Contacts of the strand formed by residues 908 - 917 (chain B) in PDB entry 5JPM
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 ALA 908 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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905B ALA* 5.6 0.2 - - - +
907B ALA* 1.3 83.3 - - + +
909B VAL* 1.3 65.2 + - - +
910B SER 4.3 0.4 + - - -
930B VAL* 4.0 12.6 - - + -
931B LEU 3.7 7.0 - - - +
932B GLN* 3.8 29.6 - - - +
933B ILE* 4.1 2.6 - - - +
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Residues in contact with VAL 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B VAL* 3.7 38.8 - - + -
873B GLU 4.0 14.4 - - - +
874B GLY* 4.8 0.9 - - - -
875B LEU* 3.8 23.8 - - + -
905B ALA* 4.4 12.1 - - + -
908B ALA* 1.3 79.0 - - - +
910B SER* 1.3 62.0 + - - +
911B LEU* 3.6 2.3 + - - +
930B VAL* 4.3 2.7 - - - -
931B LEU* 2.8 44.8 + - + +
933B ILE* 4.0 21.3 - - + +
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Residues in contact with SER 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B VAL* 4.0 20.0 - - - +
908B ALA 4.3 0.4 + - - -
909B VAL* 1.3 72.8 - - - +
911B LEU* 1.3 58.8 + - - +
912B LYS* 4.2 1.2 + - - +
928B SER* 4.6 10.3 - - - -
929B LYS 3.4 7.6 - - - -
930B VAL* 4.0 21.5 - - - +
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Residues in contact with LEU 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837B LEU* 3.7 24.6 - - + +
839B LEU* 4.2 11.4 - - + -
851B LEU* 4.1 29.2 - - + -
869B VAL* 4.5 11.4 - - + -
870B SER 5.7 0.4 - - - -
872B VAL* 4.8 6.1 - - + -
875B LEU* 4.2 25.1 - - + -
901B VAL* 6.0 0.7 - - + -
909B VAL 3.6 2.1 + - - +
910B SER* 1.3 74.7 - - - +
912B LYS* 1.3 60.8 + - - +
913B VAL* 4.1 10.3 - - + -
927B VAL 4.0 0.7 - - - +
928B SER* 3.4 1.8 - - - -
929B LYS 2.9 33.7 + - - +
931B LEU* 4.0 34.5 - - + -
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Residues in contact with LYS 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869B VAL* 3.5 4.4 - - - +
870B SER* 2.8 47.4 + - - +
910B SER 4.2 1.5 + - - +
911B LEU* 1.3 74.9 - - - +
913B VAL* 1.3 64.6 + - - +
914B VAL* 3.8 23.8 - - + -
926B ALA* 3.9 16.8 - - - +
927B VAL 3.4 10.8 - - - +
928B SER* 3.9 20.2 - - - +
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Residues in contact with VAL 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B LEU* 3.6 20.1 - - + +
837B LEU* 3.8 34.8 - - + -
851B LEU* 4.8 1.6 - - + -
853B PRO* 4.2 22.7 - - + -
867B VAL* 5.3 4.0 - - + -
868B HIS 3.6 13.5 - - - +
869B VAL* 4.1 18.4 - - + +
899B PHE* 4.7 4.3 - - + -
911B LEU* 4.1 8.1 - - + -
912B LYS* 1.3 75.5 - - - +
914B VAL* 1.3 65.8 + - - +
915B ALA* 5.8 0.2 - - + -
926B ALA* 3.3 6.4 - - - +
927B VAL* 2.9 33.8 + - + +
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Residues in contact with VAL 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867B VAL* 3.3 2.4 - - - +
868B HIS* 2.7 67.9 + - + +
870B SER* 3.6 23.6 - - - +
912B LYS* 3.8 22.7 - - + -
913B VAL* 1.3 76.2 - - - +
915B ALA* 1.3 68.8 + - - +
916B ARG* 5.1 4.5 - - + +
925B ASP 4.2 1.6 - - - -
926B ALA* 4.3 6.5 - - + -
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Residues in contact with ALA 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833B PHE* 4.1 15.5 - - + -
835B LEU* 4.2 11.2 - - + -
855B LEU* 4.3 2.7 - - + -
865B VAL* 3.9 9.0 - - + -
866B SER 3.6 4.0 - - - -
867B VAL* 3.7 21.3 - - + -
913B VAL* 4.2 0.4 - - + -
914B VAL* 1.3 77.7 - - - +
916B ARG* 1.3 61.8 + - - +
924B GLY* 3.2 3.6 - - - -
925B ASP 2.9 40.1 + - - +
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Residues in contact with ARG 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865B VAL* 3.8 4.6 - - - +
866B SER* 2.8 43.0 + - - +
868B HIS* 6.1 1.8 - - + -
914B VAL* 5.3 6.3 - - + -
915B ALA* 1.3 76.2 - - - +
917B GLY* 1.3 74.6 + - - +
918B SER 3.6 0.3 + - - -
921B PHE 5.7 0.4 - - - +
922B PRO 6.4 0.2 - - - -
923B VAL 3.9 6.5 - - - +
924B GLY* 4.2 1.3 - - - -
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Residues in contact with GLY 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863B LEU* 4.7 2.0 - - - -
864B THR 3.8 9.6 - - - -
865B VAL* 4.3 6.1 - - - +
916B ARG* 1.3 87.0 + - - +
918B SER* 1.3 67.7 + - - +
919B PHE 4.3 1.9 - - - +
921B PHE 3.4 11.3 - - - +
923B VAL* 2.8 37.0 + - - -
924B GLY* 4.4 0.2 - - - -
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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