Contacts of the helix formed by residues 80 - 83 (chain D) in PDB entry 6VSU
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 GLN 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLU* 5.9 2.9 - - - +
73D GLY* 3.2 22.0 - - - +
74D HIS* 3.2 32.3 + - - +
76D SER* 4.5 5.4 - - - +
78D PHE 5.9 0.2 - - - -
79D LEU* 1.3 73.0 - - - +
81D GLY* 1.3 63.1 + - - +
82D PRO* 3.3 4.7 - - - +
83D ALA* 3.0 25.2 + - + +
84D PHE* 4.8 3.3 - - + -
126D ARG* 4.6 5.7 + - - -
317D GLN* 4.7 0.7 - - - -
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Residues in contact with GLY 81 (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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79D LEU* 3.4 2.8 - - - +
80D GLN* 1.3 75.8 - - - +
82D PRO* 1.3 62.7 - - - +
83D ALA 3.0 0.2 - - - -
84D PHE* 2.8 28.3 + - - -
315D ASN* 3.1 24.9 - - - +
316D PRO* 3.6 10.1 - - - +
317D GLN* 3.3 22.6 + - - -
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Residues in contact with PRO 82 (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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73D GLY* 5.2 0.2 - - - -
76D SER* 4.5 4.7 - - - +
79D LEU 3.8 8.3 - - - +
80D GLN* 3.3 6.1 - - - +
81D GLY* 1.3 88.5 - - - +
83D ALA* 1.4 61.1 + - - +
84D PHE 3.0 0.2 - - - -
85D ALA* 3.0 10.5 + - + +
86D PRO* 3.9 0.2 - - - +
159D GLY* 2.7 51.4 + - - +
160D ASP* 3.9 3.4 - - + +
283D SER* 3.9 4.3 - - - +
313D GLU* 3.7 29.6 - - - +
314D PHE 3.1 23.1 - - - +
315D ASN* 3.8 11.9 - - + +
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Residues in contact with ALA 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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71D PRO* 3.0 44.3 - - - +
72D LEU 4.0 2.7 - - - +
73D GLY* 3.7 17.3 - - - +
80D GLN* 3.0 19.0 + - + +
81D GLY 2.9 0.4 + - - +
82D PRO* 1.4 77.1 - - - +
84D PHE* 1.3 73.1 + - + +
85D ALA 3.6 0.2 + - - -
86D PRO* 3.9 0.2 - - - +
87D PRO* 5.3 0.3 - - - +
123D GLN* 4.4 10.1 - - + +
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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