Contacts of the strand formed by residues 119 - 124 (chain N) in PDB entry 3DXA
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 THR 119 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6N GLN* 3.3 24.7 + - - +
8N PRO* 3.0 30.3 + - + +
11N MET* 4.0 24.2 - - + -
21N LEU* 4.5 20.6 - - + -
22N PRO* 4.6 2.9 + - + -
41N TRP* 5.7 0.7 - - - -
101N VAL* 3.5 1.2 - - - -
102N TYR* 2.7 48.7 + - - +
118N GLY* 1.3 71.6 - - - +
120N LYS* 1.3 65.6 + - - +
121N LEU 3.7 2.7 + - - +
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Residues in contact with LYS 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N THR 3.2 25.7 + - - +
10N SER* 3.6 11.9 - - - +
11N MET 2.9 24.4 + - - +
100N ALA 3.7 5.2 - - - +
101N VAL* 3.8 30.0 - - + +
117N THR* 3.9 26.5 - - - -
118N GLY 4.3 4.3 - - - +
119N THR* 1.3 75.0 - - - +
121N LEU* 1.3 60.7 + - - +
122N GLN* 3.7 16.7 + - - +
47O GLY* 4.3 16.0 + - - -
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Residues in contact with LEU 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N MET* 3.5 21.1 - - + +
12N ASP 3.8 3.8 - - - -
13N CYS* 3.6 16.8 - - + -
19N ALA* 4.3 11.4 - - + -
21N LEU* 3.4 35.4 - - + -
91N LEU* 4.2 15.9 - - + -
98N ASP* 5.2 2.0 - - + +
99N THR* 3.4 8.5 - - - -
100N ALA 3.0 26.2 + - - +
102N TYR* 4.0 19.1 - - + +
119N THR* 3.7 2.5 + - + -
120N LYS* 1.3 71.8 - - - +
122N GLN* 1.3 83.4 + - - +
123N VAL* 4.1 16.2 - - + -
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Residues in contact with GLN 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N SER* 6.1 1.5 - - - -
11N MET 3.2 7.4 + - - +
12N ASP* 3.2 21.7 - - - +
13N CYS 2.8 32.1 + - - +
99N THR* 4.3 8.2 - - - +
100N ALA 6.3 0.2 - - - -
120N LYS* 4.2 19.6 - - - +
121N LEU* 1.3 84.2 + - - +
123N VAL* 1.3 59.5 + - - +
124N ILE* 3.6 16.2 - - + +
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Residues in contact with VAL 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N CYS* 3.3 5.4 - - + +
14N ALA 3.8 4.3 - - - -
15N GLU* 3.4 37.0 - - + +
94N ALA* 3.9 19.3 - - + -
95N THR 3.6 21.5 - - - +
96N LEU* 3.1 23.8 - - - +
98N ASP* 4.7 2.9 - - + -
99N THR* 3.2 27.7 - - + +
121N LEU* 4.1 19.7 - - + -
122N GLN* 1.3 76.1 - - - +
124N ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N ASP* 4.9 11.4 - - + +
13N CYS 3.1 12.7 + - - +
14N ALA* 3.6 9.1 - - - +
15N GLU* 3.2 19.7 + - - +
122N GLN* 3.6 28.7 - - + +
123N VAL* 1.3 82.8 - - - +
125N PRO* 1.4 77.5 - - + +
126N ILE 4.2 0.2 + - - -
154N SER* 3.3 28.7 - - - +
171N LYS* 6.4 2.5 - - - -
184N ASN* 4.7 6.3 - - - +
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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