Contacts of the strand formed by residues 584 - 592 (chain E) in PDB entry 2JJD
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 VAL 584 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264D GLU* 5.1 11.2 - - + +
265D ASP* 6.2 1.6 - - + -
276D LYS* 3.8 32.3 - - + -
292D LEU* 3.4 19.8 - - + +
515E TRP* 3.8 1.1 - - - -
570E LEU* 3.6 29.8 - - + -
571E VAL 3.4 10.3 - - - +
572E THR* 3.6 16.2 - - + -
581E GLY 4.4 6.8 - - - +
582E GLU* 3.4 5.1 + - - +
583E GLN* 1.3 82.6 + - + +
585E ARG* 1.3 71.4 + - - +
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Residues in contact with ARG 585 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D LEU* 3.9 4.7 - - - -
514E ILE* 5.5 2.0 - - - -
515E TRP* 3.1 69.2 + - + +
518E LYS* 3.4 35.7 - - - +
519E SER 4.9 5.6 - - - -
520E HIS* 3.4 34.0 + - + +
570E LEU* 3.5 4.5 - - - +
571E VAL* 2.7 43.4 + - + +
582E GLU* 4.1 18.2 + - - +
584E VAL* 1.3 77.8 + - - +
586E VAL* 1.3 66.2 + - - +
587E VAL* 3.9 4.5 - - + -
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Residues in contact with VAL 586 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D CYS* 4.8 2.5 - - - -
289D ALA* 6.1 0.4 - - + -
290D PRO* 3.6 44.0 - - + +
291D ARG* 4.7 1.8 - - - -
292D LEU* 3.7 33.9 - - + +
520E HIS* 3.9 20.2 - - - +
568E ASP* 4.9 1.8 - - + +
569E PHE 3.2 14.8 - - - +
570E LEU* 4.0 12.6 - - + -
585E ARG* 1.3 76.2 - - - +
587E VAL* 1.3 65.7 + - - +
588E ARG* 4.2 1.9 + - + +
617E GLN* 5.5 2.9 + - - -
621E THR* 6.1 0.5 - - - -
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Residues in contact with VAL 587 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511E TRP* 4.6 3.8 - - + -
514E ILE* 4.3 9.9 - - + -
519E SER 4.1 18.4 - - - +
520E HIS* 3.5 12.1 - - + +
522E ILE* 3.6 34.5 - - + -
568E ASP* 3.5 3.1 - - - -
569E PHE* 2.8 46.1 + - + -
571E VAL* 3.3 31.4 - - + -
585E ARG* 3.9 8.7 + - + -
586E VAL* 1.3 78.0 - - - +
588E ARG* 1.3 63.7 - - - +
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Residues in contact with ARG 588 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D LYS* 3.9 12.5 - - - +
289D ALA* 3.2 37.5 - - - +
520E HIS 2.9 12.9 + - - +
521E THR* 3.3 4.9 - - - +
522E ILE 2.9 26.5 + - - +
566E ILE* 3.5 34.6 - - + +
567E ARG 3.2 4.5 - - - +
568E ASP* 2.8 42.2 + - - +
586E VAL* 5.3 1.3 - - + +
587E VAL* 1.3 76.0 - - - +
589E GLN* 1.3 60.4 + - - +
590E PHE* 3.8 26.0 - - + -
617E GLN* 3.0 35.7 + - + +
620E GLN* 6.0 0.2 + - - -
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Residues in contact with GLN 589 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522E ILE* 3.4 18.2 - - + +
524E MET* 3.0 21.1 - - + +
539E TYR* 2.8 39.9 + - - +
540E TRP* 3.3 10.0 - - - -
565E SER 3.7 0.5 - - - +
566E ILE* 3.6 6.1 - - - +
567E ARG* 2.7 73.3 + - + +
569E PHE* 3.7 24.0 - - + -
587E VAL 4.2 0.4 - - - -
588E ARG* 1.3 71.9 - - - +
590E PHE* 1.3 68.2 + - - +
591E HIS 3.7 0.9 + - - -
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Residues in contact with PHE 590 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521E THR* 3.7 27.8 - - + -
522E ILE 2.8 13.3 + - - +
523E VAL* 3.6 6.1 - - + +
524E MET 2.9 25.5 + - - +
564E ILE* 4.5 4.0 - - + -
565E SER 4.2 2.2 - - - -
566E ILE* 3.7 37.7 - - + -
588E ARG* 3.8 22.7 - - + -
589E GLN* 1.3 73.5 - - - +
591E HIS* 1.3 59.3 + - - +
592E PHE* 3.5 5.2 + - - +
610E LEU* 4.0 19.5 - - + -
613E ALA* 3.8 28.0 - - + -
614E VAL* 3.5 23.6 - - + -
617E GLN* 3.8 21.3 - - + -
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Residues in contact with HIS 591 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524E MET* 3.2 31.9 - - + +
526E THR 3.0 27.5 + - - -
527E GLU* 4.0 10.7 - - + -
528E VAL* 5.2 2.7 - - + -
540E TRP* 3.9 11.2 - + - -
564E ILE* 3.5 2.4 - - - +
565E SER* 3.0 40.9 + - - +
567E ARG* 3.2 40.2 + - - +
589E GLN* 3.7 1.7 + - + -
590E PHE* 1.3 69.3 - - - +
592E PHE* 1.3 68.7 + - - +
593E HIS* 3.5 28.1 + + - -
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Residues in contact with PHE 592 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524E MET 2.8 18.1 + - - +
525E LEU* 4.0 17.7 - - + +
526E THR 4.0 7.3 - - - +
563E ALA* 4.3 5.6 - - + -
564E ILE* 3.9 21.8 - - + -
590E PHE 3.5 2.1 + - - +
591E HIS* 1.3 83.0 - - - +
593E HIS* 1.3 60.0 + - - +
594E GLY* 3.4 40.4 - - - -
595E TRP* 3.8 15.4 + + + +
601E PRO* 5.5 1.3 - - + -
606E GLY* 3.7 30.1 - - - -
607E MET* 3.3 33.7 - - + -
610E LEU* 3.5 28.9 - - + -
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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