.3 62.4 + - - +
----------------------------------------------------------
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