Contacts of the strand formed by residues 126 - 137 (chain D) in PDB entry 2CFX
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 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ALA* 3.8 10.1 - - + -
72D THR 3.2 15.3 - - - +
73D VAL* 4.1 0.2 - - - -
74D LYS* 4.0 8.3 - - - +
81D PHE* 3.8 28.3 - - + -
122D THR* 3.2 17.3 + - - +
123D SER* 3.5 13.9 + - - +
124D PRO 3.7 1.2 - - - -
125D TYR* 1.3 82.1 - - - +
127D GLN* 1.3 69.0 + - - +
128D THR* 4.0 4.1 + - + +
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN* 5.3 6.8 + - - -
70D GLU 3.6 0.2 - - - +
71D ALA* 3.2 4.7 - - - -
72D THR* 2.7 59.4 + - + +
74D LYS* 3.8 24.3 - - + +
123D SER* 5.7 0.2 - - - +
126D ALA* 1.3 73.8 - - - +
128D THR* 1.3 61.0 + - - +
129D VAL* 6.4 0.4 - - + -
127F GLN* 5.7 4.8 - - - +
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Residues in contact with THR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.8 23.6 - - + -
70D GLU 3.1 8.3 - - - +
71D ALA* 4.7 7.4 - - + -
118D PHE* 5.2 1.3 - - + -
119D ILE* 3.3 34.1 - - + +
122D THR* 3.6 25.4 - - + +
123D SER* 5.5 0.7 + - - -
126D ALA 4.0 5.8 + - - +
127D GLN* 1.3 82.6 - - - +
129D VAL* 1.3 67.9 + - - +
130D THR* 4.1 2.7 + - - -
99F GLY 3.8 6.4 - - - +
100F ALA 4.1 8.8 - - - +
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE 3.8 0.9 - - - +
69D VAL* 3.4 3.4 - - - -
70D GLU* 2.9 52.4 + - + +
72D THR* 6.1 4.7 - - + -
127D GLN* 6.4 0.4 - - + -
128D THR* 1.3 77.0 - - - +
130D THR* 1.3 61.3 + - - +
131D HIS* 3.7 25.5 + - + -
99F GLY* 3.3 22.9 - - - -
100F ALA* 3.7 20.6 - - + +
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D CYS* 3.7 32.1 - - + -
68D ILE 3.7 2.9 - - - -
69D VAL* 4.1 8.8 - - + +
115D VAL* 4.1 12.6 - - + -
119D ILE* 3.1 29.4 - - - +
128D THR* 4.1 2.5 + - - -
129D VAL* 1.3 73.7 - - - +
131D HIS* 1.3 65.6 + - - +
132D VAL* 4.3 0.2 - - + -
134E PHE* 4.2 9.6 - - + -
98F ALA* 3.7 11.5 - - + +
99F GLY* 3.1 34.6 + - - -
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Residues in contact with HIS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D CYS* 3.1 3.4 - - - -
68D ILE* 2.7 54.3 + - + +
70D GLU* 2.7 32.4 + - + +
129D VAL* 3.7 24.1 - - + +
130D THR* 1.3 75.2 + - - +
132D VAL* 1.3 62.7 + - - +
133D ILE* 4.4 0.5 - - - +
99F GLY* 5.5 1.2 - - - -
70G GLU* 5.6 4.6 + - - -
97G ILE* 3.9 21.2 - - + +
98G ALA* 3.5 25.0 + - - +
99G GLY* 4.5 7.7 - - - -
100G ALA 5.5 2.7 - - - -
101G ALA* 6.2 0.9 - - + -
104G MET* 3.7 22.9 - - + +
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 5.1 2.0 - - + -
66D SER 4.0 8.7 - - - +
67D CYS* 3.8 17.7 - - - -
112D LEU* 4.5 15.5 - - + -
130D THR* 4.3 1.6 - - + -
131D HIS* 1.3 73.4 - - - +
133D ILE* 1.3 73.2 + - - +
134D PHE* 3.6 2.1 + - + -
112E LEU* 3.9 30.5 - - + -
132E VAL* 4.1 20.0 - - + -
134E PHE* 4.5 2.2 - - + -
98F ALA* 4.0 25.7 - - + +
97G ILE* 3.5 1.2 - - - -
98G ALA* 2.9 32.0 + - + +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D SER* 2.9 47.4 + - - +
67D CYS 4.0 1.1 - - - +
68D ILE* 4.0 20.4 - - + +
106D LYS* 3.8 17.9 - - - -
132D VAL* 1.3 81.5 - - - +
134D PHE* 1.3 64.8 + - - +
135D SER* 3.5 26.5 - - - +
136D GLU* 5.7 0.2 - - + -
112E LEU* 4.0 9.2 - - - +
95G TYR* 3.9 25.6 - - + -
96G ARG 3.6 4.7 - - - +
97G ILE* 4.0 15.9 - - + -
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 3.6 1.7 + - + -
133D ILE* 1.3 77.3 - - - +
135D SER* 1.3 61.5 + - - +
112E LEU* 3.8 42.2 - - + +
113E GLU* 5.0 6.6 + - - +
115E VAL* 3.9 30.7 - - + -
116E GLU* 3.3 37.9 - - + +
119E ILE* 4.6 8.5 - - + -
130E THR* 4.3 6.3 - - + -
132E VAL* 4.8 2.9 - - + -
96G ARG* 2.7 27.8 + - + +
97G ILE 3.5 28.5 - - - -
98G ALA* 3.1 28.7 - - + -
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Residues in contact with SER 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 3.5 11.1 - - - +
134D PHE* 1.3 80.2 - - - +
136D GLU* 1.3 63.5 + - - +
116E GLU* 2.9 25.8 + - - -
95G TYR* 3.5 4.3 - - - -
96G ARG* 2.7 36.3 + - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LYS* 5.7 0.3 + - - -
135D SER* 1.3 81.9 - - - +
137D ILE* 1.3 75.4 + - - +
138D ASP* 4.0 2.1 + - - -
50G LYS* 5.1 8.6 + - - -
93G PHE* 4.5 9.7 - - - +
94G CYS 3.6 7.2 - - - +
95G TYR* 3.4 37.6 + - + -
96G ARG 5.3 0.2 - - - -
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLU* 1.3 82.9 - - - +
138D ASP* 1.3 78.1 + - - +
139D THR* 3.4 18.2 + - + +
81G PHE* 4.3 4.3 - - + -
82G LYS* 3.8 41.7 - - + +
85G ILE* 4.3 6.1 - - + -
86G GLN* 3.8 21.5 - - + +
93G PHE* 5.4 0.7 - - - -
94G CYS* 2.8 33.5 + - + +
96G ARG* 5.3 0.9 - - + +
103G TYR* 3.4 35.9 - - + +
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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