Contacts of the strand formed by residues 683 - 689 (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 MET 683 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B PHE* 3.3 39.4 - - + +
411B ASP 3.2 11.2 - - - +
412B LEU* 4.0 18.4 - - + +
594B LEU* 4.7 1.6 - - + -
597B ILE* 3.0 38.4 - - + -
623B ASP 4.3 4.7 - - - +
625B ILE* 3.4 22.0 - - + +
660B GLU* 3.7 13.1 - - - +
663B ILE* 4.0 33.5 - - + +
667B PHE* 4.2 3.3 - - + -
681B MET 4.1 0.6 + - - -
682B PHE* 1.3 76.0 - - - +
684B ASP* 1.3 74.2 + - - +
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Residues in contact with ASP 684 (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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410B PHE* 3.9 4.7 - - - -
411B ASP 3.1 27.7 + - - +
413B THR* 4.3 13.3 + - - -
660B GLU* 3.7 19.5 - - - +
682B PHE* 4.5 5.2 + - - +
683B MET* 1.3 89.3 + - - +
685B ARG* 1.3 71.8 + - - +
686B GLU* 3.2 7.8 + - - +
716B GLU* 6.3 1.6 - - + -
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Residues in contact with ARG 685 (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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408B MET* 3.3 25.4 - - + -
409B SER 3.5 0.9 - - - +
410B PHE* 3.4 28.2 - - + -
652B ASP* 3.1 28.1 + - - +
655B ALA* 4.1 11.9 - - + -
656B ARG* 5.8 1.3 - - + +
660B GLU* 3.4 14.5 + - - +
684B ASP* 1.3 75.0 - - - +
686B GLU* 1.3 79.2 + - - +
687B ALA 3.9 3.8 - - - -
688B ILE* 3.4 19.7 - - - +
714B ASP* 2.3 51.3 + - - -
716B GLU* 3.2 17.6 - - - +
717B GLY* 3.2 18.8 - - - +
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Residues in contact with GLU 686 (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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409B SER* 2.5 26.1 + - - +
411B ASP* 3.3 33.6 - - - +
684B ASP* 3.2 12.4 + - - +
685B ARG* 1.3 77.2 + - - +
687B ALA* 1.3 59.2 + - - +
715B MET* 3.2 26.0 - - + +
716B GLU* 2.6 71.8 + - - +
726B LYS* 6.4 1.1 - - - -
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Residues in contact with ALA 687 (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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407B VAL 4.5 0.4 - - - -
408B MET* 3.3 6.5 - - - -
409B SER* 3.1 33.7 + - - +
685B ARG* 3.9 3.5 - - - -
686B GLU* 1.3 80.7 - - - +
688B ILE* 1.3 68.6 + - - +
689B ALA* 4.2 1.3 - - + -
710B LEU* 5.6 5.4 - - + -
712B VAL* 3.7 15.5 - - + -
714B ASP 3.4 3.6 - - - -
715B MET* 3.6 23.8 - - + -
726B LYS* 5.1 6.1 - - + -
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Residues in contact with ILE 688 (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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407B VAL 3.7 5.2 - - - +
408B MET* 4.1 7.6 - - + +
647B TRP* 3.7 26.0 - - + -
648B VAL* 3.6 28.5 - - + +
651B LEU* 4.0 15.3 - - + -
652B ASP* 3.9 14.8 - - + +
685B ARG* 3.4 42.4 - - - +
687B ALA* 1.3 74.0 - - - +
689B ALA* 1.3 62.0 + - - +
712B VAL* 3.4 3.1 - - - +
713B TRP* 2.8 27.9 + - - -
714B ASP* 3.0 21.9 + - + +
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Residues in contact with ALA 689 (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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405B LYS 4.1 1.3 - - - -
406B TYR* 3.5 3.3 - - - +
407B VAL* 3.0 33.8 + - + +
647B TRP* 3.8 10.9 - - - -
651B LEU* 5.5 0.2 - - - +
687B ALA* 4.2 1.5 - - + -
688B ILE* 1.3 75.1 - - - +
690B GLY* 1.3 57.4 + - - +
699B GLY 4.6 1.3 - - - +
710B LEU* 3.7 34.5 - - + -
711B ASN 2.9 26.7 - - - +
712B VAL* 4.0 3.6 - - + -
713B TRP* 4.2 1.1 - - - -
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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