Contacts of the strand formed by residues 125 - 131 (chain D) in PDB entry 1LNU
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 ASN 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D GLN 4.5 4.8 + - - +
124D PRO* 1.3 73.8 - - - +
126D VAL* 1.3 66.5 + - - +
127D VAL* 6.1 1.6 - - + -
145D SER 3.1 3.6 - - - +
146D VAL* 3.2 0.5 - - - -
147D THR* 3.0 44.8 + - - +
148D ASP* 2.8 36.1 + - - +
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Residues in contact with VAL 126 (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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124D PRO 3.7 4.9 + - - +
125D ASN* 1.3 82.3 - - - +
127D VAL* 1.3 72.7 + - - +
144D CYS* 4.8 7.6 - - - -
145D SER 3.2 8.1 - - - +
146D VAL* 3.9 9.6 - - + -
200D CYS 5.8 1.3 - - - +
202D VAL* 3.9 24.7 - - + -
211D ILE* 3.3 36.1 - - + -
213D VAL* 3.2 32.8 - - + +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PRO* 4.6 18.6 - - + -
125D ASN* 6.1 1.6 - - + -
126D VAL* 1.3 88.2 - - - +
128D ILE* 1.3 68.4 + - - +
129D SER* 5.3 4.3 - - - +
143D VAL 3.6 1.4 - - - +
144D CYS* 4.4 1.3 - - - -
145D SER* 3.0 35.6 + - - +
213D VAL* 4.8 5.8 - - - -
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Residues in contact with ILE 128 (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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127D VAL* 1.3 81.5 - - - +
129D SER* 1.3 69.5 + - - +
142D LEU* 5.1 2.0 - - + -
143D VAL 3.0 9.0 - - - +
144D CYS* 4.1 4.3 - - + -
158D TRP* 3.9 27.6 - - + -
199D THR* 6.0 0.2 - - - -
200D CYS* 4.1 14.8 - - + -
213D VAL* 4.0 22.4 - - + +
214D GLU 4.1 12.1 - - - +
215D TRP* 3.3 46.6 - - + -
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Residues in contact with SER 129 (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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127D VAL* 5.3 5.0 - - - +
128D ILE* 1.3 79.1 + - - +
130D LEU* 1.3 64.3 + - - +
142D LEU* 3.3 16.4 - - - +
143D VAL* 2.8 36.0 + - - -
145D SER* 6.0 1.1 - - - -
215D TRP* 5.4 4.5 - - - +
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Residues in contact with LEU 130 (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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129D SER* 1.3 80.2 - - - +
131D SER* 1.3 68.1 + - - +
140D ASN* 4.9 2.7 - - + -
141D THR 3.3 16.6 - - - +
142D LEU* 3.5 18.2 - - + -
190D MET* 4.1 11.9 - - + -
192D PRO* 6.2 1.8 - - + -
215D TRP* 5.0 17.7 - - + +
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Residues in contact with SER 131 (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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129D SER 4.2 0.4 - - - -
130D LEU* 1.3 81.9 - - - +
132D ARG* 1.3 81.0 + - - +
133D THR 3.6 7.5 + - - +
134D GLU 5.0 0.3 - - - +
140D ASN* 4.4 1.6 - - - -
141D THR* 2.8 23.5 + - - -
142D LEU* 5.1 0.2 - - - +
143D VAL* 4.3 20.2 - - - -
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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