Contacts of the helix formed by residues 73 - 81 (chain A) in PDB entry 1F16
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLU* 3.9 6.9 + - - +
70A LEU* 2.9 43.8 + - - +
71A ASP 3.3 1.3 - - - +
72A SER* 1.3 77.2 + - - +
74A MET* 1.3 62.5 + - - +
75A GLU* 4.5 2.3 - - + +
76A LEU* 3.5 23.8 - - + +
77A GLN* 2.9 29.3 + - - +
178A ALA* 5.1 4.0 - - - +
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Residues in contact with MET 74 (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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72A SER* 3.3 25.5 + - - +
73A ASN* 1.3 73.2 - - - +
75A GLU* 1.3 59.4 + - - +
77A GLN* 3.8 8.5 - - - -
78A ARG* 2.8 56.8 + - - +
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Residues in contact with GLU 75 (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 ASN* 3.2 2.8 - - + +
74A MET* 1.3 78.8 - - - +
76A LEU* 1.3 66.5 + - + +
78A ARG* 3.0 18.6 + - + +
79A MET* 3.0 19.7 + - - +
182A THR* 6.1 4.0 - - + +
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Residues in contact with LEU 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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70A LEU* 4.9 7.6 - - + +
73A ASN* 3.5 26.8 + - + +
75A GLU* 1.3 80.3 - - - +
77A GLN* 1.3 61.6 + - - +
79A MET* 3.3 6.7 + - + -
80A ILE* 3.2 42.6 + - + +
115A TYR* 5.4 7.2 - - + +
178A ALA* 4.5 13.2 - - + +
181A LEU* 3.9 23.1 - - + -
182A THR* 2.9 36.6 - - + +
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Residues in contact with GLN 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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71A ASP* 5.3 10.3 - - - +
73A ASN 2.9 21.0 + - - +
74A MET* 3.9 10.4 - - - +
76A LEU* 1.3 78.5 - - - +
78A ARG* 1.3 82.3 + - - +
79A MET 3.4 0.5 + - - -
80A ILE* 4.2 8.2 - - - +
81A ALA* 3.4 25.5 + - - +
119A LYS* 5.5 9.1 + - - +
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Residues in contact with ARG 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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74A MET* 2.8 51.7 + - - +
75A GLU* 3.0 11.5 + - + +
77A GLN* 1.3 92.9 - - - +
79A MET* 1.3 61.4 + - - +
81A ALA* 3.9 6.9 - - - +
82A ALA* 3.4 18.4 + - - +
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Residues in contact with MET 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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75A GLU* 3.0 16.3 + - - +
76A LEU* 3.4 14.6 - - + +
78A ARG* 1.3 77.8 - - - +
80A ILE* 1.3 59.1 + - - +
81A ALA 2.9 0.9 - - - -
82A ALA* 2.5 38.7 + - + +
83A VAL* 3.3 8.7 + - - +
182A THR* 4.2 17.7 - - + -
185A LEU* 3.5 52.5 - - + +
186A THR* 4.1 14.1 - - + +
189A LYS* 4.6 13.0 - - - +
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Residues in contact with ILE 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 LEU* 3.2 35.0 + - + +
77A GLN* 4.5 6.1 - - - +
79A MET* 1.3 75.3 - - - +
81A ALA* 1.3 60.5 + - - +
82A ALA 3.3 0.3 + - - -
83A VAL* 3.3 26.2 + - + +
84A ASP 4.4 1.0 + - - -
115A TYR* 4.7 11.7 - - + +
116A PHE* 6.2 8.1 - - + -
119A LYS* 3.2 46.0 - - + +
123A LYS* 6.0 4.5 - - + +
181A LEU* 5.5 1.3 - - + -
185A LEU* 4.5 9.2 - - + -
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Residues in contact with ALA 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 GLN* 3.4 30.1 + - - +
78A ARG* 3.9 8.3 - - + +
79A MET 2.9 0.8 - - - -
80A ILE* 1.3 79.5 - - - +
82A ALA* 1.3 60.1 + - - +
83A VAL 3.2 4.8 + - - +
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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