Contacts of the strand formed by residues 806 - 814 (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 TRP 806 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603A ALA* 5.1 4.5 - - + -
604A LEU 3.2 20.6 - - - +
605A ASP* 3.9 18.8 - - + -
606A THR* 4.3 1.6 - - - +
779B PRO* 4.1 26.5 - - + -
780B GLU 5.2 0.7 - - - -
782B TRP* 3.5 42.6 - + - -
799B LEU* 3.8 16.9 - - + +
800B PRO* 3.4 32.3 - - + -
801B ASP 4.6 1.1 - - - -
802B SER* 3.9 17.3 - - - -
804B THR 4.2 5.6 - - - -
805B THR* 1.3 75.2 + - - +
807B GLU* 1.3 59.3 + - - +
808B ILE* 5.7 1.1 - - + -
826B GLN* 3.7 4.3 - - - -
827B LEU* 2.7 57.1 + - + +
829B VAL* 3.5 24.3 - - + +
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Residues in contact with GLU 807 (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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603A ALA* 3.5 1.1 - - - -
604A LEU* 3.0 35.9 + - + +
605A ASP 5.6 2.3 - - - +
606A THR* 5.7 6.7 - - - +
609A TYR* 3.8 30.6 - - - +
618A PRO* 5.4 0.9 - - - +
806B TRP* 1.3 74.9 - - - +
808B ILE* 1.3 63.2 + - - +
809B HIS* 3.2 30.2 + - + +
824B PRO* 3.7 14.7 - - + +
825B VAL 3.3 7.2 - - - +
826B GLN* 2.9 34.1 + - - +
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Residues in contact with ILE 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A LEU* 4.1 10.8 - - + +
589A LEU* 4.1 28.5 - - + -
601A LEU* 4.7 2.5 - - + -
602A GLY 3.3 9.2 - - - +
603A ALA* 4.1 12.8 - - + -
782B TRP* 4.5 8.7 - - + -
783B LEU* 4.0 25.1 - - + -
797B LEU* 5.6 1.3 - - + -
806B TRP* 5.5 1.8 - - + +
807B GLU* 1.3 75.2 - - - +
809B HIS* 1.3 73.6 + - - +
824B PRO* 3.4 6.8 - - - +
825B VAL* 2.9 36.9 + - + +
827B LEU* 3.7 37.0 - - + -
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Residues in contact with HIS 809 (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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159A ARG* 6.2 0.2 - - - -
573A LEU* 4.0 4.7 - - - -
601A LEU* 3.4 9.9 - - - +
602A GLY* 2.6 38.9 + - - +
604A LEU* 4.4 18.9 - - + +
609A TYR* 6.4 0.4 - + - -
618A PRO* 3.6 33.5 - - + +
619A LEU 4.6 8.7 + - - -
807B GLU* 3.2 39.2 + - + +
808B ILE* 1.3 80.6 - - - +
810B GLY* 1.3 58.9 + - - +
821B VAL* 6.1 1.0 - - - +
822B ALA 5.3 4.4 + - - +
824B PRO* 3.7 26.7 - - + +
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Residues in contact with GLY 810 (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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571A LEU* 3.7 7.2 - - - -
573A LEU* 4.0 5.0 - - - +
600A ALA 3.4 7.9 - - - -
601A LEU* 3.9 11.7 - - - -
809B HIS* 1.3 78.8 - - - +
811B LEU* 1.3 69.4 + - - +
821B VAL* 3.7 1.6 - - - +
822B ALA* 2.8 39.4 + - - +
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Residues in contact with LEU 811 (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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144A GLN* 3.6 32.3 - - - +
159A ARG* 5.5 0.7 - - - +
161A PHE* 3.6 24.5 - - + -
571A LEU* 3.7 3.3 - - - +
598A LEU 3.3 2.1 - - - +
599A VAL* 3.2 3.3 - - - +
600A ALA* 2.7 46.7 + - + +
619A LEU* 4.4 17.5 - - + -
809B HIS* 6.5 0.2 - - + -
810B GLY* 1.3 81.1 - - - +
812B SER* 1.3 60.7 + - - +
813B LEU* 4.2 6.4 - - + +
819B LEU* 4.2 16.6 - - + -
820B CYS 3.4 2.5 - - - +
821B VAL* 3.7 35.7 - - + -
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Residues in contact with SER 812 (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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570A LYS 5.4 0.4 - - - -
571A LEU* 3.5 34.0 - - - +
593A THR* 3.5 12.0 + - - -
597A ALA* 3.4 20.3 - - - +
598A LEU 3.6 3.6 - - - -
599A VAL* 4.4 3.9 - - - +
811B LEU* 1.3 71.4 - - - +
813B LEU* 1.3 63.0 + - - +
814B SER* 4.0 2.5 + - - -
818B GLY 3.3 2.9 + - - +
819B LEU* 3.2 8.3 - - - +
820B CYS* 2.8 43.4 + - - -
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Residues in contact with LEU 813 (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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161A PHE* 3.7 39.9 - - + -
163A LEU* 3.7 30.3 - - + -
169A PRO* 4.9 10.3 - - + -
195A SER 5.4 3.1 - - - +
196A SER* 5.5 4.7 - - - +
197A ILE* 6.1 1.6 - - + -
597A ALA* 3.3 3.6 - - - +
598A LEU* 2.9 57.6 + - + +
600A ALA* 5.4 0.4 - - + -
811B LEU* 4.2 8.1 - - + +
812B SER* 1.3 77.4 + - - +
814B SER* 1.3 59.6 + - - +
815B LYS* 4.4 0.5 + - - +
818B GLY 4.8 0.2 - - - -
819B LEU* 3.7 32.8 - - + +
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Residues in contact with SER 814 (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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169A PRO* 3.3 10.6 - - - +
593A THR* 5.8 0.4 - - - -
595A SER* 2.5 29.1 + - - -
596A LEU* 3.8 4.9 + - - +
597A ALA* 4.0 9.9 - - - -
812B SER* 5.0 2.5 - - - -
813B LEU* 1.3 75.0 - - - +
815B LYS* 1.3 63.7 + - - +
816B THR* 3.5 5.0 + - - -
817B LYS* 3.3 22.8 + - - -
818B GLY* 2.9 38.9 + - - -
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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