Contacts of the helix formed by residues 629 - 635 (chain B) in PDB entry 3RMD
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 ALA 629 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406B TYR* 2.8 29.4 + - + +
407B VAL 4.4 1.3 - - - +
408B MET* 4.5 11.2 - - + -
627B VAL* 3.5 4.6 + - + +
628B SER* 1.3 70.8 - - - +
630B ASP* 1.3 66.6 + - - +
631B LYS 3.3 2.2 - - - -
632B ILE* 2.7 21.8 + - + +
633B ILE* 2.9 12.4 + - + +
651B LEU* 3.9 30.7 - - + -
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Residues in contact with ASP 630 (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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404B TYR* 5.1 2.4 - - - -
405B LYS* 3.5 19.6 + - - +
406B TYR* 2.9 42.1 + - - +
628B SER* 3.2 17.9 + - - +
629B ALA* 1.3 76.0 - - - +
631B LYS* 1.3 66.2 + - - +
633B ILE* 3.1 1.7 + - - +
634B ASP* 3.0 34.7 + - - +
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Residues in contact with LYS 631 (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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609B CYS* 3.9 15.5 - - + +
611B THR* 4.0 16.4 - - + +
614B GLU* 3.3 29.2 + - - +
616B PHE* 3.4 35.4 - - + -
628B SER 4.4 1.0 + - - +
629B ALA 3.3 0.6 - - - -
630B ASP* 1.3 80.5 - - - +
632B ILE* 1.3 59.5 + - - +
634B ASP* 3.7 14.1 + - - +
635B LYS* 3.3 23.0 + - - +
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Residues in contact with ILE 632 (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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605B LEU* 4.7 9.0 - - + -
608B VAL* 5.6 2.7 - - + -
609B CYS* 3.9 20.6 - - - -
616B PHE* 5.7 2.5 - - + -
628B SER 5.2 0.6 + - - +
629B ALA* 2.7 21.4 + - + +
631B LYS* 1.3 70.8 - - + +
633B ILE* 1.3 67.6 + - - +
634B ASP 3.1 1.6 - - - -
635B LYS* 3.0 25.2 + - + +
636B VAL 3.8 1.9 + - - -
650B PHE* 3.6 23.6 - - + -
651B LEU* 3.4 30.3 - - + -
654B PHE* 3.7 43.7 - - + -
659B MET* 6.2 0.2 - - + -
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Residues in contact with ILE 633 (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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406B TYR* 3.2 47.8 - - + +
629B ALA* 2.9 14.3 + - + +
630B ASP 3.6 6.5 - - - +
632B ILE* 1.3 76.2 - - - +
634B ASP* 1.3 52.9 + - - +
636B VAL* 3.3 5.2 + - - +
637B GLY 2.7 29.6 + - - -
638B GLU* 3.7 21.1 - - + -
641B PHE* 3.9 10.6 - - + -
647B TRP* 4.1 22.7 - - + -
650B PHE* 4.4 10.5 - - + -
651B LEU* 3.8 30.5 - - + -
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Residues in contact with ASP 634 (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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406B TYR* 5.7 0.9 - - - -
630B ASP* 3.0 25.8 + - - +
631B LYS* 3.8 16.3 - - - +
632B ILE 3.1 0.2 - - - -
633B ILE* 1.3 81.6 - - - +
635B LYS* 1.3 53.3 + - - +
636B VAL 2.7 16.7 + - - -
637B GLY* 3.2 13.3 + - - +
638B GLU* 5.1 6.4 + - - +
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Residues in contact with LYS 635 (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 VAL 3.3 24.0 + - - -
609B CYS* 3.7 33.0 - - + +
610B GLY* 4.7 0.4 - - - +
631B LYS* 3.3 13.1 + - + +
632B ILE* 3.0 19.5 + - + +
634B ASP* 1.3 77.4 - - - +
636B VAL* 1.3 62.8 + - + +
640B LYS* 5.0 2.4 + - - -
650B PHE* 6.1 0.7 - - + -
895D ALA 5.6 1.6 + - - -
896D SER 4.2 14.1 + - - -
897D LEU 5.7 2.0 - - - -
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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