Contacts of the helix formed by residues 603 - 612 (chain B) in PDB entry 4PE5
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 GLY 603 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602B ILE* 1.3 77.0 - - - +
604B LYS* 1.3 62.2 + - - -
605B ALA 3.3 0.4 + - - -
606B ILE* 4.0 9.6 + - - +
607B TRP* 4.2 6.8 + - - +
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Residues in contact with LYS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B ILE 3.3 3.2 + - - -
603B GLY* 1.3 70.7 - - - -
605B ALA* 1.3 58.9 + - - +
606B ILE 3.3 1.3 - - - -
607B TRP* 3.4 10.6 + - + +
608B LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569B VAL 3.7 18.6 - - - +
602B ILE* 3.6 23.5 + - - +
603B GLY 3.3 0.4 - - - -
604B LYS* 1.3 79.6 - - - +
606B ILE* 1.3 56.7 + - - +
608B LEU* 3.4 5.8 + - - +
609B LEU* 2.9 30.5 + - - +
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Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B LEU* 4.6 16.4 - - + +
569B VAL 4.5 0.6 + - - -
602B ILE* 4.8 13.7 - - + +
603B GLY 4.0 9.4 + - - +
605B ALA* 1.3 78.8 - - - +
607B TRP* 1.3 58.8 + - - +
609B LEU* 3.9 4.1 - - - +
610B TRP* 2.9 33.1 + - - +
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Residues in contact with TRP 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A ARG* 5.9 8.1 - - + -
603B GLY 4.2 3.9 + - - +
604B LYS* 3.4 16.2 + - + +
605B ALA 3.3 0.2 - - - -
606B ILE* 1.3 78.4 - - - +
608B LEU* 1.3 57.9 + - - +
610B TRP* 3.9 3.5 - - - +
611B GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B LYS 2.9 18.0 + - - +
605B ALA* 3.7 7.6 - - - +
607B TRP* 1.3 76.7 - - - +
609B LEU* 1.3 59.2 + - - +
611B GLY* 3.9 0.6 - - - -
612B LEU* 3.0 31.5 + - - +
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B LEU* 4.5 17.0 - - - -
569B VAL* 4.1 22.0 - - + -
605B ALA 2.9 17.3 + - - +
606B ILE* 3.9 4.0 - - - +
608B LEU* 1.3 78.0 - - - +
610B TRP* 1.3 60.5 + - - +
612B LEU* 3.5 4.6 + - - +
613B VAL* 3.4 19.8 + - - +
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Residues in contact with TRP 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A MET* 5.5 11.9 - - + -
637A ALA* 6.0 1.6 - - - +
566B LEU* 5.4 8.1 - - + -
606B ILE 2.9 18.2 + - - +
607B TRP* 4.5 3.4 - - - +
609B LEU* 1.3 75.8 - - - +
611B GLY* 1.3 61.2 + - - +
613B VAL* 3.5 18.2 + - - +
614B PHE* 4.0 6.9 + - - +
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Residues in contact with GLY 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A ALA* 6.4 2.5 - - - -
607B TRP 2.9 20.9 + - - -
608B LEU* 3.9 1.3 - - - -
610B TRP* 1.3 78.2 - - - +
612B LEU* 1.3 59.0 + - - +
613B VAL 3.2 2.6 + - - -
614B PHE* 3.6 16.8 + - - +
615B ASN 4.6 6.6 + - - +
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B LEU 3.0 18.3 + - - +
609B LEU* 3.5 5.4 + - - +
611B GLY* 1.3 74.6 - - - +
613B VAL* 1.3 62.6 + - - +
614B PHE 3.3 8.2 + - - +
632B VAL* 6.6 0.2 - - + -
635B TRP 5.9 0.7 - - - +
636B ALA* 4.8 20.3 - - + +
639B ALA* 3.6 13.1 - - - +
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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