Contacts of the strand formed by residues 838 - 842 (chain N) in PDB entry 2JA7
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 SER 838 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354M SER* 5.5 2.0 - - - -
355M GLY* 5.0 1.0 + - - -
482M PHE* 3.7 22.9 - - - -
833N TYR 3.3 13.7 + - - -
834N ASN* 2.5 41.3 + - - +
835N GLN 2.5 25.3 + - - -
837N ASP* 1.3 75.5 - - - +
839N MET* 1.3 53.9 + - - +
988N GLY 4.5 0.7 - - - -
989N THR* 2.8 21.8 - - - +
990N ILE 4.3 6.3 - - - -
991N GLY* 4.9 1.3 - - - -
1012N ILE* 5.7 1.1 - - - -
1013N ASN 4.9 1.3 + - - -
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Residues in contact with MET 839 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834N ASN* 4.3 1.1 - - - -
838N SER* 1.3 73.5 - - - +
840N ILE* 1.3 65.5 + - - +
980N PHE* 3.1 42.6 - - + +
986N GLN 5.9 1.1 - - - +
988N GLY* 3.9 17.9 - - - +
989N THR 2.8 12.6 + - - +
990N ILE* 3.2 16.4 - - + +
991N GLY* 3.0 25.5 + - - -
1010N LEU* 3.4 44.0 - - + -
1011N ILE 3.9 6.1 - - - +
1012N ILE* 3.9 25.8 - - + +
1092N TYR* 4.3 14.6 - - + -
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Residues in contact with ILE 840 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830N TYR* 3.9 21.3 - - + -
831N SER* 3.0 27.6 - - - +
833N TYR* 4.2 7.6 - - + -
834N ASN* 3.6 31.0 - - + +
839N MET* 1.3 73.4 - - - +
841N MET* 1.3 65.2 + - - +
992N ILE* 3.6 8.7 - - + +
994N TYR* 3.4 30.3 - - + -
999N MET* 4.2 3.4 - - + -
1010N LEU* 3.3 4.2 - - - +
1011N ILE* 2.8 52.6 + - + +
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Residues in contact with MET 841 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839N MET 3.9 1.6 + - - -
840N ILE* 1.3 77.2 - - - +
842N ASN* 1.3 66.1 + - - +
846N ILE* 3.3 34.8 - - + -
850N LEU* 5.3 4.9 - - + -
851N PHE* 3.8 25.4 - - + -
974N PRO* 4.4 4.0 - - - -
980N PHE* 3.2 31.9 - - + -
990N ILE* 3.7 26.0 - - + -
992N ILE 3.2 7.5 + - - -
993N THR* 3.0 26.3 - - + -
994N TYR 3.1 3.3 + - - -
1009N ASP* 3.2 13.9 - - + +
1010N LEU* 3.4 24.5 - - + -
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Residues in contact with ASN 842 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840N ILE 4.2 0.4 + - - -
841N MET* 1.3 68.5 - - - +
843N GLN* 1.3 64.1 + - - +
844N SER* 3.6 5.0 - - - -
845N SER* 2.2 65.6 + - - +
846N ILE* 3.1 15.8 - - - +
848N ARG* 4.4 2.4 - - - +
994N TYR 3.4 12.1 - - - +
995N ARG* 3.8 2.3 - - - -
996N ARG* 3.6 24.9 + - - +
999N MET* 3.9 16.2 - - - +
1007N VAL* 4.8 1.2 - - - +
1008N PRO 3.1 26.5 + - - +
1009N ASP* 2.8 13.0 + - - -
1011N ILE* 6.0 0.2 - - - +
9V SER 4.5 7.5 + - - -
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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
------------------------------------------------------------
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