Contacts of the strand formed by residues 124 - 130 (chain T) in PDB entry 2NX5
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 ALA 124 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A LYS* 5.4 5.6 - - + +
122T ASP* 3.5 6.9 + - - +
123T PRO* 1.3 76.9 - - - +
125T VAL* 1.3 64.3 + - - +
126T TYR* 3.4 38.8 - - + +
140T LEU 3.5 2.6 - - - +
141T PHE* 3.6 5.8 - - - -
142T THR 3.3 27.6 + - - +
140U HIS* 5.0 5.4 - - + -
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Residues in contact with VAL 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124T ALA* 1.3 77.7 - - - +
126T TYR* 1.3 70.3 + - - +
139T CYS* 4.3 1.3 - - + -
140T LEU 3.4 5.6 - - - +
141T PHE* 4.3 12.1 - - + -
189T CYS* 3.3 39.8 - - + +
190T ALA 6.0 0.9 - - - +
193T PHE* 3.9 37.0 - - + +
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Residues in contact with TYR 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T ASP 5.1 1.0 + - - -
124T ALA* 3.4 25.9 - - + +
125T VAL* 1.3 79.8 - - - +
127T GLN* 1.3 60.2 + - - +
128T LEU* 3.8 6.7 - - + +
139T CYS* 3.3 5.0 - - - -
140T LEU* 2.8 44.0 + - + +
142T THR* 3.5 34.3 - - + -
143T ASP* 4.9 3.0 + - - -
189T CYS* 4.4 4.3 - - - -
134U SER* 3.4 26.5 - - - +
136U ALA* 3.9 13.5 - - + -
137U GLU* 3.6 39.7 - - + -
140U HIS* 3.1 30.8 - + + -
141U THR* 3.7 7.4 - - - +
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Residues in contact with GLN 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126T TYR* 1.3 71.8 - - - +
128T LEU* 1.3 61.8 + - - +
129T ARG* 3.2 37.9 + - - +
137T SER* 4.0 26.0 + - - -
138T VAL 3.7 2.7 - - - -
187T PHE 5.1 0.7 - - - +
188T ALA* 4.7 4.7 - - - +
189T CYS* 3.6 34.8 + - + +
134U SER* 3.3 23.3 + - - -
136U ALA* 6.1 0.2 - - - +
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Residues in contact with LEU 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126T TYR* 3.8 4.3 - - + +
127T GLN* 1.3 80.1 - - - +
129T ARG* 1.3 62.3 + - - +
137T SER* 4.0 8.0 - - - -
138T VAL* 2.8 38.4 + - + +
139T CYS 5.1 0.2 - - - -
140T LEU* 3.7 32.5 - - + +
131U PHE* 4.0 14.6 - - + +
132U GLU 3.2 18.8 - - - +
134U SER* 4.0 19.5 - - - +
145U THR 3.5 21.1 - - - +
147U VAL* 3.8 35.4 - - + +
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Residues in contact with ARG 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127T GLN* 3.2 37.6 + - - +
128T LEU* 1.3 75.5 + - - +
130T ASP* 1.3 66.3 + - - +
137T SER* 5.6 3.4 - - - +
131U PHE* 3.6 7.8 - - - -
132U GLU* 3.1 34.6 + - + +
133U PRO 5.3 0.8 + - - -
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Residues in contact with ASP 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129T ARG* 1.3 81.1 - - - +
131T SER* 1.3 76.1 + - - +
132T LYS 3.0 23.7 + - - +
134T SER* 3.3 28.8 + - - +
135T ASP 4.1 17.3 + - - +
137T SER* 6.3 0.4 - - - +
131U PHE* 4.0 11.7 - - + -
132U GLU* 4.0 8.0 - - - +
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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