Contacts of the helix formed by residues 78 - 88 (chain A) in PDB entry 5FN2
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 LYS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A VAL* 3.7 8.8 - - - +
77A GLU* 1.3 90.1 - - + +
79A GLU* 1.3 70.3 + - - +
80A GLU* 3.5 28.7 - - + +
81A ASP* 3.2 37.0 + - - +
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Residues in contact with GLU 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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77A GLU 4.4 3.4 - - - +
78A LYS* 1.3 78.8 - - - +
80A GLU* 1.3 67.9 + - - +
82A LEU* 3.2 14.7 + - + +
83A GLN* 2.9 32.5 + - - +
102A HIS* 5.3 7.7 - - - +
107A LEU* 4.2 27.0 - - - +
110A LYS* 4.2 21.2 + - - +
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Residues in contact with GLU 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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78A LYS* 3.2 29.5 - - + +
79A GLU* 1.3 87.6 + - - +
81A ASP* 1.3 59.0 - - - +
83A GLN* 3.2 16.1 + - - +
84A TRP* 2.9 29.3 + - - +
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Residues in contact with ASP 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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74A HIS* 3.8 18.3 + - + +
75A VAL 3.3 19.5 - - - +
76A VAL* 3.6 13.7 - - + -
77A GLU* 4.0 16.8 + - - +
78A LYS* 3.2 33.9 - - - +
80A GLU* 1.3 76.9 - - - +
82A LEU* 1.3 59.2 + - - +
84A TRP* 3.2 9.9 + - - +
85A VAL* 2.9 32.7 + - - +
196A TYR* 5.6 0.2 + - - -
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Residues in contact with LEU 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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76A VAL* 3.8 15.8 - - + +
78A LYS 3.8 1.0 + - - -
79A GLU* 3.2 22.9 + - + +
81A ASP* 1.3 81.1 - - - +
83A GLN* 1.3 57.3 + - - +
85A VAL* 3.2 6.1 + - + +
86A LEU* 2.9 58.3 + - + +
96A VAL* 6.0 2.0 - - + -
107A LEU* 3.5 25.6 - - + +
110A LYS* 3.4 38.6 - - + +
111A LEU* 4.2 25.8 - - + -
118A ILE* 4.6 6.1 - - + -
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Residues in contact with GLN 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 GLU* 2.9 14.4 + - - +
80A GLU* 3.2 21.1 + - - +
82A LEU* 1.3 77.7 - - - +
84A TRP* 1.3 57.1 + - - +
86A LEU* 3.2 4.1 + - - +
87A THR* 2.6 55.5 + - + +
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Residues in contact with TRP 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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74A HIS* 3.1 43.6 + + - -
80A GLU 2.9 12.9 + - - +
81A ASP* 3.2 7.4 + - - +
83A GLN* 1.3 76.9 - - - +
85A VAL* 1.3 74.4 + - + +
87A THR* 4.8 0.9 - - - -
88A ASP* 3.1 47.2 + - + +
89A GLY 2.7 32.6 + - - -
90A PRO* 3.3 32.1 - - + -
91A ASN* 5.1 0.9 - - - -
94A TYR* 3.9 15.0 + + - -
202A SER* 4.5 24.2 - - - -
206A SER 5.2 6.1 - - - -
208A PRO* 4.7 11.9 - - + -
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Residues in contact with VAL 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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74A HIS* 3.3 43.7 - - + -
76A VAL* 5.4 0.4 - - + -
81A ASP 2.9 10.3 + - - +
82A LEU* 3.2 13.0 + - + +
84A TRP* 1.3 84.9 - - + +
86A LEU* 1.3 63.6 + - + +
89A GLY* 3.6 6.7 - - - +
94A TYR* 4.1 22.6 - - + -
96A VAL* 4.2 7.2 - - + -
117A ARG* 3.3 18.8 + - - +
118A ILE* 3.5 39.3 - - + -
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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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82A LEU* 2.9 57.3 + - + +
83A GLN* 3.8 3.6 - - - +
85A VAL* 1.3 83.6 - - + +
87A THR* 1.3 62.1 + - - +
88A ASP 3.4 0.2 - - - -
110A LYS* 5.3 6.3 - - + +
111A LEU* 4.9 7.6 - - - +
114A ARG* 3.4 61.6 + - + +
117A ARG* 2.5 39.7 + - + +
118A ILE* 4.4 17.3 - - + -
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Residues in contact with THR 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 GLN* 2.6 46.3 + - + +
84A TRP* 4.7 0.7 - - - +
86A LEU* 1.3 76.8 - - - +
88A ASP* 1.3 64.9 + - + +
114A ARG* 4.5 18.5 + - - +
117A ARG* 4.4 3.6 + - - -
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Residues in contact with ASP 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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84A TRP* 3.1 49.3 + - + +
87A THR* 1.3 84.1 - - + +
89A GLY* 1.3 67.3 + - - +
90A PRO* 3.4 13.5 - - - +
117A ARG* 3.1 10.0 + - - -
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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