Contacts of the strand formed by residues 624 - 628 (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 SER 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B SER* 5.7 0.2 - - - -
410B PHE 3.2 9.2 - - - -
411B ASP* 2.4 30.4 + - - -
594B LEU* 3.7 2.2 - - - +
620B GLY* 3.2 3.8 - - - -
621B ASP 2.9 31.3 + - - -
622B THR 3.9 0.2 - - - -
623B ASP* 1.3 85.3 + - - +
625B ILE* 1.3 64.1 + - - +
626B TYR* 3.7 26.4 + - - -
115H A 4.4 10.8 - - - -
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Residues in contact with ILE 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B MET 4.0 0.5 - - - +
409B SER* 3.2 3.3 - - - -
410B PHE* 3.0 43.4 + - + -
594B LEU* 3.5 34.8 - - + +
597B ILE* 4.3 7.9 - - + +
598B GLU* 5.0 4.5 - - + -
601B VAL* 3.8 30.1 - - + -
617B VAL* 4.0 18.8 - - + -
619B TYR 3.4 4.9 - - - -
620B GLY* 4.6 3.4 - - - -
624B SER* 1.3 71.9 - - - +
626B TYR* 1.3 64.1 + - - +
627B VAL* 4.2 9.9 - - + -
663B ILE* 5.1 0.2 - - + -
683B MET* 3.4 24.0 - - + -
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Residues in contact with TYR 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 4.1 6.7 - - + -
408B MET 3.6 2.5 - - - -
409B SER* 3.4 25.6 - - - -
411B ASP* 5.3 1.8 + - - -
617B VAL* 3.4 4.3 - - - -
618B LEU* 2.9 34.4 + - + +
619B TYR* 2.8 38.1 + + - +
621B ASP* 5.5 0.7 - - + -
624B SER* 3.7 28.5 + - - -
625B ILE* 1.3 77.2 - - - +
627B VAL* 1.3 62.1 + - - +
702B TRP* 3.9 29.8 - + + -
708B TYR* 2.6 38.1 + + - -
710B LEU* 4.3 12.1 - - + -
726B LYS* 3.6 10.9 + - - -
115H A 3.4 8.6 + - - -
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Residues in contact with VAL 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 3.1 6.6 - - - +
408B MET* 2.7 48.2 + - + +
410B PHE* 4.3 13.2 - - + -
601B VAL* 4.0 22.2 - - + -
605B LEU* 3.5 28.7 - - + -
616B PHE* 3.1 12.8 - - + +
617B VAL* 4.4 4.3 - - + -
618B LEU* 3.9 3.8 - - - -
625B ILE* 4.2 15.9 - - + -
626B TYR* 1.3 78.1 - - - +
628B SER* 1.3 74.1 + - - +
629B ALA* 3.5 1.9 + - - +
659B MET* 5.2 5.4 - - + -
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Residues in contact with SER 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B TYR* 4.3 14.7 - - - +
406B TYR 3.4 7.9 + - - -
615B ALA 5.2 2.7 - - - -
616B PHE* 2.7 35.3 + - - -
618B LEU* 3.9 14.1 - - - +
627B VAL* 1.3 79.6 - - - +
629B ALA* 1.3 61.2 + - - +
630B ASP* 3.5 26.3 + - - +
631B LYS 4.4 2.4 + - - -
632B ILE* 5.2 0.5 + - - +
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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
------------------------------------------------------------
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