Contacts of the helix formed by residues 75 - 87 (chain A) in PDB entry 2FBW
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 ASN 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.7 5.8 - - - +
74A ASP* 1.3 88.9 + - - +
76A TRP* 1.3 66.5 + - - +
77A ARG* 2.9 58.6 + - - +
78A TRP* 3.0 51.6 + - + +
79A HIS 3.4 3.3 + - - -
137A PHE* 5.9 1.4 - - - -
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Residues in contact with TRP 76 (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 ALA* 3.6 18.4 - - + +
75A ASN* 1.3 75.5 + - - +
77A ARG* 1.3 92.6 + - + +
79A HIS* 3.1 7.8 + - - +
80A PHE* 2.8 25.5 + - + -
97A HIS* 3.5 33.4 - + - -
100A THR* 3.6 35.0 + - - +
101A GLU* 3.3 37.8 + - + +
104A PRO* 5.0 8.3 - - + -
610A ASP* 3.5 20.2 - - - -
611A CYS* 3.7 31.4 - - + -
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Residues in contact with ARG 77 (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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75A ASN* 2.9 37.6 + - - +
76A TRP* 1.3 122.4 - - + +
78A TRP* 1.3 56.5 + - - +
80A PHE* 3.2 7.5 - - + +
81A TYR 2.9 21.8 + - - -
101A GLU* 5.5 0.2 + - - -
137A PHE* 3.5 31.2 - - + -
610A ASP* 3.0 49.3 + - - +
611A CYS* 4.5 8.3 - - - +
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Residues in contact with TRP 78 (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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73A ASP* 3.7 26.9 - - + -
74A ASP* 3.4 24.2 - - - -
75A ASN* 3.0 28.3 + - + +
77A ARG* 1.3 74.2 - - - +
79A HIS* 1.3 59.4 + - - +
81A TYR* 3.3 7.5 + - - +
82A ASP* 2.9 34.9 + - - +
134A SER 3.9 6.7 - - - +
135A LEU* 3.8 17.0 - - + -
136A GLN* 3.3 50.6 + - + +
137A PHE* 3.4 47.2 - + - +
145A ARG* 3.7 9.2 - - - +
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Residues in contact with HIS 79 (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 ASN* 3.5 27.9 + - + +
66A ALA* 4.7 3.0 - - - -
67A ALA* 4.8 3.6 + - + +
75A ASN 3.4 1.4 + - - +
76A TRP* 3.1 16.0 + - - +
78A TRP* 1.3 75.1 - - - +
80A PHE* 1.3 64.5 + - - +
82A ASP* 3.4 3.4 + - + +
83A THR* 2.8 38.1 + - - -
100A THR* 3.6 20.1 + - + +
103A ALA* 4.5 5.8 - - + +
133A GLN* 3.7 16.8 - - - -
145A ARG* 3.7 27.7 - - - +
409A LEU* 5.2 0.9 - - + -
412A ASN* 2.9 22.8 + - - -
415A LEU* 3.5 23.3 - - + -
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Residues in contact with PHE 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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76A TRP* 2.8 14.0 + - + +
77A ARG* 3.2 15.7 - - + +
79A HIS* 1.3 73.5 - - - +
81A TYR* 1.3 71.1 + - + +
83A THR* 3.1 2.8 + - - -
84A VAL* 3.0 38.1 + - + +
93A GLN* 3.6 41.5 - - - -
96A ILE* 3.6 15.7 - - + -
97A HIS* 3.6 20.6 - - + -
100A THR* 3.4 17.8 - - - +
137A PHE* 5.7 1.8 - + - -
605A THR* 3.8 14.1 - - + -
611A CYS* 3.5 21.8 - - - -
612A SER 3.6 14.4 - - - -
614A VAL* 3.7 16.4 - - + -
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Residues in contact with TYR 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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77A ARG 2.9 17.0 + - - +
78A TRP* 3.3 6.9 + - - +
80A PHE* 1.3 80.9 - - + +
82A ASP* 1.3 73.3 + - - +
83A THR 3.1 0.2 + - - -
84A VAL* 3.3 3.2 + - - +
