Contacts of the helix formed by residues 257 - 262 (chain D) in PDB entry 3HYW
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 PRO 257 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D THR* 3.2 24.5 - - - +
106D GLY 4.3 5.2 - - - +
108D LYS* 3.9 10.0 - - + +
255D GLN 3.9 4.2 - - - +
256D GLY* 1.3 89.3 - - - +
258D GLU* 1.3 66.6 + - - +
259D VAL* 3.7 14.8 - - + -
260D VAL* 3.3 19.0 + - + +
261D ALA* 3.2 17.8 + - - +
273D LYS* 4.5 0.3 - - - +
295D VAL* 3.7 17.3 - - + -
433D SO4 3.5 22.2 - - - +
441D FAD 5.1 5.2 - - - +
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Residues in contact with GLU 258 (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 GLU 4.4 4.3 - - - +
108D LYS* 4.8 5.7 - - - -
255D GLN* 4.6 6.6 + - - -
256D GLY 4.8 0.3 - - - +
257D PRO* 1.3 71.2 - - - +
259D VAL* 1.3 59.4 + - - +
261D ALA* 3.2 10.1 + - - +
262D SER* 2.9 31.5 + - - -
273D LYS* 3.1 33.4 + - - +
433D SO4 2.8 33.4 + - - +
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 5.5 2.0 - - + -
78D ALA* 3.4 35.7 - - + +
79D GLU 3.4 22.3 + - - +
80D SER 3.8 3.8 - - - +
81D ILE* 3.4 31.7 - - + +
105D THR* 4.0 11.9 - - + -
257D PRO* 3.7 24.0 - - + -
258D GLU* 1.3 77.5 - - - +
260D VAL* 1.3 61.5 + - + +
262D SER* 2.8 17.7 + - - -
433D SO4 3.9 2.9 + - - +
441D FAD 3.7 17.3 - - - +
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Residues in contact with VAL 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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81D ILE* 4.5 4.9 - - + -
103D ILE* 3.8 30.5 - - + -
257D PRO* 3.3 28.1 + - + +
258D GLU 3.2 0.6 - - - -
259D VAL* 1.3 77.4 - - + +
261D ALA* 1.3 65.1 + - - +
262D SER 3.1 1.6 - - - -
263D ALA* 3.0 19.3 + - - +
267D VAL* 4.3 6.3 - - + +
268D ALA* 3.4 23.9 - - + +
273D LYS 3.2 24.7 - - - +
275D VAL* 3.8 21.3 - - + +
295D VAL* 4.2 1.6 - - + -
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Residues in contact with ALA 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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257D PRO 3.2 6.9 + - - +
258D GLU* 3.2 23.0 + - - +
260D VAL* 1.3 78.3 - - - +
262D SER* 1.3 59.5 + - - +
263D ALA 3.1 1.5 + - - -
264D GLY* 3.4 12.8 + - - +
268D ALA* 3.7 12.6 - - - +
273D LYS* 3.8 32.9 + - + +
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Residues in contact with SER 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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79D GLU 4.6 1.6 - - - -
80D SER* 3.2 18.2 - - - -
81D ILE 3.0 24.1 + - - +
83D PRO* 5.2 0.3 - - - +
258D GLU 2.9 12.8 + - - -
259D VAL 2.8 19.6 + - - -
260D VAL 3.1 0.2 - - - -
261D ALA* 1.3 75.5 - - - +
263D ALA* 1.3 57.0 + - - +
264D GLY 3.3 2.9 + - - -
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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