Contacts of the helix formed by residues 247 - 251 (chain A) in PDB entry 3HJW
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 GLU 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.7 10.2 - - + +
41A ARG* 2.8 44.1 + - - -
245A PRO* 2.9 13.5 + - + +
246A MET* 1.3 81.5 + - - +
248A LYS* 1.3 59.3 + - - +
250A VAL* 2.9 34.8 + - - +
251A GLU* 3.5 7.2 + - - +
255A LYS* 5.3 1.2 + - - -
293A MET* 4.0 9.4 - - + -
297A ASP 3.4 20.6 - - - +
298A GLU* 3.4 1.4 - - - -
299A LEU* 2.7 38.1 + - + +
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 6.0 0.2 - - + -
210A PRO* 3.4 28.7 - - - +
211A PHE* 4.1 22.9 - - + +
214A ASP* 4.2 12.1 + - - -
216A THR* 4.0 25.2 - - - +
244A GLN* 4.1 21.3 - - + +
245A PRO* 3.0 18.4 + - + +
247A GLU* 1.3 72.3 - - - +
249A ALA* 1.3 57.9 + - - +
250A VAL 2.8 10.4 + - - -
251A GLU* 3.1 51.7 + - - +
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.4 6.3 - - + -
102A VAL* 4.0 26.5 - - + -
105A ALA* 3.7 8.8 - - - +
106A LEU* 3.4 14.2 - - + +
210A PRO* 4.2 0.2 - - - -
211A PHE* 3.8 27.5 - - + -
245A PRO 4.3 0.2 + - - -
246A MET 3.0 14.6 + - - +
248A LYS* 1.3 76.8 - - - +
250A VAL* 1.3 57.6 + - - +
251A GLU 3.7 0.2 - - - -
252A HIS* 3.1 22.2 - - - -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 5.2 3.4 - - + -
105A ALA* 4.7 3.1 - - + -
246A MET 4.4 3.6 - - - +
247A GLU* 2.9 16.9 + - - +
249A ALA* 1.3 81.4 - - - +
251A GLU* 1.3 62.5 + - - +
252A HIS* 3.2 5.6 - - - -
253A LEU* 3.1 43.1 + - + +
255A LYS* 3.6 18.4 - - - -
291A ALA* 3.8 17.9 - - + -
293A MET* 4.1 13.2 - - + -
299A LEU* 4.2 14.4 - - + -
302A LEU* 3.8 19.7 - - + -
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Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 5.4 1.6 + - - -
210A PRO* 4.1 10.5 - - + +
212A LYS* 5.8 1.6 + - - -
247A GLU 3.5 4.0 + - - +
248A LYS* 3.1 58.4 + - - +
249A ALA 3.7 0.6 - - - -
250A VAL* 1.3 77.8 - - - +
252A HIS* 1.3 59.5 + - - +
253A LEU 3.2 5.1 + - - +
255A LYS* 4.2 18.1 + - - +
281A HIS* 5.9 1.6 - - - -
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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