Contacts of the strand formed by residues 118 - 123 (chain B) in PDB entry 2QNJ
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 LEU 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.4 8.7 - - + +
107B MET* 4.1 35.0 + - + +
108B LYS* 3.8 31.9 - - + +
110B LEU 5.3 0.8 + - - -
111B ASN* 5.6 3.4 + - - +
116B VAL 4.0 1.0 + - - -
117B LYS* 1.3 75.4 - - - +
119B PHE* 1.3 74.3 + - - +
120B GLU 3.5 21.5 - - - +
121B VAL* 4.1 15.9 - - + -
130B LEU* 4.3 7.2 - - + -
131B ILE 3.6 9.9 - - - +
132B MET* 3.8 15.4 - - - +
354B TYR* 3.5 29.6 - - + -
362B LEU* 4.3 4.3 - - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU 5.9 0.4 - - - -
82B VAL* 4.2 7.0 - - + -
117B LYS* 4.3 12.8 - - + -
118B LEU* 1.3 79.2 - - - +
120B GLU* 1.3 61.9 + - + +
131B ILE* 2.7 25.2 + - + +
132B MET 3.9 3.8 - - - -
133B GLU* 3.6 40.8 - - + -
354B TYR* 3.8 14.0 - - - +
358B THR* 5.2 0.2 - - - +
359B ALA* 3.3 25.3 + - + +
362B LEU* 4.0 29.2 - - + +
363B LEU* 3.6 35.7 - - + -
367B LYS* 4.1 36.8 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLY* 5.9 0.2 - - - -
55B ASN* 5.2 2.4 + - - -
56B TYR* 2.5 43.8 + - + +
75B HIS* 4.6 2.4 - - - -
118B LEU* 3.5 8.2 - - - +
119B PHE* 1.3 80.9 - - - +
121B VAL* 1.3 72.3 + - - +
122B ILE* 3.8 20.5 - - + +
129B TYR 3.8 0.3 - - - +
131B ILE* 2.9 32.3 + - + +
354B TYR* 3.6 15.3 - - - +
355B ASP* 3.8 1.0 - - - -
356B GLU* 3.3 35.5 + - - +
359B ALA* 3.3 13.3 - - + +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 5.6 3.4 - - + -
104B VAL* 4.1 12.8 - - + -
108B LYS* 4.4 7.0 - - - +
118B LEU* 4.1 18.4 - - + -
120B GLU* 1.3 78.6 - - - +
122B ILE* 1.3 67.2 + - - +
123B GLU* 4.2 6.4 + - + +
128B LEU* 3.7 27.8 - - + -
129B TYR 3.4 5.4 - - - +
130B LEU* 4.0 16.6 - - + -
354B TYR* 3.0 25.5 + - + +
355B ASP* 5.0 2.4 - - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE* 4.2 22.2 - - + +
54B GLY* 3.8 30.7 - - - +
56B TYR* 4.0 22.2 - - + -
120B GLU* 3.8 22.0 - - + +
121B VAL* 1.3 77.9 - - - +
123B GLU* 1.3 66.3 + - - +
124B THR* 5.2 4.0 - - + -
128B LEU* 3.8 0.5 - - - +
129B TYR* 2.7 48.7 + - + +
131B ILE* 4.1 9.9 - - + -
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LYS* 2.7 31.6 + - - +
101B PHE* 3.2 40.1 - - - -
121B VAL* 4.1 7.7 + - + +
122B ILE* 1.3 77.6 - - - +
124B THR* 1.3 62.7 + - - +
127B THR 3.8 2.5 - - - +
128B LEU* 3.5 16.3 - - + +
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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