Contacts of the strand formed by residues 123 - 135 (chain C) in PDB entry 1V8C
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 ALA 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C ARG* 3.7 1.7 - - - +
120C LEU* 2.9 33.8 + - + +
121C PRO 3.2 0.2 - - - -
122C GLY* 1.3 81.8 - - - +
124C VAL* 1.3 68.9 + - - +
125C VAL* 5.3 0.7 - - + -
147C VAL* 4.0 15.9 - - + -
148C GLU 3.2 12.3 - - - +
149C GLY* 4.3 1.1 - - - -
151C GLU 4.3 4.9 - - - -
155C TRP* 3.6 27.1 - - + -
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Residues in contact with VAL 124 (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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117C VAL* 4.1 15.7 - - + -
118C TYR 3.4 10.3 - - - +
119C ARG* 3.3 31.0 - - + +
123C ALA* 1.3 80.0 - - - +
125C VAL* 1.3 66.8 + - - +
126C ARG* 3.4 36.8 + - + +
146C GLU 3.7 0.7 - - - +
147C VAL* 3.4 4.3 - - - -
148C GLU* 2.8 36.8 + - + +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.8 1.1 - - + -
105C LEU* 4.2 9.6 - - + -
116C GLY 3.6 1.2 - - - +
117C VAL* 3.4 4.5 - - - -
118C TYR* 2.8 46.0 + - + +
120C LEU* 3.8 29.8 - - + -
123C ALA* 5.3 0.2 - - + -
124C VAL* 1.3 78.5 - - - +
126C ARG* 1.3 63.3 + - - +
127C PHE* 4.3 15.3 - - + -
145C VAL* 4.1 11.2 - - + -
146C GLU 3.5 7.2 - - - +
147C VAL* 4.2 15.3 - - + -
155C TRP* 5.2 0.7 - - + -
159C ILE* 3.9 27.1 - - + -
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Residues in contact with ARG 126 (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 GLY 3.1 8.1 - - - +
117C VAL* 4.5 17.7 - - + +
124C VAL* 3.4 31.2 + - + +
125C VAL* 1.3 77.4 - - - +
127C PHE* 1.3 61.5 + - - +
144C ARG 3.8 0.3 - - - +
145C VAL* 3.5 1.7 - - - +
146C GLU* 2.7 63.0 + - + +
148C GLU* 3.5 28.2 + - - +
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Residues in contact with PHE 127 (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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98C PRO* 4.1 18.4 - - + -
101C LEU* 3.7 27.6 - - + -
102C GLU* 3.6 36.3 - - + -
105C LEU* 3.9 10.8 - - + -
116C GLY* 2.9 44.4 + - - +
118C TYR* 3.7 26.9 - + - -
125C VAL* 4.3 9.6 - - + -
126C ARG* 1.3 78.3 - - - +
128C ARG* 1.3 64.6 + - - +
143C LEU* 4.2 15.9 - - + -
144C ARG 3.1 11.7 - - - +
145C VAL* 4.1 5.6 - - + -
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Residues in contact with ARG 128 (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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127C PHE* 1.3 79.5 - - - +
129C GLU* 1.3 76.6 + - - +
130C VAL* 3.5 10.5 + - - +
143C LEU* 3.3 5.7 - - - +
144C ARG* 2.9 70.0 + - + +
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Residues in contact with GLU 129 (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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98C PRO* 3.4 38.5 - - + +
128C ARG* 1.3 89.1 + - + +
130C VAL* 1.3 64.0 + - - +
142C GLN 3.6 8.5 - - - +
143C LEU* 4.0 1.8 - - + -
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Residues in contact with VAL 130 (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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92C THR* 3.9 15.7 - - + +
128C ARG* 3.8 18.4 - - - +
129C GLU* 1.3 82.9 - - - +
131C GLU* 1.3 70.9 + - - +
132C PRO* 3.3 7.1 - - - +
141C PRO* 5.6 0.2 - - - +
142C GLN* 2.9 45.2 + - + +
143C LEU 4.3 0.2 - - - +
144C ARG* 3.8 27.1 - - + +
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Residues in contact with GLU 131 (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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130C VAL* 1.3 75.4 - - - +
132C PRO* 1.3 81.2 - - + +
133C LEU* 5.2 1.7 - - - +
142C GLN* 3.2 15.1 - - - +
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Residues in contact with PRO 132 (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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130C VAL 3.3 6.0 - - - +
131C GLU* 1.3 101.2 - - - +
133C LEU* 1.3 60.4 + - - +
134C LYS* 4.1 1.4 + - - +
139C SER* 3.6 25.8 - - - +
140C ILE 3.1 21.3 - - - +
141C PRO* 4.1 7.0 - - + -
142C GLN* 3.7 4.3 - - + +
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Residues in contact with LEU 133 (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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94C GLY* 5.7 0.9 - - - -
131C GLU 5.2 1.3 - - - +
132C PRO* 1.3 76.8 - - - +
134C LYS* 1.3 62.7 + - - +
135C VAL* 5.3 2.9 - - + -
138C LEU 3.8 0.5 - - - +
139C SER* 3.5 4.0 + - - -
140C ILE* 2.8 51.6 + - + +
142C GLN* 3.1 40.2 - - + +
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Residues in contact with LYS 134 (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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132C PRO 4.1 1.7 + - - +
133C LEU* 1.3 76.4 - - - +
135C VAL* 1.3 68.3 + - - +
136C GLY 3.3 24.0 - - - +
137C SER* 4.1 14.2 + - - +
138C LEU 3.5 8.5 - - - +
139C SER* 4.0 21.8 - - - -
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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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133C LEU* 4.2 3.1 - - + -
134C LYS* 1.3 79.0 - - - +
136C GLY* 1.3 62.1 + - - +
137C SER 3.1 0.5 + - - -
138C LEU* 2.8 36.9 + - + +
140C ILE* 3.8 23.8 - - + -
18D LEU* 4.2 24.7 - - + -
19D GLU 3.8 14.6 - - - +
20D LEU* 3.7 24.9 - - + -
35D ALA* 3.4 9.5 - - + +
36D TYR* 4.5 1.1 - - + +
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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