Contacts of the strand formed by residues 143 - 147 (chain D) in PDB entry 1LO5
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 VAL 143 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D LYS 3.5 0.3 - - - -
125D VAL* 2.5 55.8 + - + +
127D ILE* 3.0 28.5 - - + -
140D LEU 4.0 3.2 + - - -
141D GLU 3.3 1.5 - - - -
142D THR* 1.3 83.1 - - + +
144D LYS* 1.3 56.2 + - - +
155D LEU* 3.5 39.9 - - + +
158D GLN* 3.4 13.9 - - + +
159D ALA* 4.1 23.1 - - + +
226D ILE* 4.8 3.1 - - + -
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLU* 3.4 39.5 + - + +
123D LYS 3.3 10.1 - - - +
124D LYS* 4.5 7.4 - - + +
140D LEU 5.3 0.2 - - - +
141D GLU* 2.9 38.9 - - + +
142D THR 4.6 1.1 - - - +
143D VAL* 1.3 75.0 - - - +
145D THR* 1.3 70.3 + - - +
155D LEU* 4.6 0.3 - - - +
158D GLN* 2.9 28.6 + - - +
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Residues in contact with THR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU* 4.0 0.5 - - - +
122D GLU* 4.6 1.9 + - - +
123D LYS* 3.0 38.6 + - + +
125D VAL* 3.5 26.5 - - + -
144D LYS* 1.3 81.5 - - - +
146D ASN* 1.3 63.9 + - - +
147D LYS 3.4 15.1 + - - -
150D VAL* 3.5 22.3 - - + +
154D GLU* 3.5 14.0 + - - -
155D LEU* 4.0 7.2 - - + -
221D SER* 4.8 6.7 - - - -
224D MET* 5.4 0.2 - - + -
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Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLU* 6.1 1.6 - - - +
117D ASN 3.6 0.7 - - - +
118D ARG* 3.7 21.7 - - - +
119D LEU* 2.9 41.7 + - - +
121D GLU* 4.5 1.6 - - - +
122D GLU* 3.5 44.7 - - - +
145D THR* 1.3 72.8 + - - +
147D LYS* 1.3 66.0 + - + +
154D GLU* 4.5 3.4 + - - -
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LYS* 6.2 0.2 - - - +
39D GLU* 4.3 15.2 + - - -
86D ASP* 3.6 26.7 - - - +
87D LEU 4.9 4.4 + - - -
88D TYR* 4.5 9.0 - - - +
112D THR* 3.1 33.7 - - + +
117D ASN* 3.0 27.4 - - - +
118D ARG* 5.0 0.2 - - - +
119D LEU* 3.5 5.6 - - - +
145D THR* 3.4 9.0 + - - +
146D ASN* 1.3 83.9 - - + +
148D LYS* 1.3 59.6 + - - +
149D ASN 3.7 10.1 - - - +
150D VAL* 4.2 6.6 + - - -
151D THR* 5.4 0.7 - - + -
154D GLU* 3.0 32.8 + - - +
221D SER* 3.3 17.7 + - - -
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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