Contacts of the strand formed by residues 988 - 994 (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 GLY 988 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483M ASP* 3.9 7.0 + - - +
837N ASP 3.2 19.7 - - - -
838N SER* 4.6 1.1 - - - -
839N MET* 3.9 12.1 - - - +
979N LYS* 3.9 2.0 - - - +
980N PHE* 2.7 32.5 + - - +
986N GLN 3.6 1.3 + - - -
987N LYS* 1.3 75.2 - - - +
989N THR* 1.3 64.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 989 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352M VAL* 4.7 4.1 - - + +
353M ILE 4.5 4.7 + - - -
354M SER* 4.9 1.2 - - - -
482M PHE* 2.8 31.6 + - - +
483M ASP 3.7 1.1 - - - -
484M GLY* 3.2 23.6 - - - +
837N ASP 3.5 5.5 + - - -
838N SER* 2.8 11.8 - - - -
839N MET* 2.8 23.8 + - - -
976N ILE 4.7 0.2 + - - -
977N GLY* 3.9 14.0 - - - +
978N ASP 3.2 16.6 - - - +
979N LYS* 4.0 10.3 - - + -
980N PHE 4.6 0.2 - - - +
988N GLY* 1.3 76.7 - - - +
990N ILE* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 990 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354M SER* 4.2 6.9 - - - -
838N SER* 4.3 0.5 - - - -
839N MET* 3.2 14.8 - - + +
841N MET* 3.7 27.8 - - + -
846N ILE* 4.9 2.0 - - + -
974N PRO* 4.7 2.2 - - + -
975N GLN 2.8 30.1 - - - +
976N ILE* 2.9 26.4 - - - +
978N ASP* 3.1 11.9 + - + +
980N PHE* 3.6 33.7 - - + -
989N THR* 1.3 87.2 + - - +
991N GLY* 1.3 71.2 + - - +
992N ILE 3.5 24.0 - - - +
993N THR* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 991 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354M SER* 4.5 6.7 - - - -
355M GLY 5.3 0.7 - - - -
469M ARG* 2.5 33.8 + - - -
833N TYR* 4.1 17.5 - - - -
838N SER* 4.9 2.2 - - - -
839N MET 3.0 8.5 + - - -
976N ILE* 3.1 16.2 - - - +
990N ILE* 1.3 75.5 - - - +
992N ILE* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 992 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833N TYR* 3.2 37.0 - - + -
839N MET 4.2 1.0 + - - -
840N ILE* 3.6 7.2 - - + +
841N MET 3.2 21.7 + - - -
976N ILE* 4.0 7.9 - - + -
990N ILE* 3.5 2.9 - - - +
991N GLY* 1.3 81.8 - - - +
993N THR* 1.3 73.5 + - - +
994N TYR* 3.7 27.6 - - + -
66W PRO* 3.4 41.7 - - + -
67W PHE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 993 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465M TYR* 4.8 10.7 + - - -
841N MET* 3.0 13.7 - - + +
843N GLN* 3.2 35.0 + - - +
846N ILE* 4.0 16.4 - - + -
974N PRO 5.3 1.8 - - - +
975N GLN* 5.0 5.2 - - - +
976N ILE* 4.5 14.2 - - + +
990N ILE* 4.6 12.1 - - + -
992N ILE* 1.3 89.1 - - - +
994N TYR* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 994 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830N TYR* 4.8 5.8 - + - -
831N SER* 2.7 41.0 - - - -
833N TYR* 4.2 1.9 - - - -
840N ILE* 3.4 27.1 - - + -
841N MET 3.1 6.3 + - - -
842N ASN* 3.3 3.4 - - - -
843N GLN* 2.3 40.3 + - - +
992N ILE* 3.7 33.1 - - + +
993N THR* 1.3 75.2 - - - +
995N ARG* 1.3 62.5 + - - +
998N ASP* 3.6 30.3 - - + -
999N MET* 3.5 26.9 - - + -
1076N HIS* 4.9 10.0 + + - -
66W PRO* 4.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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