Contacts of the strand formed by residues 838 - 841 (chain M) in PDB entry 5D4C
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 LYS 838 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564M MET* 4.5 1.2 - - - -
567M GLN* 4.4 3.8 + - - -
836M GLY 3.8 0.6 + - - +
837M ASP* 1.3 73.2 - - - +
839M LEU* 1.3 70.1 + - - +
846M LYS* 3.9 15.7 - - - +
847M GLY 3.8 9.4 - - - +
848M VAL* 4.1 12.8 - - + -
996M LYS* 3.7 2.4 - - - +
997M LEU* 2.9 56.1 + - + +
999M HIS* 3.4 49.2 + - + +
741N ASP 3.4 21.8 - - - +
742N GLY* 4.8 5.8 - - - -
1605N C 3.0 25.3 + - - -
1608N ATP 3.6 9.8 + - - +
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Residues in contact with LEU 839 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688M ILE* 4.1 20.2 - - + +
690M ILE* 4.1 15.9 - - + -
700M TYR* 4.6 10.5 - - + -
833M LEU* 4.1 28.5 - - + -
837M ASP 4.4 0.2 - - - +
838M LYS* 1.3 82.0 - - - +
840M ALA* 1.3 64.0 + - - +
846M LYS* 3.4 1.6 - - - +
847M GLY 2.9 37.4 + - - +
849M VAL* 3.6 29.4 - - + -
869M VAL* 5.3 3.1 - - + -
994M ILE* 3.9 17.0 - - + -
995M MET 3.3 6.3 - - - +
996M LYS* 3.9 20.2 - - + -
997M LEU* 4.6 1.1 - - - -
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Residues in contact with ALA 840 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564M MET* 3.8 19.3 - - + -
688M ILE* 5.9 0.4 - - - -
839M LEU* 1.3 77.3 - - - +
841M ASN* 1.3 62.7 + - - +
845M ASN 3.3 11.4 - - - +
846M LYS* 3.8 2.9 - - + -
994M ILE* 4.1 4.7 - - - -
995M MET* 2.9 44.4 + - + +
997M LEU* 3.7 26.7 - - + -
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Residues in contact with ASN 841 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561M GLY* 4.2 5.7 - - - -
564M MET* 4.3 0.7 - - - +
840M ALA* 1.3 81.5 - - - +
842M ARG* 1.3 64.6 + - - +
843M HIS* 3.0 15.9 + - + -
844M GLY 3.3 5.0 + - - -
845M ASN* 2.9 42.3 + - - +
871M LEU* 4.8 0.8 - - - +
884M GLN* 2.8 33.9 + - - +
992M MET* 3.5 27.8 - - + -
993M PHE 3.5 19.5 - - - +
994M ILE* 4.3 4.0 - - + +
995M MET* 4.0 6.7 - - - +
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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