Contacts of the strand formed by residues 683 - 689 (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 MET 683 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D PHE* 3.6 29.6 - - + +
411D ASP 3.1 14.8 - - - +
412D LEU* 3.3 26.5 - - + -
597D ILE* 3.5 37.0 - - + -
601D VAL* 4.9 4.0 - - + -
625D ILE* 3.9 17.5 - - + -
660D GLU* 2.8 27.6 - - - +
663D ILE* 3.7 33.2 - - + +
667D PHE* 4.4 3.7 - - + -
681D MET 4.2 0.8 + - - -
682D PHE* 1.3 76.0 - - - +
684D ASP* 1.3 65.7 + - - +
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Residues in contact with ASP 684 (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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410D PHE* 3.3 4.9 - - - -
411D ASP* 2.9 32.2 + - - +
413D THR* 4.0 16.9 + - - +
660D GLU* 3.4 6.8 - - - +
682D PHE* 4.4 3.6 - - - +
683D MET* 1.3 84.0 + - - +
685D ARG* 1.3 70.7 + - - +
686D GLU* 3.2 10.2 + - - +
716D GLU* 5.7 0.5 - - - +
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Residues in contact with ARG 685 (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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408D MET* 3.9 5.8 - - - -
409D SER 4.1 1.8 - - - +
410D PHE* 3.3 38.1 - - + -
652D ASP* 3.2 21.3 + - - -
655D ALA* 3.8 19.5 - - + -
656D ARG* 5.6 1.3 - - - +
660D GLU* 3.6 6.9 + - - +
684D ASP* 1.3 73.2 - - - +
686D GLU* 1.3 89.2 + - - +
687D ALA 3.9 3.6 - - - -
688D ILE* 3.0 40.3 - - + +
714D ASP* 2.8 24.0 + - - -
716D GLU* 3.7 7.8 - - - -
717D GLY* 2.8 31.1 - - - +
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Residues in contact with GLU 686 (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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409D SER* 2.4 37.0 + - - +
411D ASP* 3.5 42.9 - - + +
684D ASP* 3.2 11.6 + - - +
685D ARG* 1.3 80.5 + - - +
687D ALA* 1.3 62.6 + - + +
715D MET* 3.3 12.0 - - - +
716D GLU* 2.6 76.8 + - - +
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Residues in contact with ALA 687 (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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407D VAL 4.5 0.2 - - - -
408D MET* 3.2 10.6 - - - +
409D SER* 2.9 35.2 + - - +
626D TYR* 6.2 0.7 - - + -
685D ARG* 3.9 0.9 - - - -
686D GLU* 1.3 79.5 - - + +
688D ILE* 1.3 64.9 + - - +
689D ALA* 4.2 1.1 - - + -
710D LEU* 5.3 6.1 - - + -
712D VAL* 3.8 19.7 - - + -
714D ASP 3.3 3.6 - - - -
715D MET* 3.7 21.5 - - + -
726D LYS* 5.8 2.0 - - - +
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Residues in contact with ILE 688 (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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407D VAL 3.7 3.4 - - - +
408D MET* 3.5 13.0 - - + -
647D TRP* 3.9 19.7 - - + -
648D VAL* 3.6 30.7 - - + +
651D LEU* 4.3 15.5 - - + -
652D ASP* 3.7 33.2 - - + +
685D ARG* 3.0 34.8 - - - +
687D ALA* 1.3 76.7 - - - +
689D ALA* 1.3 61.8 + - - +
712D VAL* 3.4 2.8 - - - +
713D TRP* 3.0 27.4 + - - -
714D ASP* 2.9 10.7 + - + +
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Residues in contact with ALA 689 (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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405D LYS 4.1 0.7 - - - -
406D TYR* 3.4 3.3 - - - -
407D VAL* 2.8 38.4 + - + +
647D TRP* 3.6 11.9 - - - -
651D LEU* 5.6 0.2 - - - +
687D ALA* 5.6 1.1 - - + -
688D ILE* 1.3 75.8 - - - +
690D GLY* 1.3 57.1 + - - +
699D GLY 4.7 1.6 - - - +
710D LEU* 3.9 30.7 - - + -
711D ASN 3.1 25.8 - - - +
712D VAL* 4.0 2.9 - - + -
713D TRP* 4.1 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