Contacts of the helix formed by residues 82 - 90 (chain L) in PDB entry 1VEQ
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 THR 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F LEU* 5.1 2.0 - - - -
34F THR* 4.7 3.6 - - - +
37F HIS* 3.7 35.5 - - + +
94F ASP* 3.8 16.5 + - - -
95F TYR* 3.8 28.4 + - + +
80L LYS* 3.8 3.2 - - - +
81L GLY* 1.3 78.0 + - - +
83L PRO* 1.3 77.0 - - + +
84L GLY 2.8 3.6 + - - -
85L ALA* 3.2 24.1 + - - +
86L ILE* 3.0 15.8 + - - +
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Residues in contact with PRO 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ASP* 2.9 33.0 - - - +
33F LEU* 4.5 15.4 - - + -
34F THR* 4.3 7.9 - - - +
83F PRO* 5.6 4.3 - - + +
86F ILE* 3.5 32.5 - - + -
87F ILE* 5.5 7.3 - - + +
90F ARG* 3.7 13.7 - - - +
94F ASP* 4.0 4.5 - - + -
82L THR* 1.3 87.8 - - - +
84L GLY* 1.3 59.4 + - - +
86L ILE* 2.8 24.5 - - + +
87L ILE* 3.4 12.2 + - - +
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Residues in contact with GLY 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ILE* 5.8 1.1 - - - -
90F ARG* 5.1 2.0 - - - -
94F ASP* 3.0 27.3 + - - -
82L THR 2.8 2.6 + - - -
83L PRO* 1.3 78.0 - - - +
85L ALA* 1.3 67.1 + - - +
86L ILE 2.8 0.5 + - - -
87L ILE* 2.8 31.2 + - - +
88L LYS* 3.3 5.6 + - - +
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Residues in contact with ALA 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ASP* 5.1 0.4 + - - -
26L SER* 4.2 0.4 - - - -
80L LYS* 3.6 52.7 - - + +
82L THR* 3.2 18.1 + - - +
84L GLY* 1.3 71.1 - - - +
86L ILE* 1.3 63.0 + - - +
88L LYS* 3.4 10.2 + - - +
89L ASP* 3.1 33.4 + - - +
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Residues in contact with ILE 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 5.3 6.1 - - + -
83F PRO* 3.5 31.4 - - + -
26L SER* 3.7 26.3 + - - +
29L ASN* 3.9 13.0 - - + +
30L ASP* 3.5 33.2 - - + +
33L LEU* 5.2 4.0 - - + -
80L LYS 5.3 0.2 + - - -
81L GLY* 5.5 1.7 - - - -
82L THR 3.0 13.0 + - - +
83L PRO* 2.8 35.0 - - + +
84L GLY 2.8 4.0 + - - -
85L ALA* 1.3 69.5 - - - +
87L ILE* 1.3 59.0 + - - +
88L LYS 2.8 10.3 + - - -
89L ASP* 3.3 1.9 + - - +
90L ARG* 3.2 27.0 + - + +
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Residues in contact with ILE 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PRO* 5.4 9.2 - - + +
84F GLY* 5.8 2.2 - - - +
87F ILE* 5.5 22.2 - - + -
83L PRO 3.4 11.4 - - - +
84L GLY* 2.8 34.0 + - - +
86L ILE* 1.3 78.2 - - - +
88L LYS* 1.3 59.1 + - + +
90L ARG* 3.2 51.6 - - - +
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Residues in contact with LYS 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L LYS* 4.9 13.3 - - - +
84L GLY 3.3 8.9 + - - +
85L ALA* 3.5 12.6 - - - +
86L ILE 2.8 2.0 + - - -
87L ILE* 1.3 79.1 - - + +
89L ASP* 1.3 70.7 + - - +
90L ARG 3.1 11.0 + - - +
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Residues in contact with ASP 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L GLN* 3.3 28.6 + - - +
23L LYS* 4.7 23.1 - - + +
26L SER* 3.1 33.5 + - - +
80L LYS* 5.5 1.2 - - - +
85L ALA* 3.1 15.9 + - - +
86L ILE 3.3 0.2 + - - -
88L LYS* 1.3 84.2 - - - +
90L ARG* 1.3 59.9 + - - +
91L THR* 3.9 9.4 + - - +
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Residues in contact with ARG 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PRO* 3.6 11.7 - - - +
84F GLY 4.9 0.2 - - - +
26L SER* 5.0 4.4 - - - +
27L THR* 6.2 0.2 - - - -
30L ASP* 3.2 18.4 + - + -
86L ILE* 3.2 18.7 + - + +
87L ILE* 3.2 45.9 - - - +
88L LYS 3.1 9.7 - - - +
89L ASP* 1.3 81.0 - - - +
91L THR* 1.3 63.1 + - - +
92L TRP* 3.4 45.5 + - + +
93L ASP* 4.2 1.8 - - - +
94L ASP* 3.1 57.9 + - - +
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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