Contacts of the strand formed by residues 718 - 728 (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 THR 718 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714D ASP* 3.0 4.9 - - - +
715D MET* 2.8 42.5 + - - +
716D GLU* 3.1 4.6 + - - +
717D GLY* 1.3 74.6 - - - +
719D ARG* 1.3 65.1 + - - +
720D TYR* 3.7 24.2 + - + -
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Residues in contact with ARG 719 (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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645D ASN* 3.3 29.2 + - - +
648D VAL* 2.7 54.3 + - - +
649D ASP* 2.6 40.8 + - - +
652D ASP* 4.9 5.7 - - - +
713D TRP 3.6 6.7 + - - +
714D ASP* 3.0 20.7 + - - +
717D GLY 3.4 7.6 + - - +
718D THR* 1.3 74.7 - - - +
720D TYR* 1.3 66.6 + - - +
721D ALA 3.8 0.7 + - - -
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Residues in contact with TYR 720 (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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645D ASN* 5.7 0.7 - - - +
712D VAL* 4.0 18.2 - - + -
713D TRP* 2.9 28.7 + - - +
715D MET* 3.4 39.7 - - + +
718D THR* 4.3 18.1 - - + +
719D ARG* 1.3 79.9 - - - +
721D ALA* 1.3 65.2 + - - +
722D GLU 3.2 18.7 - - - +
723D PRO* 4.8 0.9 - - + -
724D LYS* 3.4 32.1 - - + -
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Residues in contact with ALA 721 (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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713D TRP* 5.8 1.9 - - - -
719D ARG 3.8 1.8 + - - -
720D TYR* 1.3 75.0 - - - +
722D GLU* 1.3 63.9 + - + +
723D PRO* 4.3 3.3 - - - +
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Residues in contact with GLU 722 (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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720D TYR* 3.2 11.8 - - - +
721D ALA* 1.3 81.6 - - + +
723D PRO* 1.3 85.7 - - + +
724D LYS* 2.9 22.0 - - + +
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Residues in contact with PRO 723 (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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692D PRO* 5.6 0.2 - - + -
711D ASN* 2.8 27.4 - - - +
712D VAL 3.3 11.7 - - - +
713D TRP* 3.7 41.0 - - + -
720D TYR* 4.8 2.0 - - + -
721D ALA 4.3 2.9 - - - +
722D GLU* 1.3 103.1 - - + +
724D LYS* 1.3 67.8 + - - +
725D LEU* 4.2 7.6 + - - +
754D GLN* 4.3 20.8 + - - +
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Residues in contact with LYS 724 (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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711D ASN* 4.7 1.3 - - - -
712D VAL* 2.9 36.3 + - + +
720D TYR* 3.4 39.3 - - + -
722D GLU* 2.9 30.1 - - + +
723D PRO* 1.3 77.7 - - - +
725D LEU* 1.3 72.3 + - - +
726D LYS* 5.5 0.2 - - - -
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Residues in contact with LEU 725 (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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710D LEU 3.5 7.0 - - - +
711D ASN* 4.8 2.7 - - - +
723D PRO 4.4 6.5 - - - +
724D LYS* 1.3 86.8 - - - +
726D LYS* 1.3 61.1 + - - +
727D ILE* 3.7 18.6 + - + +
746D LYS* 3.8 33.2 - - + +
749D ILE* 4.5 9.9 - - + -
750D ARG* 3.6 43.5 - - + +
753D LEU* 5.0 7.6 - - + -
754D GLN* 4.4 10.5 - - - +
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Residues in contact with LYS 726 (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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626D TYR* 4.9 2.4 + - - -
687D ALA* 5.8 1.4 - - - +
708D TYR* 3.6 32.5 + - + +
709D ALA* 3.1 4.3 - - - -
710D LEU* 2.9 54.2 + - + +
712D VAL* 3.9 9.4 - - + -
715D MET* 4.0 24.2 - - + +
724D LYS 3.7 0.6 + - - -
725D LEU* 1.3 72.5 - - - +
727D ILE* 1.3 60.2 + - - +
728D MET* 4.1 14.1 - - + -
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Residues in contact with ILE 727 (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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708D TYR 3.5 1.6 - - - -
709D ALA* 4.2 5.8 - - + -
725D LEU* 3.7 24.2 + - + +
726D LYS* 1.3 78.4 - - - +
728D MET* 1.3 81.6 + - - +
729D GLY 4.3 0.2 + - - -
730D LEU* 3.1 43.3 - - + +
732D THR* 4.3 15.3 - - + +
746D LYS* 5.2 11.2 - - + -
749D ILE* 3.5 33.4 - - + -
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Residues in contact with MET 728 (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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284D ASN* 5.9 11.7 - - + +
706D LYS* 3.7 6.5 - - + +
707D ARG* 3.1 5.2 - - - -
708D TYR* 2.8 77.4 + - + +
726D LYS* 4.1 14.5 + - + -
727D ILE* 1.3 100.1 - - - +
729D GLY* 1.3 60.9 + - - +
730D LEU 3.2 4.4 + - - -
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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