Contacts of the helix formed by residues 70 - 77 (chain A) in PDB entry 5V35
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 GLU 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LYS 5.4 2.7 - - - +
69A LEU* 1.3 71.6 - - - +
71A PHE* 1.3 57.9 + - - +
72A TRP* 3.6 42.5 - - + -
73A GLU* 2.4 71.5 + - - +
74A ILE* 2.9 9.5 + - - -
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Residues in contact with PHE 71 (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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9A VAL* 6.0 2.5 - - + -
12A VAL* 3.9 15.0 - - + -
69A LEU 4.0 1.4 + - - -
70A GLU* 1.3 71.2 - - - +
72A TRP* 1.3 70.3 + + + +
74A ILE* 3.4 24.3 - - + +
75A LEU* 3.4 28.8 - - + +
89A CYS* 3.8 29.8 - - + -
93A HIS* 2.8 62.8 - + + -
149A PHE* 5.3 5.2 - + - -
201A FAR 6.2 1.6 - - + -
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Residues in contact with TRP 72 (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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61A ILE* 4.3 14.5 - - + +
70A GLU* 2.8 41.7 + - + -
71A PHE* 1.3 86.1 - + + +
73A GLU* 1.3 85.4 + - + +
75A LEU* 3.2 10.0 + - - +
76A LEU* 2.8 43.7 + - + +
96A VAL* 6.0 5.2 - - + -
100A LEU* 4.2 25.1 - - + -
201A FAR 3.6 77.6 - - + +
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Residues in contact with GLU 73 (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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61A ILE* 4.3 5.8 - - + +
62A ILE 4.4 1.7 - - - +
63A ILE* 3.5 41.5 + - + +
64A GLY 3.7 6.9 + - - -
65A ASN 5.1 1.1 + - - +
68A LYS 4.3 1.7 - - - +
69A LEU* 3.2 20.2 - - + +
70A GLU* 2.4 64.1 + - - +
72A TRP* 1.3 89.1 + - + +
74A ILE* 1.3 51.1 + - - -
76A LEU* 4.3 6.3 - - - +
77A THR* 2.5 48.0 + - + +
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Residues in contact with ILE 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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9A VAL* 3.9 31.2 - - + -
12A VAL* 6.1 0.2 - - + -
69A LEU* 4.2 25.2 - - + +
70A GLU 2.9 17.0 + - - +
71A PHE* 3.4 24.0 - - + +
73A GLU* 1.3 74.6 - - - +
75A LEU* 1.4 72.3 + - + +
77A THR* 3.2 14.5 + - - -
78A SER* 3.6 14.4 + - - -
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Residues in contact with LEU 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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12A VAL* 4.3 14.6 - - + -
71A PHE* 3.4 44.9 - - + +
72A TRP* 3.2 10.5 + - - +
73A GLU 3.2 0.4 - - - -
74A ILE* 1.4 82.2 - - + +
76A LEU* 1.3 63.2 + - - +
78A SER* 2.9 22.9 + - - -
79A MET* 3.5 1.4 - - - +
87A PHE* 3.1 61.6 - - + -
89A CYS* 4.2 5.4 - - - -
149A PHE* 4.6 7.6 - - + -
151A ILE* 4.6 12.1 - - + -
201A FAR 5.1 5.6 - - + -
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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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27A PHE* 3.4 10.1 - - + -
33A VAL* 4.3 17.9 - - + -
35A PHE* 3.9 33.7 - - + -
61A ILE* 3.8 33.2 - - + -
63A ILE* 5.8 0.2 - - + -
72A TRP* 2.8 33.4 + - + +
73A GLU* 4.1 4.5 - - - +
75A LEU* 1.3 75.4 - - + +
77A THR* 1.3 64.0 + - + +
78A SER 3.1 1.8 + - - -
79A MET* 3.1 25.4 + - - +
151A ILE* 3.8 33.9 - - + -
153A LEU* 4.3 4.3 - - + +
201A FAR 6.2 1.1 - - + -
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Residues in contact with THR 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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24A LEU* 3.7 12.3 - - - +
27A PHE* 3.0 53.9 - - + +
63A ILE* 4.3 12.3 - - + -
69A LEU* 4.1 25.4 - - + +
73A GLU* 2.5 38.1 + - - +
74A ILE* 3.2 11.1 + - - -
76A LEU* 1.3 71.6 - - + +
78A SER* 1.3 54.9 + - - +
79A MET 3.2 1.7 + - - -
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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