Contacts of the helix formed by residues 86 - 98 (chain A) in PDB entry 1EFT
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY 3.5 3.1 + - - -
85A HIS* 1.3 74.4 - - + +
87A ASP* 1.3 60.7 + - - +
88A TYR 2.9 10.9 + - - -
89A ILE* 3.4 25.5 + - + +
115A GLN* 4.1 24.6 + - - +
118A GLU* 5.6 0.4 - - - +
389A ARG* 4.5 6.9 + - - -
392A GLY 5.6 6.9 - - - +
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Residues in contact with ASP 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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59A ARG* 3.0 29.4 + - - +
85A HIS* 3.1 20.3 + - + -
86A ALA* 1.3 77.4 - - - +
88A TYR* 1.3 81.4 + - + +
89A ILE 3.6 0.9 - - - -
90A LYS* 3.6 16.9 + - - -
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Residues in contact with TYR 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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59A ARG* 2.5 40.2 + - - -
61A ILE* 3.5 22.2 - - + -
62A THR 4.3 2.7 - - - -
63A ILE* 3.7 37.5 - - + +
83A PRO* 3.5 20.5 - - + +
85A HIS* 3.1 24.3 + - + +
86A ALA 2.9 1.2 + - - -
87A ASP* 1.3 95.8 - - + +
89A ILE* 1.3 63.9 + - - +
90A LYS* 3.2 9.6 - - - +
91A ASN* 3.1 24.3 + - - +
92A MET* 3.4 8.2 + - - +
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Residues in contact with ILE 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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83A PRO 5.9 0.4 - - - +
85A HIS 4.6 2.5 - - - +
86A ALA* 3.4 24.0 + - + +
87A ASP 3.6 0.8 + - - -
88A TYR* 1.3 78.9 - - - +
90A LYS* 1.3 62.2 + - - +
92A MET* 3.1 7.8 + - + +
93A ILE* 3.0 24.1 + - + +
115A GLN* 4.2 7.4 - - + -
118A GLU* 3.7 23.8 - - - +
119A HIS* 3.7 29.8 - - + +
122A LEU* 3.4 24.7 - - + -
389A ARG* 3.9 34.3 - - - +
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Residues in contact with LYS 90 (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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87A ASP 3.6 22.4 + - - -
88A TYR* 4.8 5.4 - - - +
89A ILE* 1.3 78.7 - - - +
91A ASN* 1.3 69.7 + - - +
93A ILE* 3.6 9.6 + - - +
94A THR* 2.9 31.2 + - + +
300A ARG* 4.6 9.6 - - - +
343A TYR* 3.9 33.7 - - + +
348A ASP* 4.9 11.9 - - - +
389A ARG* 5.6 1.0 - - - +
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Residues in contact with ASN 91 (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 ILE* 2.7 35.6 + - - +
64A ASN* 4.5 6.6 + - - +
65A THR* 3.2 19.7 - - + +
83A PRO* 3.7 5.4 - - + -
88A TYR* 3.1 25.3 + - - +
89A ILE 3.1 0.4 - - - -
90A LYS* 1.3 82.5 - - - +
92A MET* 1.3 65.7 + - - +
93A ILE 3.2 1.3 - - - -
94A THR* 3.6 4.6 + - - -
95A GLY 3.2 16.8 + - - -
300A ARG* 3.0 30.2 + - - +
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Residues in contact with MET 92 (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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17A ILE* 4.7 6.1 - - + -
82A CYS* 3.8 23.4 - - + -
83A PRO* 3.9 16.0 - - - +
88A TYR 3.4 4.7 + - - +
89A ILE* 3.1 19.5 + - + +
91A ASN* 1.3 77.9 - - - +
93A ILE* 1.3 61.6 + - + +
95A GLY* 3.3 1.7 + - - -
96A ALA* 2.8 36.6 + - - +
119A HIS* 3.6 48.9 - - + +
122A LEU* 3.2 43.1 - - + -
123A ALA* 5.2 0.9 - - - -
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Residues in contact with ILE 93 (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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89A ILE* 3.0 26.0 + - + +
90A LYS* 3.8 5.8 - - - +
91A ASN 3.2 0.2 - - - -
92A MET* 1.3 80.1 - - + +
94A THR* 1.3 59.0 + - + +
96A ALA* 3.2 4.4 + - - +
97A ALA* 2.8 27.9 + - - +
122A LEU* 3.8 43.5 - - + +
126A VAL* 3.8 23.5 - - + +
343A TYR* 3.9 44.6 - - + -
345A ARG 4.1 8.5 - - - +
387A ALA* 5.1 1.8 - - + -
389A ARG* 4.5 5.6 - - - -
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Residues in contact with THR 94 (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 THR* 4.6 3.6 + - - +
90A LYS 2.9 19.7 + - - +
91A ASN* 3.7 5.9 + - - -
92A MET 3.4 0.2 - - - -
93A ILE* 1.3 77.7 - - + +
95A GLY* 1.3 61.8 + - - +
97A ALA* 3.6 11.5 - - - +
98A GLN* 2.8 25.0 + - - +
226A GLU* 3.9 15.9 + - - +
300A ARG* 3.5 37.5 + - - +
343A TYR* 6.4 0.9 - - + -
345A ARG 4.4 2.0 - - - +
346A THR* 4.1 26.0 - - - +
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Residues in contact with GLY 95 (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 THR* 4.0 5.4 - - - -
80A VAL* 3.9 20.4 - - - +
82A CYS* 4.2 1.6 - - - -
91A ASN 3.2 11.8 + - - -
92A MET 3.6 3.4 - - - -
94A THR* 1.3 83.1 + - - +
96A ALA* 1.3 59.8 + - - +
98A GLN* 3.4 23.0 + - - +
99A MET* 3.4 21.6 - - - +
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Residues in contact with ALA 96 (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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17A ILE* 5.1 2.9 - - + -
92A MET* 2.8 29.9 + - - +
93A ILE* 3.2 2.9 + - - +
95A GLY* 1.3 71.7 - - - +
97A ALA* 1.3 57.5 + - - +
98A GLN 3.0 10.2 + - - -
99A MET* 3.1 28.5 + - + +
122A LEU 5.6 0.2 - - - -
123A ALA* 4.5 9.9 - - + -
126A VAL* 3.4 16.9 - - + +
127A GLY 5.4 0.2 - - - -
128A VAL* 3.3 24.9 - - + +
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Residues in contact with ALA 97 (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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93A ILE 2.8 16.2 + - - +
94A THR 3.6 9.6 - - - +
96A ALA* 1.3 76.2 - - - +
98A GLN* 1.3 57.8 + - - +
99A MET 3.5 0.7 - - - -
126A VAL* 3.4 18.5 - - + +
224A PRO* 6.2 0.2 - - - +
241A ARG* 3.7 16.4 + - - +
243A GLU* 4.8 4.0 - - - +
345A ARG* 3.5 36.4 - - + +
346A THR* 4.0 8.0 - - + +
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Residues in contact with GLN 98 (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 ASN* 3.2 22.9 - - - +
67A HIS* 2.9 29.2 + - - -
80A VAL* 4.0 5.3 - - + +
94A THR 2.8 25.0 + - - +
95A GLY* 3.4 11.7 + - - +
96A ALA 3.0 1.4 - - - -
97A ALA* 1.3 79.3 - - + +
99A MET* 1.3 61.5 + - - +
226A GLU* 3.2 38.9 + - + +
240A GLY* 5.2 0.2 - - - -
241A ARG* 3.3 40.5 + - + +
285A ASN* 3.3 13.6 + - - +
346A THR* 5.1 5.4 - - + -
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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