Contacts of the helix formed by residues 73 - 78 (chain A) in PDB entry 3EHN
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 SER 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLN 3.9 0.2 + - - -
68A ASN 2.9 27.1 + - - -
69A THR* 3.1 16.1 + - - -
71A LEU 3.4 1.0 - - - -
72A ILE* 1.3 78.0 - - - +
74A SER* 1.3 69.1 + - - -
75A GLY 3.3 0.7 - - - -
76A ASN* 2.8 21.1 + - - +
77A TYR* 2.9 31.9 + - - -
92A GLU* 3.8 9.2 - - - -
503A PHE* 3.7 22.2 - - - -
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Residues in contact with SER 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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69A THR 2.7 25.6 + - - -
70A ASP* 3.3 7.6 - - - -
73A SER* 1.3 80.6 + - - +
75A GLY* 1.3 67.6 + - - +
76A ASN 3.2 0.7 + - - -
77A TYR* 3.3 14.5 + - - +
78A ILE* 3.2 28.0 + - - +
463A ALA* 3.4 20.8 - - - +
464A VAL* 3.6 5.2 - - - +
467A TRP* 3.4 28.4 - - - -
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Residues in contact with GLY 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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70A ASP 2.6 25.4 + - - -
74A SER* 1.3 76.0 + - - +
76A ASN* 1.3 58.1 + - - +
78A ILE* 3.9 4.2 - - - +
79A GLY 3.3 1.0 + - - -
80A TYR* 2.9 30.0 + - - -
81A PHE* 3.0 19.8 + - - -
463A ALA* 3.4 15.5 - - - +
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Residues in contact with ASN 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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71A LEU 3.6 8.0 + - - +
72A ILE 3.2 21.2 + - - +
73A SER 2.8 9.7 + - - +
75A GLY* 1.3 76.0 - - - +
77A TYR* 1.3 73.7 + - - +
79A GLY* 3.1 13.0 + - - -
81A PHE 3.8 11.5 - - - +
83A ASN* 3.3 24.5 + - - +
93A ALA 3.1 26.7 + - - -
326A PRO* 3.8 13.9 - - - +
327A THR* 3.0 33.5 + - - +
328A ASN 4.7 0.2 + - - -
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Residues in contact with TYR 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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73A SER* 2.9 31.5 + - - -
74A SER* 3.3 10.7 + - - +
76A ASN* 1.3 93.1 - - - +
78A ILE* 1.3 61.5 + - - +
79A GLY* 3.1 1.6 + - - -
92A GLU* 2.7 33.0 + - - +
95A TRP* 3.8 21.5 - + - -
97A PHE* 3.6 4.2 - - - -
326A PRO* 4.6 6.8 - - - +
327A THR* 4.5 3.8 - - - -
467A TRP* 3.9 22.0 - + + -
478A LEU* 4.2 5.4 - - - +
479A MET 4.9 3.1 - - - +
498A ARG 4.3 3.8 - - - +
499A VAL* 3.6 30.9 - - + +
500A PRO* 3.5 27.6 - - + -
503A PHE* 3.5 29.2 - + - -
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Residues in contact with ILE 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 SER 3.2 9.8 + - - +
75A GLY* 3.9 6.5 - - - +
77A TYR* 1.3 74.0 - - - +
79A GLY* 1.3 55.0 + - - +
80A TYR* 3.7 27.8 - - + +
289A THR* 3.4 12.3 - - - +
456A TYR* 2.6 32.5 + - + -
463A ALA* 3.5 14.6 - - - +
466A ALA* 3.3 34.1 - - + +
467A TRP* 3.3 38.6 - - + +
470A TYR* 4.5 11.0 - - + -
478A LEU* 3.4 16.8 - - + +
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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