Contacts of the helix formed by residues 76 - 85 (chain A) in PDB entry 2FY2
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.6 16.4 - - + -
74A ASN* 2.9 17.3 + - - +
75A TRP* 1.3 103.0 - - + +
77A SER* 1.3 60.9 + - - +
78A GLU 3.3 2.9 - - - -
79A TYR* 3.2 10.5 + - + -
80A TRP* 2.7 41.6 + - + +
441A ILE* 5.2 3.1 - - + -
449A VAL 5.7 0.4 - - - +
504A ASN* 3.9 35.9 - - + +
507A LEU* 4.1 16.6 - - + -
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Residues in contact with SER 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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74A ASN* 3.0 29.9 + - - +
75A TRP 3.7 0.2 - - - -
76A VAL* 1.3 76.9 - - - +
78A GLU* 1.3 57.3 + - - +
80A TRP* 4.0 5.5 - - - +
81A LEU* 3.0 32.4 + - - +
446A GLU* 3.0 35.1 + - - +
448A ARG* 6.5 1.3 - - - -
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Residues in contact with GLU 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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68A ARG* 3.8 24.7 + - - +
74A ASN 5.0 0.6 + - - -
76A VAL 3.3 0.2 - - - -
77A SER* 1.3 77.8 - - - +
79A TYR* 1.3 76.7 + - - +
81A LEU* 3.8 6.3 - - - +
82A ASN* 3.2 42.8 + - - +
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 3.3 44.6 + - - -
75A TRP 3.8 9.9 - - - -
76A VAL* 3.2 7.0 + - + +
78A GLU* 1.3 87.1 - - + +
80A TRP* 1.3 57.9 + - - +
82A ASN* 3.4 5.3 + - - +
83A ASP* 2.8 32.7 + - - +
507A LEU* 3.8 19.0 - - + +
508A ALA* 3.5 42.8 - - + -
511A GLU* 3.7 30.5 + - + -
512A LEU* 3.4 25.7 + - + +
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Residues in contact with TRP 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 VAL* 2.7 33.6 + - + +
77A SER* 4.0 5.2 - - - +
79A TYR* 1.3 71.7 - - - +
81A LEU* 1.3 76.7 + - + +
83A ASP* 4.5 1.1 - - + +
84A MET* 2.8 66.8 + - + +
85A TYR* 3.5 28.3 - + - -
325A SER 4.8 0.7 - - - -
328A ASP* 4.1 4.9 - - - -
436A TYR* 5.1 1.8 + - - -
448A ARG* 3.6 55.6 - - + -
449A VAL* 3.5 37.8 + - + +
450A ASP* 5.4 1.0 - - - +
504A ASN* 3.5 21.9 + - - -
507A LEU* 3.7 11.6 - - + +
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Residues in contact with LEU 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 SER 3.0 20.0 + - - +
78A GLU* 3.8 6.7 - - - +
80A TRP* 1.3 88.4 - - + +
82A ASN* 1.3 58.7 + - - +
85A TYR* 3.2 13.4 + - + +
86A LEU* 3.2 52.8 + - + -
172A LEU* 4.3 22.4 - - + -
325A SER* 4.1 25.4 - - - +
448A ARG* 5.1 2.0 - - - +
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Residues in contact with ASN 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 GLU* 3.2 33.4 + - - +
79A TYR* 3.8 4.9 - - - +
80A TRP 3.2 0.4 - - - -
81A LEU* 1.3 78.3 - - - +
83A ASP* 1.3 65.6 + - - +
84A MET 3.4 0.3 + - - -
85A TYR 3.6 1.2 + - - -
86A LEU* 3.5 23.4 - - - +
87A ASN* 2.9 43.8 + - - +
169A GLN* 3.2 34.7 + - - +
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Residues in contact with ASP 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 TYR 2.8 21.7 + - - +
80A TRP* 4.0 2.4 - - + +
82A ASN* 1.3 75.9 - - - +
84A MET* 1.3 64.0 + - - +
87A ASN* 4.0 12.5 + - - +
88A ASN* 5.3 2.9 + - - +
507A LEU* 3.8 22.1 - - + +
510A ARG* 2.8 31.6 + - - +
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Residues in contact with MET 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 TRP* 2.8 50.3 + - + +
83A ASP* 1.3 79.1 + - - +
85A TYR* 1.3 99.7 + - + +
88A ASN* 4.6 12.2 + - - +
436A TYR* 4.5 27.8 - - + +
535A PHE* 6.4 2.0 - - + -
555A VAL* 5.5 11.0 - - + -
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Residues in contact with TYR 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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80A TRP* 3.5 25.7 - + - -
81A LEU* 3.2 11.3 + - + +
83A ASP 3.6 0.6 - - - -
84A MET* 1.3 115.2 - - + +
86A LEU* 1.3 68.3 + - - +
87A ASN 3.2 2.2 - - - -
88A ASN* 2.9 18.8 + - - +
96A SER* 3.8 21.1 - - - -
163A ARG* 2.8 31.3 + - - +
324A HIS* 3.0 59.9 + + + -
325A SER* 3.9 21.3 - - - -
328A ASP* 4.3 1.6 + - - -
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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