85A LYS* 3.0 50.9 + - + +
89A TRP* 5.5 4.2 - + - -
137A PHE* 3.2 58.0 + + + -
138A GLY* 3.7 9.7 - - - -
614A VAL* 3.8 34.8 - - + -
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Residues in contact with ASP 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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78A TRP 2.9 20.2 + - - +
79A HIS* 3.8 6.5 - - + +
80A PHE 3.3 0.2 - - - -
81A TYR* 1.3 83.4 - - - +
83A THR* 1.3 57.5 + - - +
85A LYS* 4.1 4.8 - - - +
86A GLY* 2.9 23.4 + - - -
132A GLY 3.8 13.7 - - - +
133A GLN* 3.4 3.8 - - + -
134A SER* 2.7 53.1 + - - +
145A ARG* 2.9 20.8 + - - +
409A LEU* 3.4 17.1 - - + +
621A TYR* 4.8 0.7 + - - -
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Residues in contact with THR 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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79A HIS* 2.8 24.9 + - - -
82A ASP* 1.3 76.3 - - - +
84A VAL* 1.3 66.2 + - - +
86A GLY* 3.3 0.5 + - - -
87A SER* 3.0 23.9 + - - -
96A ILE* 3.7 21.3 - - + -
99A MET* 4.4 6.1 - - + -
100A THR* 3.8 3.6 - - - +
403A VAL 3.4 23.6 - - - +
404A HIS* 5.3 2.0 - - - +
407A ASN 5.3 0.2 - - - +
409A LEU* 3.8 9.1 - - + +
412A ASN* 3.1 31.7 + - - +
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Residues in contact with VAL 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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80A PHE* 3.0 49.6 + - + +
81A TYR* 3.7 4.0 - - - +
83A THR* 1.3 75.6 - - - +
85A LYS* 1.3 61.6 + - - +
87A SER* 2.6 25.0 + - - +
88A ASP 3.4 3.5 + - - -
89A TRP* 3.5 32.4 + - + +
91A GLY 5.8 1.1 - - - +
93A GLN* 3.7 22.7 - - + +
96A ILE* 4.0 17.0 - - + -
614A VAL* 3.9 13.5 - - + -
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Residues in contact with LYS 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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81A TYR* 3.0 44.9 + - + +
82A ASP* 4.1 4.0 - - - +
84A VAL* 1.3 77.7 - - - +
86A GLY* 1.3 64.2 + - - +
88A ASP* 2.9 12.3 + - - -
89A TRP* 3.9 29.4 - - + -
138A GLY* 6.0 3.6 - - - -
618A ILE 5.1 2.5 - - - -
619A ARG* 2.9 23.5 + - + +
620A SER* 2.7 40.4 + - - +
621A TYR* 3.7 29.5 - - + +
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Residues in contact with GLY 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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82A ASP 2.9 19.1 + - - -
83A THR 3.7 1.8 - - - -
84A VAL 3.3 0.2 - - - -
85A LYS* 1.3 77.0 - - - +
87A SER* 1.3 59.3 + - - +
407A ASN* 3.2 19.5 - - - +
409A LEU* 4.1 14.8 - - - -
619A ARG* 3.0 21.7 + - - -
621A TYR* 3.4 16.4 + - - -
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Residues in contact with SER 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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83A THR 3.0 12.1 + - - -
84A VAL* 2.6 23.0 + - - +
86A GLY* 1.3 73.6 - - - +
88A ASP* 1.3 67.6 + - - +
89A TRP* 3.3 2.6 + - - -
90A LEU 3.4 4.3 + - - -
91A GLY* 3.3 19.7 + - - -
96A ILE* 5.1 0.4 - - - -
403A VAL 4.7 1.6 - - - -
404A HIS* 3.3 35.4 - - - -
405A GLY* 3.6 6.1 - - - -
406A ALA* 3.0 20.7 + - - +
407A ASN 3.7 2.0 + - - -
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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