Contacts of the strand formed by residues 617 - 621 (chain D) 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 VAL 617 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D LYS* 2.9 28.3 + - + +
598D GLU* 3.9 24.5 - - + +
601D VAL* 3.5 24.2 - - + -
602D ASN* 3.1 31.4 - - - +
615D ALA* 4.7 7.3 - - - +
616D PHE* 1.3 73.8 - - - +
618D LEU* 1.3 59.8 + - - +
619D TYR 3.4 2.2 - - - +
625D ILE* 3.3 33.2 - - + -
626D TYR 3.3 4.7 - - - +
627D VAL* 4.1 5.4 - - + -
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Residues in contact with LEU 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D LYS* 4.2 9.7 - - - +
399D PRO* 3.8 20.5 - - + +
400D ILE 4.6 2.1 + - - -
404D TYR* 3.8 42.3 + - + +
407D VAL* 3.9 21.1 - - + -
615D ALA 5.6 1.1 - - - -
616D PHE 3.4 3.7 + - - +
617D VAL* 1.3 73.4 - - - +
619D TYR* 1.3 76.0 + - + +
626D TYR* 2.9 28.9 + - + +
628D SER* 4.1 13.2 - - - +
702D TRP* 3.7 36.3 - - + -
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Residues in contact with TYR 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D VAL* 4.8 3.8 - - - +
397D LYS* 3.3 35.0 - - - -
399D PRO* 3.5 22.7 - - + -
598D GLU* 5.8 0.2 - - - -
617D VAL* 3.4 2.5 - - - -
618D LEU* 1.3 100.3 - - + +
620D GLY* 1.3 72.5 + - - +
621D ASP* 2.7 40.9 + - + +
625D ILE* 3.5 3.2 - - - +
626D TYR* 2.8 52.9 + + + -
702D TRP* 4.3 11.4 - - - +
705D LYS* 4.0 2.9 - - + -
706D LYS* 3.1 37.6 - - + +
708D TYR* 6.1 2.0 - + - -
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Residues in contact with GLY 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D PHE 4.4 0.4 - - - -
397D LYS* 3.2 34.3 + - - +
594D LEU* 4.1 11.7 - - - -
598D GLU* 4.4 7.0 - - - -
619D TYR* 1.3 83.6 - - - +
621D ASP* 1.3 65.8 + - - +
624D SER 3.2 10.5 - - - -
625D ILE* 4.3 5.2 - - - -
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Residues in contact with ASP 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D PHE 3.3 8.7 - - - +
396D VAL* 4.6 6.1 - - + -
594D LEU* 3.6 3.2 - - - +
619D TYR* 2.7 37.7 + - - +
620D GLY* 1.3 69.7 - - - +
622D THR* 1.3 62.0 + - - +
623D ASP* 2.3 25.5 + - - +
624D SER* 2.9 28.9 + - - -
706D LYS* 3.4 21.8 - - + +
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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