Contacts of the helix formed by residues 141 - 148 (chain A) in PDB entry 1OCU
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 HIS 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A VAL* 3.9 24.5 - - + +
105A MET 5.6 3.6 - - - -
137A SER 3.6 8.8 + - - +
138A VAL* 3.5 13.2 - - - +
139A ALA 3.2 2.0 - - - -
140A GLY* 1.3 76.9 - - - +
142A PRO* 1.3 76.1 - - + +
143A LEU* 3.1 41.2 + - + +
144A LEU* 3.0 20.8 + - + +
145A GLN* 2.9 23.2 + - - +
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Residues in contact with PRO 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 3.4 9.6 - - - +
141A HIS* 1.3 94.5 - - + +
143A LEU* 1.3 68.3 + - + +
145A GLN* 3.3 13.6 + - - +
146A SER* 3.2 23.4 + - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 5.9 0.7 - - - +
101A HIS* 4.1 43.0 + - + +
104A VAL* 5.2 8.1 - - + -
141A HIS* 3.1 22.8 + - + -
142A PRO* 1.3 83.4 - - + +
144A LEU* 1.3 63.2 + - + +
146A SER* 3.5 8.2 + - - +
147A GLY* 2.9 28.4 + - - -
148A SER 4.0 0.3 + - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.2 16.6 - - + -
96A ILE* 3.2 31.4 - - + -
101A HIS* 6.4 0.9 - - + -
104A VAL* 4.9 9.4 - - + -
106A VAL* 5.3 5.4 - - + -
138A VAL* 3.4 41.3 - - + +
139A ALA* 5.7 0.2 - - - -
141A HIS* 3.0 26.3 + - + +
143A LEU* 1.3 79.7 - - + +
145A GLN* 1.3 63.8 + - + +
148A SER* 2.9 43.2 + - - +
151A LEU* 4.5 10.5 - - + +
152A VAL* 5.9 0.2 - - - +
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE 5.7 0.2 - - - -
36A LEU* 3.9 23.0 + - + +
68A LEU* 3.8 34.9 - - + +
69A PRO* 6.1 0.3 - - - +
70A SER* 2.9 25.8 + - - -
71A PHE* 4.7 5.5 - - - -
139A ALA 2.8 28.3 + - - +
140A GLY* 3.6 15.5 + - - +
141A HIS 2.9 19.6 + - - +
142A PRO* 3.3 15.1 + - - +
144A LEU* 1.3 77.4 - - - +
146A SER* 1.3 57.0 + - - +
151A LEU* 5.4 5.1 - - + +
152A VAL* 5.5 0.3 - - - +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 6.3 3.4 - - - -
70A SER* 3.4 13.2 + - - -
142A PRO 3.2 10.6 + - - -
143A LEU* 3.5 13.7 + - - +
145A GLN* 1.3 81.3 - - - +
147A GLY* 1.3 61.2 + - - +
148A SER 3.8 0.2 - - - -
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 5.6 0.2 - - - -
95A GLU* 4.3 0.5 - - - +
99A LEU* 3.5 26.0 - - - +
101A HIS* 6.3 0.4 - - - -
143A LEU 2.9 14.0 + - - -
146A SER* 1.3 82.2 + - - +
148A SER* 1.3 59.9 + - - +
149A LYS* 3.4 12.8 + - - +
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 5.1 2.4 + - - -
92A LEU* 3.6 8.8 - - - +
95A GLU* 2.4 25.8 + - - -
96A ILE* 5.5 0.7 - - - -
99A LEU* 4.8 2.0 - - - -
143A LEU 4.0 0.6 + - - -
144A LEU* 2.9 40.8 + - - +
146A SER 3.8 0.6 - - - -
147A GLY* 1.3 70.3 - - - +
149A LYS* 1.3 62.5 + - - +
151A LEU* 3.0 28.4 + - - +
152A VAL* 3.6 19.4 + - - +
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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