Contacts of the strand formed by residues 707 - 715 (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 ARG 707 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702D TRP* 3.5 4.8 - - - -
703D THR* 2.8 59.6 + - - +
704D GLY* 2.9 20.5 + - - +
705D LYS* 3.6 17.8 + - - +
706D LYS* 1.3 75.8 - - - +
708D TYR* 1.3 60.0 + - - +
728D MET 3.1 4.5 - - - -
729D GLY* 3.6 21.9 + - - +
730D LEU* 4.5 7.6 - - + +
731D GLU* 6.2 1.0 - - - +
6K A 5.1 2.0 - - - -
7K A 3.4 36.8 + - - -
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Residues in contact with TYR 708 (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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619D TYR* 6.1 2.0 - + - -
626D TYR* 2.7 32.8 + + - -
701D PHE* 3.3 6.3 - - - +
702D TRP* 3.1 47.1 - + + +
706D LYS* 4.8 6.5 - - + -
707D ARG* 1.3 75.5 - - - +
709D ALA* 1.3 69.5 + - - +
710D LEU* 3.8 22.2 - - + +
726D LYS* 3.6 41.2 + - + +
727D ILE* 3.5 0.9 - - - -
728D MET* 2.8 64.7 + - + +
730D LEU* 3.6 10.2 - - - +
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Residues in contact with ALA 709 (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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700D GLY* 3.1 4.4 - - - -
701D PHE* 3.0 45.6 + - + +
702D TRP* 5.1 0.5 - - - -
708D TYR* 1.3 81.5 - - - +
710D LEU* 1.3 62.7 - - - +
726D LYS 3.1 10.3 - - - +
727D ILE* 4.2 11.0 - - + -
730D LEU* 3.5 22.4 - - + -
749D ILE* 4.4 9.4 - - + -
753D LEU* 4.4 2.4 - - + +
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Residues in contact with LEU 710 (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* 4.1 15.5 - - + -
626D TYR* 4.0 15.9 - - + -
687D ALA* 5.3 6.5 - - + -
689D ALA* 3.9 12.8 - - + -
699D GLY 3.5 9.6 - - - +
700D GLY* 4.4 2.7 - - - -
702D TRP* 3.4 32.8 - - + -
708D TYR* 3.8 8.3 - - + -
709D ALA* 1.3 77.3 - - - +
711D ASN* 1.3 61.4 + - - +
712D VAL* 3.2 37.0 + - + -
725D LEU* 3.5 2.3 - - - +
726D LYS* 2.9 53.1 + - + +
753D LEU* 3.7 6.9 - - - +
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Residues in contact with ASN 711 (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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689D ALA* 3.1 20.9 - - - +
690D GLY 3.0 25.9 + - - +
692D PRO* 3.8 4.8 - - - +
699D GLY 3.0 14.3 + - - +
710D LEU* 1.3 69.1 - - - +
712D VAL* 1.3 59.3 + - - +
713D TRP* 3.2 22.4 - - - -
723D PRO* 2.8 32.8 - - - +
724D LYS 3.9 3.5 - - - +
725D LEU* 4.8 2.6 - - + +
753D LEU* 3.5 21.4 + - + +
754D GLN* 3.6 27.5 + - - +
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Residues in contact with VAL 712 (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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687D ALA* 3.8 15.3 - - + -
688D ILE 3.4 9.2 - - - +
689D ALA* 4.0 2.2 - - + -
710D LEU* 3.2 34.3 - - + +
711D ASN* 1.3 71.6 - - - +
713D TRP* 1.3 65.4 + - - +
714D ASP 3.3 28.7 - - - +
715D MET* 4.3 12.1 - - + -
720D TYR* 4.0 11.5 - - + -
723D PRO* 3.3 5.9 - - - +
724D LYS* 2.9 41.8 + - + +
726D LYS* 3.9 9.9 - - + -
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Residues in contact with TRP 713 (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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644D THR* 3.6 22.9 - - + -
645D ASN* 6.2 0.9 - - - +
647D TRP* 3.9 12.9 - + - -
648D VAL* 3.9 20.6 - - + -
688D ILE 3.0 9.5 + - - -
689D ALA* 4.1 0.4 - - - -
690D GLY 2.7 30.0 + - - -
692D PRO* 3.4 44.9 - - + -
711D ASN* 3.2 30.8 + - - -
712D VAL* 1.3 73.7 - - - +
714D ASP* 1.3 61.5 + - - +
719D ARG* 3.6 3.7 - - - +
720D TYR* 2.9 38.8 + - - +
721D ALA 5.8 1.3 - - - -
723D PRO* 3.7 37.7 - - + -
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Residues in contact with ASP 714 (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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648D VAL* 4.1 12.3 - - + -
652D ASP* 5.4 2.5 - - - -
685D ARG* 2.8 40.2 + - - +
687D ALA* 3.3 4.0 - - - -
688D ILE* 2.9 32.1 + - + -
712D VAL* 3.3 4.4 - - - +
713D TRP* 1.3 82.6 - - - +
715D MET* 1.3 60.9 + - - +
717D GLY* 2.9 16.4 + - - +
718D THR 3.0 22.7 - - - -
719D ARG* 3.0 31.6 + - - +
720D TYR* 5.0 0.2 - - - -
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Residues in contact with MET 715 (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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686D GLU* 3.3 26.0 - - - +
687D ALA* 3.7 20.6 - - + -
712D VAL* 4.3 14.4 - - + -
714D ASP* 1.3 72.6 + - - +
716D GLU* 1.3 85.0 + - + +
717D GLY 3.3 0.7 - - - -
718D THR* 2.8 28.1 + - - +
720D TYR* 3.4 34.1 - - + +
726D LYS* 4.0 28.5 - - + +
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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
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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