Contacts of the strand formed by residues 79 - 89 (chain A) in PDB entry 2F2D
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 ARG 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLN* 4.5 0.7 - - - +
72A THR 3.6 4.5 - - - +
73A SER* 3.5 18.5 + - - +
78A THR* 1.4 87.8 + - + +
80A VAL* 1.3 62.1 + - - +
81A GLN 5.4 0.2 - - - -
82A GLU* 2.6 55.7 + - + +
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Residues in contact with VAL 80 (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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72A THR* 3.0 14.1 + - + +
73A SER 4.1 2.2 - - - -
74A LEU* 3.8 36.6 - - + +
78A THR 3.6 13.5 - - - +
79A ARG* 1.3 74.8 - - - +
81A GLN* 1.3 61.2 + - - +
82A GLU 4.3 0.2 - - - -
130A TYR* 3.3 60.9 - - + +
131A ILE* 3.9 13.2 - - + -
137A LEU* 5.0 3.4 - - + -
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Residues in contact with GLN 81 (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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70A LEU 4.9 0.3 - - - +
72A THR* 3.4 30.0 + - - -
80A VAL* 1.3 86.0 - - + +
82A GLU* 1.3 60.9 + - - +
83A GLU* 3.6 26.2 + - + +
122A TYR* 6.4 0.4 - - - -
127A ARG* 3.2 57.5 + - - +
130A TYR* 5.1 13.7 - - + +
131A ILE* 4.7 14.8 - - + +
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Residues in contact with GLU 82 (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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69A HIS* 5.2 6.7 - - - +
71A GLN* 4.0 30.9 - - + +
72A THR 4.7 0.2 - - - +
79A ARG* 2.6 64.0 + - + +
80A VAL 4.3 0.2 - - - -
81A GLN* 1.3 71.0 - - - +
83A GLU* 1.3 57.6 + - - +
84A PRO* 3.5 12.1 - - + +
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Residues in contact with GLU 83 (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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70A LEU* 2.8 31.7 + - - +
71A GLN* 4.6 0.2 - - - +
81A GLN* 3.6 19.2 + - + +
82A GLU* 1.3 73.2 - - - +
84A PRO* 1.4 63.3 - - + +
85A GLU 3.5 12.4 + - - +
86A LEU* 5.1 9.9 + - + +
127A ARG* 2.6 47.1 + - - -
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Residues in contact with PRO 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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69A HIS* 3.4 53.7 - - + +
82A GLU* 3.5 14.4 - - + +
83A GLU* 1.4 83.1 - - - +
85A GLU* 1.3 60.2 + - + +
86A LEU 4.2 0.2 - - - -
144A LYS* 3.4 14.9 - - - -
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Residues in contact with GLU 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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67A THR* 3.0 20.0 - - - +
83A GLU* 3.5 11.6 + - - +
84A PRO* 1.3 79.1 - - + +
86A LEU* 1.3 59.0 + - - +
87A VAL* 4.1 7.8 + - + +
144A LYS* 2.6 34.5 + - - -
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Residues in contact with LEU 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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67A THR* 3.6 3.8 - - - -
68A VAL* 3.1 50.7 + - + +
70A LEU* 3.7 34.5 - - + -
83A GLU* 5.3 10.8 - - + +
85A GLU* 1.3 75.0 + - - +
87A VAL* 1.3 65.9 + - - +
88A PHE* 3.6 11.0 - - + -
94A ASP* 4.9 5.4 - - - +
95A VAL* 4.2 26.0 - - + -
99A LEU* 5.3 1.3 - - + -
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Residues in contact with VAL 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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65A VAL* 3.6 24.7 - - + -
66A VAL 3.8 3.4 - - - +
67A THR* 3.6 26.2 - - + +
85A GLU* 4.1 7.9 + - + +
86A LEU* 1.3 77.4 - - - +
88A PHE* 1.3 66.9 + - - +
94A ASP* 4.8 2.1 - - - +
147A VAL* 6.1 0.7 - - + -
150A PRO* 5.9 1.8 - - + -
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Residues in contact with PHE 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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65A VAL* 3.7 6.2 - - - +
66A VAL* 3.0 65.2 + - + +
68A VAL* 3.9 28.3 - - + -
86A LEU* 3.6 14.6 - - + -
87A VAL* 1.3 77.9 - - - +
89A THR* 1.3 78.9 + - - +
91A GLY 5.5 0.7 - - - -
92A ASP 6.0 0.2 - - - -
94A ASP* 3.5 24.9 - - + +
95A VAL* 3.6 40.2 - - + -
99A LEU* 4.7 3.6 - - + -
103A VAL* 3.8 32.1 - - + -
106A MET* 4.5 2.2 - - + -
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Residues in contact with THR 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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63A GLY* 5.5 3.6 - - - -
64A GLN 3.8 13.0 - - - +
65A VAL* 4.6 12.7 - - + +
88A PHE* 1.3 86.4 - - - +
90A LEU* 1.3 72.3 + - - +
91A GLY 3.3 3.9 + - - +
92A ASP* 3.5 38.4 + - - +
94A ASP* 5.8 2.3 - - - +
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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