Contacts of the strand formed by residues 118 - 125 (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 ARG 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D GLU* 3.7 39.6 + - - +
114D HIS* 4.4 24.4 + - + +
116D ASN* 3.7 2.8 - - - +
117D ASN* 1.3 82.3 + - - +
119D LEU* 1.3 69.8 + - - +
120D THR 4.2 0.3 + - - -
146D ASN* 3.8 23.9 - - - +
147D LYS* 6.2 0.2 - - - -
148D LYS* 5.4 0.7 - - - +
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Residues in contact with LEU 119 (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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118D ARG* 1.3 81.4 - - - +
120D THR* 1.3 66.5 + - - +
121D GLU* 3.2 18.8 + - - +
123D LYS* 3.4 33.2 - - + -
145D THR 4.0 2.5 - - - +
146D ASN* 2.9 31.8 + - - +
147D LYS 3.5 10.3 - - - +
148D LYS* 3.4 38.1 - - + +
221D SER* 3.8 8.1 - - - +
222D GLU* 3.7 24.2 - - + +
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Residues in contact with THR 120 (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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118D ARG 4.2 0.6 + - - -
119D LEU* 1.3 73.5 - - - +
121D GLU* 1.3 72.4 + - - +
222D GLU* 5.5 2.6 + - - -
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Residues in contact with GLU 121 (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* 3.1 22.2 - - - +
120D THR* 1.3 93.0 + - - +
122D GLU* 1.3 74.0 + - - +
123D LYS* 3.2 2.8 + - - -
124D LYS* 6.0 1.9 - - - -
146D ASN* 4.5 0.4 - - - -
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Residues in contact with GLU 122 (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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121D GLU* 1.3 80.8 - - - +
123D LYS* 1.3 63.9 + - - +
124D LYS* 3.8 17.5 + - + +
144D LYS* 3.4 49.7 + - + +
145D THR 4.4 2.0 - - - +
146D ASN* 3.5 38.5 - - - +
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Residues in contact with LYS 123 (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* 3.4 20.4 - - + -
121D GLU 3.2 2.1 + - - -
122D GLU* 1.3 72.4 - - - +
124D LYS* 1.3 79.8 + - - +
125D VAL* 4.4 4.9 - - + +
126D PRO* 4.4 15.8 - - - +
144D LYS* 3.3 5.1 - - - +
145D THR* 3.0 52.6 + - + +
221D SER* 4.0 25.8 - - - +
222D GLU* 4.3 15.3 - - + +
223D ASN* 4.2 14.6 - - - +
224D MET* 4.4 6.1 + - - -
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Residues in contact with LYS 124 (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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121D GLU* 6.0 2.0 - - - -
122D GLU* 3.8 17.9 + - + +
123D LYS* 1.3 85.2 + - - +
125D VAL* 1.3 59.3 + - - +
126D PRO* 3.2 15.1 - - - +
140D LEU* 3.6 38.5 - - + +
141D GLU* 4.8 19.3 - - + +
143D VAL 3.7 4.3 - - - -
144D LYS* 4.5 9.6 - - - +
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Residues in contact with VAL 125 (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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123D LYS* 4.1 7.9 - - + +
124D LYS* 1.3 69.9 - - - +
126D PRO* 1.3 70.0 - - + +
127D ILE* 3.3 11.6 + - - +
139D PRO 5.5 0.7 - - - +
140D LEU* 4.2 9.3 + - - +
143D VAL* 2.5 45.8 + - + +
145D THR* 3.5 30.5 - - + -
155D LEU* 3.6 5.8 - - + -
224D MET* 4.0 21.1 - - + -
225D HIS* 4.2 1.6 - - - -
226D ILE* 3.4 36.1 - - + -
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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