Contacts of the helix formed by residues 493 - 504 (chain B) in PDB entry 4P0S
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 SER 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487B GLN* 3.6 4.9 - - - +
492B VAL* 1.3 74.8 - - - +
494B LEU* 1.3 60.1 + - - +
495B GLU* 3.7 8.1 + - - +
496B MET* 3.5 23.8 + - - +
497B ALA* 2.8 30.3 + - - +
51L C 3.2 31.0 + - - -
52L A 2.6 18.2 + - - -
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Residues in contact with LEU 494 (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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483B ARG* 3.2 37.7 - - - +
487B GLN* 3.3 17.1 - - - +
493B SER* 1.3 73.7 - - - +
495B GLU* 1.3 64.7 + - + +
497B ALA* 3.6 3.5 - - - +
498B SER* 2.8 45.5 + - - +
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Residues in contact with GLU 495 (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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493B SER* 3.3 6.3 + - - +
494B LEU* 1.3 87.9 - - + +
496B MET* 1.3 68.5 + - - +
498B SER* 3.7 4.9 + - - -
499B ALA* 3.4 20.8 + - - +
532B VAL* 3.8 20.9 - - + +
533B ARG* 3.5 47.2 + - + +
534B ARG* 4.6 5.1 + - - -
51L C 3.7 25.2 + - - +
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Residues in contact with MET 496 (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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491B ARG 4.5 4.0 - - - +
492B VAL* 4.8 4.3 - - + -
493B SER* 3.5 16.2 + - - +
495B GLU* 1.3 76.4 - - - +
497B ALA* 1.3 64.0 + - - +
499B ALA* 3.3 12.7 + - - +
500B VAL* 3.3 18.9 + - + +
532B VAL* 4.3 9.2 - - + -
541B THR* 4.1 11.0 - - + -
544B ARG 4.5 11.7 - - - +
545B ILE* 3.8 28.5 - - + +
549B LEU* 4.0 22.4 - - + -
50L G 3.9 3.6 - - - +
51L C 3.3 45.8 - - - +
52L A 4.2 6.3 - - - -
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Residues in contact with ALA 497 (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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483B ARG* 4.0 19.7 - - + +
486B ILE* 4.0 17.2 - - + +
487B GLN* 3.8 21.3 - - + -
492B VAL* 4.1 2.0 - - + +
493B SER 2.8 20.8 + - - +
494B LEU* 3.6 5.4 - - - +
495B GLU 3.3 0.2 - - - -
496B MET* 1.3 79.4 - - - +
498B SER* 1.3 62.7 + - - +
500B VAL* 3.5 2.3 + - - +
501B VAL* 3.3 26.0 + - - +
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ARG* 3.7 23.3 - - - +
494B LEU* 2.8 30.6 + - - +
495B GLU* 4.1 5.6 - - - -
497B ALA* 1.3 72.4 - - - +
499B ALA* 1.3 59.1 + - - +
501B VAL* 3.1 5.9 + - - +
502B ASN* 2.9 41.9 + - - -
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Residues in contact with ALA 499 (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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495B GLU 3.4 11.3 + - - +
496B MET* 3.4 11.7 - - - +
498B SER* 1.3 77.2 - - - +
500B VAL* 1.3 66.8 + - - +
502B ASN* 3.6 15.9 + - - +
503B ALA* 3.7 8.8 + - - +
530B ILE* 3.9 23.0 - - + +
531B GLN 3.9 22.9 - - - +
532B VAL* 4.7 6.3 - - + -
545B ILE* 4.8 2.5 - - + -
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Residues in contact with VAL 500 (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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482B TRP* 6.2 2.7 - - + -
486B ILE* 4.4 26.7 - - + -
496B MET 3.3 14.3 + - - +
497B ALA 4.0 5.6 - - - +
498B SER 3.4 0.2 - - - -
499B ALA* 1.3 77.7 - - - +
501B VAL* 1.3 63.0 + - - +
503B ALA* 3.6 6.2 + - - +
504B TYR* 3.5 21.5 + - + +
510B LEU* 5.9 5.4 - - + -
527B LEU* 3.8 28.3 - - + -
530B ILE* 4.5 8.1 - - + -
545B ILE* 4.4 18.4 - - + -
549B LEU* 6.1 0.7 - - + -
553B ILE* 4.1 23.6 - - + -
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Residues in contact with VAL 501 (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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479B ALA 4.9 4.0 - - - +
482B TRP* 3.8 24.2 - - + +
483B ARG* 3.5 36.8 - - + +
486B ILE* 3.6 17.5 - - + -
497B ALA 3.3 13.2 + - - +
498B SER* 3.1 10.9 + - - +
500B VAL* 1.3 74.0 - - + +
502B ASN* 1.3 67.5 + - - +
503B ALA 3.2 2.0 - - - -
504B TYR 3.2 24.7 - - - -
505B PRO* 3.2 8.8 - - + +
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Residues in contact with ASN 502 (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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498B SER* 2.9 33.5 + - - +
499B ALA* 4.0 9.1 - - - +
500B VAL 3.5 0.4 - - - -
501B VAL* 1.3 74.8 - - - +
503B ALA* 1.3 62.0 + - - +
504B TYR 3.8 0.2 + - - -
505B PRO* 4.1 10.0 - - - +
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Residues in contact with ALA 503 (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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499B ALA 3.7 8.1 + - - +
500B VAL 3.6 7.4 + - - +
501B VAL 3.2 0.6 - - - -
502B ASN* 1.3 78.9 - - - +
504B TYR* 1.3 90.9 + - + +
505B PRO* 3.7 5.4 - - - +
509B LEU* 5.8 0.3 - - - +
530B ILE* 4.3 14.4 - - + -
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Residues in contact with TYR 504 (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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482B TRP* 2.8 21.9 + - + -
500B VAL* 3.5 12.3 + - + +
501B VAL* 3.2 6.7 + - - +
503B ALA* 1.3 100.3 - - + +
505B PRO* 1.3 51.4 - - - -
506B SER 2.6 22.9 + - - +
509B LEU* 3.8 26.0 - - + -
510B LEU* 4.0 24.7 - - + -
513B ALA* 3.7 21.0 - - + +
526B LEU* 3.4 27.4 + - + +
527B LEU* 3.9 24.2 - - + -
530B ILE* 5.1 1.1 - - + -
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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