Contacts of the helix formed by residues 499 - 513 (chain X) in PDB entry 3F6E
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350X ALA* 3.3 29.0 + - - +
351X GLY 3.4 9.4 - - - +
353X LEU* 3.9 10.0 - - - +
497X ALA* 3.5 0.8 - - - +
498X ASP* 1.3 80.4 + - - +
500X LEU* 1.3 60.5 + - - +
501X GLU* 3.2 12.9 + - - +
502X GLN* 2.9 52.7 + - - +
503X LEU* 2.9 26.5 + - - +
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Residues in contact with LEU 500 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348X GLN* 4.5 15.7 - - + +
349X ASP 5.4 4.2 + - - +
350X ALA* 5.5 0.8 - - - +
351X GLY 4.5 1.0 + - - -
353X LEU* 3.7 12.6 - - + +
357X THR* 3.8 21.5 - - + -
361X THR* 3.7 22.9 - - - +
499X ASN* 1.3 72.3 - - - +
501X GLU* 1.3 68.3 + - - +
503X LEU* 3.1 9.9 + - + -
504X LYS* 2.9 51.8 + - + +
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Residues in contact with GLU 501 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499X ASN* 3.2 12.4 + - - +
500X LEU* 1.3 78.4 - - - +
502X GLN* 1.3 64.1 + - + +
504X LYS* 3.4 9.2 + - - +
505X GLY* 3.1 23.0 + - - -
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Residues in contact with GLN 502 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496X LYS* 3.7 12.1 - - - +
497X ALA* 3.8 11.9 - - - -
498X ASP* 2.8 38.8 + - - +
499X ASN* 2.9 32.1 + - - +
501X GLU* 1.3 79.5 - - + +
503X LEU* 1.3 61.7 + - - +
505X GLY* 4.4 1.8 - - - +
506X SER* 2.8 35.4 + - - +
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Residues in contact with LEU 503 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353X LEU* 3.7 23.6 - - + -
357X THR 4.6 0.2 - - - +
358X VAL* 4.0 31.0 - - + -
361X THR* 4.0 20.4 - - + +
451X VAL* 5.4 2.0 - - + -
497X ALA* 3.5 8.4 - - + +
499X ASN 2.9 13.9 + - - +
500X LEU* 3.1 15.0 + - + +
502X GLN* 1.3 74.8 - - - +
504X LYS* 1.3 57.3 + - - +
506X SER* 3.2 1.5 + - - -
507X LEU* 2.8 51.4 + - + +
519X ILE* 5.0 4.7 - - + -
521X VAL* 3.9 27.8 - - + -
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Residues in contact with LYS 504 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361X THR* 4.2 20.1 + - + +
364X ASP* 4.9 8.7 + - - +
365X MET* 3.6 20.9 - - + +
500X LEU* 2.9 50.7 + - + +
501X GLU* 3.8 6.5 - - - +
503X LEU* 1.3 78.7 - - - +
505X GLY* 1.3 56.9 + - - +
507X LEU 3.4 0.3 + - - -
508X GLN* 3.0 29.1 + - - +
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Residues in contact with GLY 505 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501X GLU 3.1 14.8 + - - -
502X GLN* 3.9 2.5 - - - -
504X LYS* 1.3 77.1 - - - +
506X SER* 1.3 58.1 + - - +
508X GLN* 3.3 10.2 + - - +
509X GLU* 3.0 29.9 + - - +
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Residues in contact with SER 506 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495X LEU* 3.6 26.9 - - - +
496X LYS 3.6 17.7 + - - -
502X GLN* 2.8 23.8 + - - +
503X LEU* 3.7 3.6 - - - -
505X GLY* 1.3 74.8 - - - +
507X LEU* 1.3 59.0 + - - +
509X GLU* 3.3 1.5 + - - -
510X ALA* 2.8 30.0 + - - +
519X ILE* 3.8 27.6 - - - -
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Residues in contact with LEU 507 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361X THR* 3.8 28.7 - - + +
362X LEU* 3.7 35.9 - - + +
365X MET* 3.9 20.2 - - + -
423X ILE* 5.7 2.2 - - + -
449X ILE* 5.1 7.0 - - + -
451X VAL* 4.6 7.2 - - + -
503X LEU* 2.8 38.1 + - + +
506X SER* 1.3 74.9 - - - +
508X GLN* 1.3 57.8 + - - +
510X ALA* 3.9 1.5 - - + +
511X LEU* 2.8 46.2 + - + +
519X ILE* 3.7 21.3 - - + -
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Residues in contact with GLN 508 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365X MET* 3.7 14.9 - - + +
504X LYS 3.0 16.6 + - - +
505X GLY* 3.6 9.1 - - - +
506X SER 3.3 0.2 - - - -
507X LEU* 1.3 77.0 - - - +
509X GLU* 1.3 63.4 - - - +
511X LEU* 3.5 4.4 + - - +
512X SER* 2.9 32.8 + - - +
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Residues in contact with GLU 509 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493X GLN* 2.9 30.6 + - - +
495X LEU* 4.0 22.2 - - + +
505X GLY 3.0 17.3 + - - +
506X SER* 3.8 3.9 - - - +
508X GLN* 1.3 79.1 - - - +
510X ALA* 1.3 63.1 + - - +
512X SER* 3.1 15.8 + - - -
513X ALA* 3.1 13.5 + - + +
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Residues in contact with ALA 510 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421X GLN* 5.3 1.0 - - - +
449X ILE* 3.8 23.3 - - + +
495X LEU* 4.4 0.2 - - - +
506X SER 2.8 18.0 + - - +
507X LEU* 3.9 3.6 - - + +
509X GLU* 1.3 76.6 - - - +
511X LEU* 1.3 64.0 + - - +
513X ALA* 3.1 17.0 + - - +
515X GLY 5.2 0.7 - - - +
517X VAL* 3.8 38.7 - - + +
519X ILE* 3.9 14.8 - - + -
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Residues in contact with LEU 511 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365X MET* 3.5 42.4 - - + +
366X ALA* 4.4 2.7 - - - +
367X PRO* 4.1 17.3 - - + -
421X GLN* 4.1 22.2 - - + +
423X ILE* 4.7 6.5 - - + -
449X ILE* 3.9 20.4 - - + -
507X LEU* 2.8 35.4 + - + +
508X GLN* 4.1 4.5 - - - +
510X ALA* 1.3 74.2 - - - +
512X SER* 1.3 58.7 + - - +
513X ALA 3.7 2.3 + - - +
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Residues in contact with SER 512 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508X GLN* 2.9 24.6 + - - +
509X GLU* 3.1 8.0 + - - -
510X ALA 3.1 0.8 - - - -
511X LEU* 1.3 75.9 - - - +
513X ALA* 1.3 65.9 + - - +
514X LYS* 3.9 18.3 + - - +
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Residues in contact with ALA 513 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447X PRO* 5.5 3.1 - - - +
493X GLN* 4.0 12.8 - - - +
509X GLU* 3.1 9.0 + - + +
510X ALA 3.1 17.1 + - - +
511X LEU 4.6 2.6 - - - +
512X SER* 1.3 83.3 - - - +
514X LYS* 1.3 68.0 + - - +
515X GLY 3.4 7.9 - - - +
517X VAL* 3.5 25.6 - - + -
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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