Contacts of the strand formed by residues 134 - 145 (chain C) in PDB entry 5IXG
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 GLU 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C TYR* 2.6 30.6 + - + -
46C ARG* 4.6 6.0 + - - -
125C CYS* 3.8 19.2 - - - +
126C MET* 3.4 17.6 + - - +
127C PRO* 4.4 2.9 - - + -
133C ARG* 1.3 72.8 - - - +
135C VAL* 1.3 70.6 + - - +
136C CYS* 4.3 0.4 - - - -
172C VAL* 3.6 4.5 - - - +
173C LYS* 3.0 59.5 + - + +
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C TYR* 5.1 0.2 - - - -
12C ASP* 6.3 0.2 - - + -
124C LYS 4.0 0.5 - - - +
125C CYS* 3.3 1.7 - - - +
126C MET* 2.9 51.7 + - + +
128C HIS* 4.0 28.5 - - + -
131C LEU* 5.8 0.2 - - + -
133C ARG 3.5 0.2 + - - -
134C GLU* 1.3 75.4 - - - +
136C CYS* 1.3 71.8 + - - +
170C GLU* 4.2 18.6 - - + +
171C ALA 3.2 15.9 - - - +
172C VAL* 4.5 11.2 - - + -
28D LEU* 3.9 20.3 - - + +
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Residues in contact with CYS 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C TYR* 3.6 33.4 - - + -
44C LEU* 4.6 2.2 - - - -
123C PHE* 4.6 0.9 - - + -
124C LYS 3.3 3.1 - - - +
125C CYS* 2.1 46.7 - - - -
134C GLU* 4.3 2.2 - - - -
135C VAL* 1.3 75.3 - - - +
137C GLY* 1.3 58.6 + - - +
170C GLU* 3.3 2.9 - - - +
171C ALA* 2.8 34.5 + - + +
201C OTP 3.5 26.1 - - + +
28D LEU* 4.1 2.0 - - - -
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Residues in contact with GLY 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C SER 4.4 0.2 - - - -
123C PHE* 3.3 1.9 - - - -
124C LYS 2.7 37.4 + - - -
136C CYS* 1.3 73.0 - - - +
138C VAL* 1.3 67.7 + - - +
169C ALA 3.3 8.5 - - - -
170C GLU* 4.3 2.2 - - - -
27D GLY 5.2 0.2 - - - +
28D LEU* 3.2 31.5 - - - +
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ILE* 4.6 9.4 - - + -
122C SER* 3.2 12.3 - - - +
123C PHE* 3.5 26.0 - - + -
137C GLY* 1.3 80.2 - - - +
139C ASP* 1.3 63.8 + - - +
140C ALA* 5.0 0.9 - - + +
167C ILE* 3.7 2.1 - - + +
168C THR* 3.8 2.5 - - - -
169C ALA* 2.9 49.4 + - + +
201C OTP 3.6 47.8 - - + -
28D LEU 3.6 5.0 + - - -
29D SER* 4.1 6.7 - - - -
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 3.7 1.4 - - - +
121C ASP* 2.8 33.9 + - + +
122C SER* 3.1 28.4 + - - +
138C VAL* 1.3 73.5 - - - +
140C ALA* 1.3 65.3 + - - +
141C VAL* 5.0 4.7 - - - +
167C ILE 3.0 8.7 - - - +
168C THR* 4.2 2.3 + - - -
29D SER* 5.6 0.4 - - - -
30D VAL* 3.8 24.3 + - + +
32D ARG* 2.8 45.4 + - - -
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.4 7.4 - - + -
119C LYS 3.1 17.3 - - - +
120C ILE* 4.3 4.0 - - + -
121C ASP 4.3 0.9 - - - +
138C VAL* 4.2 0.9 - - + -
139C ASP* 1.3 77.5 - - - +
141C VAL* 1.3 71.8 + - - +
166C LEU* 3.6 0.5 - - - -
167C ILE* 2.8 41.7 + - + -
201C OTP 3.6 31.2 - - + -
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.4 6.8 - - - -
119C LYS* 2.7 57.1 + - + +
121C ASP* 3.6 26.0 - - - +
139C ASP* 5.0 6.1 - - - +
140C ALA* 1.3 82.9 - - - +
142C GLY* 1.3 60.1 + - - +
164C LYS* 4.4 22.0 - - - +
165C LEU 3.2 10.3 - - - +
166C LEU* 4.5 10.5 - - + -
167C ILE* 5.2 0.2 - - - -
32D ARG* 5.7 0.2 - - - +
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.8 1.6 - - - -
117C THR 4.0 14.4 - - - -
118C LEU* 4.1 11.2 - - - +
141C VAL* 1.3 77.7 - - - +
143C GLU* 1.4 68.8 + - - +
164C LYS* 3.6 3.3 - - - +
165C LEU* 2.8 35.0 + - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 3.2 33.7 - - - +
116C LEU* 3.5 14.6 - - - +
117C THR 4.8 0.4 + - - -
142C GLY* 1.4 79.1 - - - +
144C PHE* 1.3 67.0 + - - +
162C LYS* 3.1 35.0 + - + +
163C THR 3.3 9.2 - - - +
164C LYS* 4.4 17.8 - - + +
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 4.3 11.2 - - + -
109C LEU* 4.1 11.9 - - + -
115C PRO 5.9 1.8 - - - +
116C LEU* 4.4 10.1 - - + -
143C GLU* 1.3 78.4 - - - +
145C SER* 1.3 64.1 + - - +
146C ARG* 3.7 23.6 - - + -
148C ASP* 5.9 0.4 - - - +
149C PHE* 3.6 33.4 - + + -
161C MET 3.5 0.2 - - - +
162C LYS* 3.6 3.5 - - - -
163C THR* 2.7 54.8 + - + -
165C LEU* 3.8 38.8 - - + -
201C OTP 4.1 21.1 - - + -
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASP* 5.2 2.6 + - - -
144C PHE* 1.3 78.2 - - - +
146C ARG* 1.3 65.2 + - - +
147C ASP* 2.4 25.8 + - - -
148C ASP* 2.9 37.4 + - - +
149C PHE* 3.9 0.9 - - - -
161C MET* 3.2 18.6 - - - +
162C LYS* 4.5 3.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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