Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 2XFR
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 LYS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN* 2.9 34.8 + - - +
13A TYR* 3.9 13.4 + - + +
46A ASP* 3.1 28.5 + - - +
47A GLY* 3.1 2.6 - - - -
48A VAL 2.9 23.3 + - - -
77A VAL* 3.9 2.6 - - - +
81A GLY 4.2 0.6 + - - +
82A LEU* 1.3 77.0 - - - +
84A LEU* 1.3 63.9 + - - +
170A GLY 3.9 18.2 - - - +
171A VAL* 3.5 6.1 - - - +
173A VAL* 3.8 21.1 - - + -
445A ARG* 6.2 0.2 - - - +
446A ASP 4.5 2.6 + - - -
447A PRO* 4.1 22.7 + - - +
449A VAL* 4.2 15.4 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 5.7 0.4 - - + -
48A VAL* 3.3 23.6 - - + +
50A VAL* 4.1 18.2 - - + -
73A LEU* 6.4 0.2 - - + -
74A PHE* 3.5 45.5 - - + -
77A VAL* 4.3 10.3 - - + -
83A LYS* 1.3 76.5 - - - +
85A GLN* 1.3 77.6 + - - +
86A ALA* 4.8 1.1 - - + +
171A VAL* 2.8 27.6 + - + +
172A ILE* 3.4 22.8 - - + +
173A VAL* 3.0 28.2 + - - +
174A ASP 3.9 0.5 + - - -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.7 43.8 + - + -
48A VAL 2.9 7.2 + - - +
49A MET* 3.2 33.2 - - + +
50A VAL 3.0 25.8 + - - -
84A LEU* 1.3 79.7 - - - +
86A ALA* 1.3 59.0 + - - +
173A VAL* 4.4 4.1 - - + +
174A ASP* 3.4 42.7 + - + +
289A GLN* 4.2 9.9 - - - +
338A ASN* 5.8 0.3 + - - -
415A THR* 3.7 12.1 + - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.7 5.6 - - - -
52A VAL* 4.1 8.1 - - + -
74A PHE* 4.6 6.7 - - + -
84A LEU* 4.2 3.5 - - + -
85A GLN* 1.3 73.6 - - - +
87A ILE* 1.3 62.9 + - - +
88A MET* 3.9 7.6 + - + -
159A PHE* 3.8 29.4 - - + -
172A ILE* 4.8 5.6 - - + -
174A ASP 3.0 10.7 + - - +
175A ILE* 3.4 10.6 - - + +
176A GLU* 2.9 24.2 + - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A MET* 4.2 18.4 - - + -
49A MET* 3.7 30.3 - - + -
50A VAL 2.9 22.0 + - - +
51A ASP* 3.8 20.0 - - - +
52A VAL* 2.9 31.2 + - - +
86A ALA* 1.3 72.1 - - - +
88A MET* 1.3 69.2 + - - +
89A SER* 3.1 17.7 + - - +
91A HIS* 5.0 5.4 - - + -
176A GLU* 3.3 28.9 - - + +
178A GLY* 4.6 6.5 - - - +
183A GLY* 5.6 2.9 - - - +
293A LYS* 6.3 0.2 - - + -
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.3 6.7 - - + -
86A ALA* 4.0 12.1 - - + +
87A ILE* 1.3 76.8 - - - +
89A SER* 1.3 58.8 + - - +
90A PHE* 3.3 31.7 + - + -
155A TYR* 4.2 14.1 - - - -
156A MET* 3.9 28.5 - - + -
159A PHE* 3.8 49.1 - - + -
175A ILE* 3.8 24.7 - - + -
176A GLU 2.8 12.8 + - - +
177A VAL* 4.4 2.9 - - - -
178A GLY* 2.9 26.4 + - - +
283A PHE* 5.0 0.7 - - - -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.5 9.4 + - - +
52A VAL 3.2 23.1 + - - -
53A TRP* 3.7 18.6 - - - -
54A TRP* 3.0 24.1 + - - +
87A ILE* 3.1 26.9 + - - +
88A MET* 1.3 67.6 - - - +
90A PHE* 1.3 57.2 + - - +
91A HIS* 3.1 34.8 + - - +
155A TYR* 5.0 1.0 - - - -
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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