Contacts of the helix formed by residues 499 - 512 (chain B) in PDB entry 4K9N
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 ASN 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B ALA* 3.4 26.6 + - - +
351B GLY 3.5 4.0 - - - +
353B LEU* 3.5 13.0 - - - +
497B ALA 3.5 0.6 - - - -
498B ASP* 1.3 81.5 + - - +
500B LEU* 1.3 61.3 + - - +
501B GLU* 3.2 14.0 + - - +
502B GLN* 2.9 43.8 + - - +
503B LEU* 2.9 26.5 + - - +
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Residues in contact with LEU 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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345B LYS* 6.4 1.8 - - - +
348B GLN* 4.5 19.3 - - + +
349B ASP 5.3 4.5 + - - +
350B ALA* 5.9 0.4 - - - +
351B GLY 4.6 1.4 + - - -
353B LEU* 3.8 12.2 - - + +
357B THR* 3.7 28.5 - - + -
361B THR* 3.7 15.9 - - - +
499B ASN* 1.3 75.7 - - - +
501B GLU* 1.3 63.4 + - - +
503B LEU* 3.1 8.9 + - + -
504B LYS* 3.0 51.4 + - + +
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Residues in contact with GLU 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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499B ASN* 3.2 11.8 + - - +
500B LEU* 1.3 78.4 - - - +
502B GLN* 1.3 65.3 + - + +
504B LYS* 3.5 9.3 + - - +
505B GLY* 3.2 18.2 + - - -
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Residues in contact with GLN 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LYS* 3.4 30.8 + - - +
497B ALA* 3.7 12.4 - - - -
498B ASP* 2.8 35.4 + - - +
499B ASN* 2.9 34.1 + - - +
501B GLU* 1.3 78.1 - - + +
503B LEU* 1.3 61.0 + - - +
505B GLY* 4.4 1.6 - - - +
506B SER* 2.8 36.1 + - - +
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Residues in contact with LEU 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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353B LEU* 4.0 20.2 - - + -
357B THR 4.5 0.2 - - - +
358B VAL* 4.0 34.3 - - + -
361B THR* 4.0 19.7 - - + +
451B VAL* 5.7 1.3 - - + -
497B ALA* 3.6 12.3 - - + +
499B ASN 2.9 16.5 + - - +
500B LEU* 3.1 9.1 + - + +
502B GLN* 1.3 77.3 - - - +
504B LYS* 1.3 64.7 + - - +
506B SER* 3.9 0.4 - - - -
507B LEU* 2.9 47.3 + - + +
519B ILE* 5.1 3.6 - - + -
521B VAL* 4.1 27.1 - - + -
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Residues in contact with LYS 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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361B THR* 4.3 15.9 + - + +
365B MET* 3.5 20.4 - - + +
500B LEU* 3.0 51.8 + - + +
501B GLU* 3.8 7.9 - - - +
503B LEU* 1.3 76.8 - - - +
505B GLY* 1.3 57.1 + - - +
508B GLN* 3.0 28.9 + - - +
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Residues in contact with GLY 505 (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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501B GLU 3.2 12.1 + - - -
502B GLN* 3.8 2.9 - - - -
504B LYS* 1.3 77.3 - - - +
506B SER* 1.3 58.5 + - - +
508B GLN* 3.4 12.9 + - - +
509B GLU* 3.0 30.0 + - - +
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Residues in contact with SER 506 (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 LEU* 3.5 22.0 - - - +
496B LYS 3.0 21.5 + - - -
497B ALA* 4.6 0.4 - - - -
502B GLN* 2.8 23.2 + - - -
503B LEU* 3.9 3.4 - - - -
505B GLY* 1.3 72.5 - - - +
507B LEU* 1.3 58.3 + - - +
509B GLU* 3.3 2.8 + - - -
510B ALA* 2.8 30.5 + - - +
519B ILE* 3.9 25.8 - - - -
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B THR* 3.7 30.5 - - + -
362B LEU* 3.8 37.2 - - + +
365B MET* 3.9 12.1 - - + -
423B ILE* 5.8 1.6 - - + -
449B ILE* 5.3 4.5 - - + -
451B VAL* 4.7 7.6 - - + -
503B LEU* 2.9 35.4 + - + +
504B LYS 3.9 2.9 - - - +
506B SER* 1.3 73.8 - - - +
508B GLN* 1.3 60.2 + - - +
510B ALA* 3.8 3.0 - - + +
511B LEU* 2.9 47.4 + - + +
519B ILE* 3.7 20.2 - - + -
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Residues in contact with GLN 508 (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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365B MET* 3.6 14.8 - - + +
504B LYS 3.0 18.6 + - - +
505B GLY* 3.6 11.3 - - - +
506B SER 3.3 0.2 - - - -
507B LEU* 1.3 77.9 - - - +
509B GLU* 1.3 62.8 + - - +
511B LEU* 3.5 5.0 + - - +
512B SER* 3.3 21.4 + - - +
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Residues in contact with GLU 509 (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 GLN* 3.5 22.5 + - - +
495B LEU* 3.8 27.0 - - + +
505B GLY 3.0 17.1 + - - +
506B SER* 3.3 5.3 + - - +
508B GLN* 1.3 77.0 - - - +
510B ALA* 1.3 66.2 + - - +
512B SER* 3.3 8.7 + - - +
513B ALA* 3.1 21.0 + - + +
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Residues in contact with ALA 510 (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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421B GLN* 5.4 0.2 - - - +
449B ILE* 3.7 24.8 - - + +
495B LEU* 4.2 0.8 - - - +
506B SER 2.8 21.7 + - - +
507B LEU* 3.8 4.3 - - + +
509B GLU* 1.3 75.1 - - - +
511B LEU* 1.3 62.3 + - - +
513B ALA* 3.0 18.2 + - - +
515B GLY 5.2 0.2 - - - +
517B VAL* 3.8 27.9 - - + +
519B ILE* 3.8 20.4 - - + -
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Residues in contact with LEU 511 (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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365B MET* 3.6 39.9 - - + +
366B ALA* 4.5 1.3 - - + -
367B PRO* 4.0 24.9 - - + -
421B GLN* 4.2 20.6 - - + +
423B ILE* 4.6 9.6 - - + -
449B ILE* 4.0 19.5 - - + -
507B LEU* 2.9 34.0 + - + +
508B GLN* 4.0 5.4 - - - +
509B GLU 3.3 0.2 - - - -
510B ALA* 1.3 77.0 - - - +
512B SER* 1.3 58.8 + - - +
513B ALA 3.8 2.1 + - - +
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Residues in contact with SER 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B GLN* 3.3 11.4 + - - +
509B GLU* 3.3 12.2 + - - -
511B LEU* 1.3 77.6 - - - +
513B ALA* 1.3 63.5 + - - +
514B LYS* 3.8 3.6 + - - +
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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