Contacts of the helix formed by residues 559 - 564 (chain W) in PDB entry 6NE3
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 THR 559 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505W PHE* 3.5 30.6 + - + +
506W SER 3.4 11.7 + - - -
507W GLN* 3.8 22.6 + - - +
558W SER* 1.3 73.9 - - - +
560W ARG* 1.3 62.7 + - + +
563W GLY* 2.9 28.6 + - - -
578W ASP 5.2 2.9 + - - +
580W ASP* 4.8 5.6 - - - +
585W VAL* 4.4 17.9 - - + +
586W ASP* 5.1 6.7 - - - +
589W ALA* 3.8 22.4 - - + +
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Residues in contact with ARG 560 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I G 5.1 22.8 + - - +
155I G 5.4 10.1 - - - -
54J G 5.3 11.4 + - - +
55J C 3.7 28.4 + - - +
56J T 3.7 15.8 + - - +
507W GLN* 3.3 38.4 + - - +
558W SER* 3.4 0.4 - - - -
559W THR* 1.3 76.4 - - + +
561W ALA* 1.3 60.9 + - - +
564W LEU* 3.0 44.1 + - + +
580W ASP* 4.0 9.5 + - - +
585W VAL* 5.9 10.2 - - + +
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Residues in contact with ALA 561 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J T 3.2 25.4 + - - +
57J T 3.7 26.2 - - - +
239W SER* 2.9 33.8 + - - +
529W LEU* 5.6 1.8 - - - +
531W GLY* 3.8 11.4 - - - -
538W ARG* 4.5 2.4 + - - +
558W SER* 3.6 4.2 + - - +
560W ARG* 1.3 78.6 - - - +
562W GLY* 1.3 59.0 + - - +
564W LEU* 4.5 8.3 + - - +
565W GLY 5.7 0.2 + - - -
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Residues in contact with GLY 562 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529W LEU* 4.9 9.9 - - - -
557W LEU* 3.7 22.4 - - - -
558W SER* 3.3 17.0 + - - -
560W ARG 3.2 0.2 - - - -
561W ALA* 1.3 78.2 - - - +
563W GLY* 1.3 57.3 + - - +
564W LEU 3.1 8.9 + - - -
565W GLY 4.1 0.7 + - - -
566W ILE* 3.3 30.8 - - - +
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Residues in contact with GLY 563 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505W PHE* 4.2 10.3 - - - -
558W SER 3.6 3.4 + - - -
559W THR 2.9 24.0 + - - -
562W GLY* 1.3 70.5 - - - +
564W LEU* 1.3 59.2 + - - +
565W GLY 3.6 0.4 - - - -
588W GLN* 3.9 14.2 - - - +
589W ALA* 4.0 4.7 + - - -
592W ARG* 3.0 40.9 + - - +
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Residues in contact with LEU 564 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W PRO* 3.7 31.4 - - + -
239W SER* 6.2 1.6 - - - -
287W TYR* 5.5 3.8 - - + -
309W GLU* 3.7 37.8 - - + +
312W ARG* 5.8 3.8 - - - +
560W ARG* 3.0 23.8 + - + +
561W ALA* 4.8 8.1 - - - +
562W GLY 3.1 2.2 + - - -
563W GLY* 1.3 77.3 - - - +
565W GLY* 1.3 59.7 + - - +
585W VAL* 5.8 7.6 - - + -
588W GLN* 3.9 14.2 + - + -
592W ARG* 3.3 16.0 + - - -
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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