Contacts of the strand formed by residues 120 - 126 (chain B) in PDB entry 1C04
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 LEU 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS* 3.2 18.4 + - - -
116B PRO* 3.4 18.5 - - + +
117B GLU* 3.2 19.9 + - + +
119B GLY* 1.3 86.6 - - - +
121B GLU* 1.3 63.9 + - - +
132B VAL* 4.6 3.1 - - + -
133B LYS 3.7 11.4 - - - +
134B GLY* 4.4 1.3 - - - -
136B ASP* 5.1 1.6 - - + +
139B ARG* 3.9 55.6 - - + +
140B VAL* 4.1 23.6 - - + -
143B LEU* 3.9 24.0 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 4.1 15.0 - - - +
116B PRO* 4.7 0.2 - - - -
119B GLY 5.7 1.1 - - - +
120B LEU* 1.3 76.8 - - - +
122B ILE* 1.3 68.9 - - - +
123B GLU* 3.7 20.5 - - + +
132B VAL* 3.4 6.4 - - - +
133B LYS* 2.9 48.5 + - + +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS* 3.0 34.6 + - - +
100B LYS* 5.1 0.8 - - - +
102B LEU* 4.0 32.5 - - + +
114B ILE* 4.4 7.0 - - + -
116B PRO* 3.7 33.4 - - + +
121B GLU* 1.3 81.4 - - - +
123B GLU* 1.3 68.2 + - - +
124B VAL* 4.5 1.6 - - + -
130B ILE* 3.5 30.3 - - + -
131B ILE 3.2 5.2 - - - +
132B VAL* 4.7 2.9 - - + -
143B LEU* 4.1 21.5 - - + -
147B ILE* 4.3 12.1 - - + -
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS* 5.0 1.1 - - - +
121B GLU* 3.7 20.0 - - - +
122B ILE* 1.3 79.5 - - - +
124B VAL* 1.3 64.2 + - - +
125B PRO* 3.6 7.9 - - + +
130B ILE* 3.4 4.3 - - - +
131B ILE* 2.7 45.1 + - + +
133B LYS* 2.9 41.2 + - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 3.5 32.3 - - + +
96B SER* 4.1 10.1 - - - +
97B LYS* 4.1 23.4 - - + +
102B LEU* 3.7 29.6 - - + -
122B ILE* 4.5 2.2 - - + -
123B GLU* 1.3 79.6 - - - +
125B PRO* 1.3 63.9 - - - +
126B SER* 3.3 20.7 + - - +
127B GLN* 4.5 0.2 - - - -
129B LYS 3.5 8.3 - - - +
130B ILE* 4.7 1.8 - - + -
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU* 3.6 11.2 - - + +
124B VAL* 1.3 88.2 - - - +
126B SER* 1.3 59.7 + - - +
129B LYS* 3.6 33.0 - - + +
131B ILE* 4.2 20.2 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.3 8.8 - - - +
125B PRO* 1.3 80.1 - - - +
127B GLN* 1.3 61.1 + - - +
128B THR* 2.9 18.0 + - - -
129B LYS* 3.1 38.7 + - - +
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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