Contacts of the helix formed by residues 258 - 262 (chain D) in PDB entry 5D0A
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 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D GLY* 3.0 30.5 - - - -
20D ASP* 2.7 27.4 + - - -
75D LEU* 3.7 9.8 - - + +
76D ALA 3.2 23.8 - - - -
78D PRO* 5.6 0.7 - - + +
256D HIS* 3.4 3.5 - - - +
257D LEU* 1.3 92.7 + - + +
259D PRO* 1.4 57.9 - - - +
260D GLU* 3.2 10.1 - - - +
261D MET* 2.8 58.7 + - + +
262D GLU* 3.9 6.7 + - - +
505D PO4 2.7 29.9 + - - +
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Residues in contact with PRO 259 (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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256D HIS 5.6 0.7 - - - +
257D LEU 3.9 6.5 - - - +
258D HIS* 1.4 84.4 - - - +
260D GLU* 1.3 61.5 + - - +
261D MET 3.2 1.0 + - - -
262D GLU* 3.3 27.2 + - + +
505D PO4 3.6 13.5 - - - +
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Residues in contact with GLU 260 (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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102D GLY* 3.4 4.2 - - - -
103D LYS* 2.8 45.6 + - + +
108D VAL* 3.5 33.9 - - + +
112D LYS* 5.3 0.3 - - - -
258D HIS* 3.6 7.8 - - - -
259D PRO* 1.3 73.5 - - - +
261D MET* 1.3 58.6 + - + +
262D GLU 3.3 2.0 - - - +
505D PO4 2.5 44.4 + - - -
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Residues in contact with MET 261 (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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75D LEU* 3.9 31.0 - - + -
76D ALA 3.7 18.4 - - - +
77D TYR* 3.9 6.3 - - + -
78D PRO* 3.6 20.8 - - + +
101D TRP* 3.2 22.4 - - - +
102D GLY* 3.9 1.8 - - - -
103D LYS 4.4 3.8 - - - +
105D TYR* 5.9 0.2 - - - -
108D VAL* 4.2 17.5 - - + -
109D LEU* 4.7 1.3 - - + -
168D TYR* 3.7 38.6 - - + -
258D HIS* 2.8 31.9 + - + +
260D GLU* 1.3 84.4 - - + +
262D GLU* 1.3 64.1 + - - +
263D PRO* 3.3 5.9 - - - +
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Residues in contact with GLU 262 (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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78D PRO* 4.2 5.2 - - - +
82D LYS* 5.1 12.0 + - - +
102D GLY* 3.7 9.7 - - - -
256D HIS* 2.4 52.6 + - - +
258D HIS 4.5 3.0 - - - +
259D PRO* 3.3 25.9 + - + +
260D GLU 3.3 1.8 - - - +
261D MET* 1.3 77.7 - - - +
263D PRO* 1.3 80.4 - - - +
264D ASP* 3.5 2.8 + - - +
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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