Contacts of the helix formed by residues 80 - 84 (chain D) in PDB entry 3SPD
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 HIS 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASN* 3.4 53.4 + - + +
701A SO4 6.0 1.6 - - - -
78D ASP* 2.9 10.3 + - - +
79D PRO* 1.3 78.6 - - - +
81D LEU* 1.3 82.0 + - + +
82D THR 3.1 1.6 - - - -
83D HIS* 3.1 17.0 + - - +
84D VAL* 3.6 22.8 + - + +
93D HIS* 5.0 6.8 - + - -
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Residues in contact with LEU 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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76D THR* 4.0 4.9 - - + +
78D ASP* 3.1 34.1 + - + +
80D HIS* 1.3 90.6 - - + +
82D THR* 1.3 63.7 + - - +
84D VAL* 3.0 25.4 + - + +
89D ILE* 4.3 4.0 - - + -
93D HIS* 3.5 36.3 - - + +
96D LEU* 3.8 35.9 - - + -
146D LEU* 4.0 9.9 - - - +
703D SO4 3.7 17.3 - - - +
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Residues in contact with THR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 3.5 18.8 - - + +
75D MET* 5.2 0.2 - - - +
76D THR* 3.7 18.0 + - - +
78D ASP 2.9 20.1 + - - +
79D PRO* 3.5 17.9 - - + +
81D LEU* 1.3 76.6 - - - +
83D HIS* 1.3 74.0 + - + +
84D VAL 4.2 0.9 - - - +
144D ASN 3.0 7.8 - - - +
145D ASN* 2.9 37.1 + - - +
146D LEU* 2.8 29.2 + - - +
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Residues in contact with HIS 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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202A ARG 5.5 6.1 - - - +
701A SO4 2.6 33.4 + - - +
36D ASP* 4.9 5.9 + - - -
79D PRO 4.3 5.5 + - - +
80D HIS 3.1 10.1 + - - +
82D THR* 1.3 90.9 - - + +
84D VAL* 1.3 63.8 + - - +
85D HIS 3.7 1.4 + - - -
144D ASN* 3.3 34.6 - - + +
145D ASN* 3.6 17.2 + - - -
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Residues in contact with VAL 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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80D HIS* 3.7 39.3 - - + +
81D LEU* 3.0 22.2 + - + +
82D THR 4.2 2.6 - - - +
83D HIS* 1.3 79.5 - - - +
85D HIS* 1.3 72.7 + - - +
86D PRO* 3.6 2.3 - - - +
88D GLU* 3.6 18.4 - - + -
89D ILE* 3.6 21.8 - - + +
93D HIS* 4.1 11.9 - - - +
144D ASN 5.5 0.3 - - - +
146D LEU* 3.7 16.6 - - - +
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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