Contacts of the helix formed by residues 82 - 90 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D LYS* 3.8 3.4 - - - +
81D GLY* 1.3 79.7 + - - +
83D PRO* 1.3 75.9 - - + +
84D GLY 2.8 3.0 + - - -
85D ALA* 3.2 23.8 + - - +
86D ILE* 3.0 16.1 + - - +
33G LEU* 5.2 1.6 - - - -
34G THR* 4.7 4.0 - - - +
37G HIS* 3.7 35.2 - - + +
94G ASP* 3.7 16.3 + - - -
95G TYR* 3.8 30.6 + - + +
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Residues in contact with PRO 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D THR* 1.3 86.3 - - - +
84D GLY* 1.3 59.7 + - - +
86D ILE* 2.7 26.2 - - + +
87D ILE* 3.4 11.8 + - - +
30G ASP* 2.9 33.7 - - - +
33G LEU* 4.6 15.2 - - + -
34G THR* 4.3 8.5 - - - +
83G PRO* 5.7 3.1 - - - +
86G ILE* 3.6 30.7 - - + -
87G ILE* 5.4 7.8 - - + +
90G ARG* 3.6 14.1 - - - +
94G ASP* 3.9 5.6 - - + -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D THR 2.8 2.8 + - - -
83D PRO* 1.3 73.4 - - - +
85D ALA* 1.3 67.3 + - - +
86D ILE 2.8 3.5 + - - -
87D ILE* 2.8 29.7 + - - +
88D LYS* 3.3 5.6 + - - +
87G ILE* 5.8 1.3 - - - -
90G ARG* 5.1 1.6 - - - -
94G ASP* 3.0 28.4 + - - -
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 4.2 0.4 - - - -
80D LYS* 3.5 54.1 - - + +
81D GLY* 4.7 0.2 - - - -
82D THR* 3.2 18.7 + - - +
84D GLY* 1.3 71.4 - - - +
86D ILE* 1.3 62.0 + - - +
88D LYS* 3.3 10.1 + - - +
89D ASP* 3.1 34.0 + - - +
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 3.7 28.9 + - - +
29D ASN* 4.0 14.1 - - + +
30D ASP* 3.5 39.0 - - + +
33D LEU* 5.2 4.5 - - + -
80D LYS 5.4 0.4 + - - -
81D GLY* 5.5 2.0 - - - -
82D THR 3.0 13.0 + - - +
83D PRO* 2.7 35.0 - - + +
84D GLY 2.8 1.2 + - - -
85D ALA* 1.3 69.4 - - - +
87D ILE* 1.3 58.4 + - + +
88D LYS 2.8 11.1 + - - -
89D ASP* 3.3 1.7 + - - +
90D ARG* 3.2 26.5 + - + +
33G LEU* 5.4 4.7 - - + -
83G PRO* 3.6 24.2 - - + -
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO 3.4 11.4 - - - +
84D GLY* 2.8 33.8 + - - +
86D ILE* 1.3 77.7 - - + +
88D LYS* 1.3 60.6 + - + +
90D ARG* 3.2 53.0 + - - +
83G PRO* 5.6 7.6 - - + +
84G GLY* 5.9 2.0 - - - +
87G ILE* 5.5 22.0 - - + -
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LYS* 4.9 13.8 - - - +
84D GLY 3.3 9.4 + - - +
85D ALA* 3.5 14.8 - - - +
86D ILE 2.8 2.4 + - - -
87D ILE* 1.3 78.6 - - + +
89D ASP* 1.3 70.2 + - - +
90D ARG 3.1 11.2 + - - +
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLN* 3.2 30.3 + - - +
23D LYS* 4.6 23.5 - - + +
26D SER* 3.1 34.1 + - - +
80D LYS* 5.5 0.7 - - - +
85D ALA* 3.1 14.1 + - - +
88D LYS* 1.3 84.9 - - - +
90D ARG* 1.3 60.1 + - - +
91D THR* 3.9 9.4 + - - +
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 5.0 4.7 - - - +
27D THR* 6.2 0.2 - - - -
30D ASP* 3.2 19.4 + - + -
86D ILE* 3.2 18.1 + - + +
87D ILE* 3.2 45.7 - - - +
88D LYS 3.1 10.5 - - - +
89D ASP* 1.3 80.8 - - - +
91D THR* 1.3 63.5 + - - +
92D TRP* 3.3 47.1 + - + +
93D ASP* 4.2 1.8 - - - +
94D ASP* 3.1 58.0 + - - +
83G PRO* 3.7 11.8 - - - +
84G GLY 5.0 0.2 - - - +
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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