Contacts of the strand formed by residues 463 - 471 (chain E) in PDB entry 1P8J
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 LYS 463 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461E ILE* 3.2 1.1 + - - -
462E GLY* 1.3 73.5 - - - -
464E ARG* 1.3 66.0 + - + +
552E GLU* 3.6 2.0 - - - +
553E ASN* 2.9 61.1 + - + +
554E THR 4.9 1.6 - - - -
555E SER 3.2 18.2 + - - +
556E GLU* 4.4 10.1 + - - +
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Residues in contact with ARG 464 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460E ASP 5.0 0.9 - - - +
461E ILE 3.2 9.7 + - - +
463E LYS* 1.3 87.2 - - + +
465E LEU* 1.3 78.2 + - - +
466E GLU* 3.2 34.6 + - + +
550E GLU* 3.7 27.2 + - - +
551E ILE 3.4 13.2 - - - -
552E GLU* 3.8 20.7 + - + -
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Residues in contact with LEU 465 (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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459E LYS* 3.8 39.0 - - + +
460E ASP 3.9 18.2 - - - +
461E ILE* 4.0 20.4 - - + +
464E ARG* 1.3 80.9 + - - +
466E GLU* 1.3 76.0 + - - +
467E VAL* 4.2 7.0 - - + -
549E LEU 3.8 0.6 - - - +
550E GLU* 3.6 3.3 - - - -
551E ILE* 2.8 46.3 + - + +
563E LEU* 4.0 29.2 - - + -
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Residues in contact with GLU 466 (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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459E LYS* 4.2 5.7 + - - -
464E ARG* 3.2 30.4 + - - +
465E LEU* 1.3 83.5 - - - +
467E VAL* 1.3 66.4 + - - +
468E ARG* 2.4 47.9 + - + +
548E VAL* 3.7 19.2 - - + +
549E LEU 3.3 3.6 - - - +
550E GLU* 4.3 5.7 - - + +
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Residues in contact with VAL 467 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454E ILE* 3.8 28.9 - - + +
455E LEU* 4.2 22.2 - - + -
459E LYS* 4.1 20.6 - - - +
465E LEU* 4.2 16.2 - - + -
466E GLU* 1.3 76.3 - - - +
468E ARG* 1.3 65.7 + - - +
547E TRP 3.7 1.0 - - - +
548E VAL* 3.3 3.5 - - - -
549E LEU* 2.8 49.6 + - + +
563E LEU* 4.2 11.4 - - + -
566E PHE* 4.3 6.8 - - + -
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Residues in contact with ARG 468 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459E LYS* 5.6 0.4 - - - +
466E GLU* 2.4 55.7 + - + +
467E VAL* 1.3 81.7 - - - +
469E LYS* 1.3 67.0 + - - +
546E GLU* 2.9 41.0 + - - +
547E TRP 3.3 4.9 - - - +
548E VAL* 3.8 19.4 - - + +
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Residues in contact with LYS 469 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452E VAL* 5.5 1.8 - - + -
453E GLU 5.5 3.6 - - - +
454E ILE* 3.7 54.3 - - + +
467E VAL 4.3 0.2 + - - -
468E ARG* 1.3 80.0 - - - +
470E ALA* 1.3 81.6 + - - +
471E VAL* 3.5 5.5 + - + +
546E GLU* 4.2 6.1 - - - +
547E TRP* 2.8 37.5 + - + +
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Residues in contact with ALA 470 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475C LEU* 4.4 18.6 - - + -
480C HIS* 4.8 9.4 - - + +
482C THR* 6.3 0.7 - - + -
469E LYS* 1.3 93.8 - - - +
471E VAL* 1.3 60.8 + - - +
472E THR* 4.3 2.2 + - - +
545E GLY 3.6 6.3 - - - +
546E GLU* 4.1 9.4 + - + +
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Residues in contact with VAL 471 (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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475C LEU* 3.3 5.2 - - - +
452E VAL* 4.4 19.3 - - + -
454E ILE* 4.3 16.8 - - + -
469E LYS* 3.8 7.4 - - + +
470E ALA* 1.3 77.9 - - - +
472E THR* 1.3 62.8 + - - +
473E ALA* 3.3 19.1 - - - +
543E PRO 4.4 2.0 - - - +
544E ALA* 3.5 4.0 - - - -
545E GLY 2.7 40.2 + - - +
547E TRP* 3.5 26.9 - - + +
568E LEU* 4.2 10.5 - - + -
570E LEU* 4.3 16.2 - - + -
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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