Contacts of the helix formed by residues 411 - 425 (chain B) in PDB entry 6FF7
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 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ASN 4.8 4.3 - - - +
413A LEU* 3.3 24.5 - - + +
415A SER 5.9 0.4 - - - +
410B LEU* 1.3 79.9 - - - +
412B ILE* 1.3 60.9 + - - +
413B ARG* 3.3 5.4 - - + +
414B PRO* 3.6 8.0 - - + +
415B LEU* 3.0 28.1 + - - +
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Residues in contact with ILE 412 (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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412A ASN 5.2 5.0 + - - +
413A LEU 3.9 7.0 + - - +
414A ARG* 5.3 8.4 - - + +
384B VAL 5.8 3.8 - - - +
385B VAL* 6.0 7.0 - - + -
411B ASN* 1.3 76.3 - - - +
413B ARG* 1.3 57.0 + - - +
415B LEU* 3.9 5.5 - - - +
416B LEU* 2.9 30.7 + - - +
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ASN* 3.3 3.7 - - + +
412B ILE* 1.3 77.8 - - - +
414B PRO* 1.4 58.2 - - - +
416B LEU* 3.4 5.3 + - - +
417B ARG* 2.9 28.4 + - - +
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Residues in contact with PRO 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG 5.0 11.2 - - - +
161B TYR* 6.0 3.6 - - + -
410B LEU* 4.6 13.2 - - + -
411B ASN* 3.6 12.3 - - + +
413B ARG* 1.4 73.9 - - - +
415B LEU* 1.3 60.8 + - - +
417B ARG* 3.8 6.5 - - + +
418B LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLU 4.7 15.0 - - - +
408B LEU* 5.3 6.3 - - - +
410B LEU* 4.6 8.8 - - + +
411B ASN 3.0 20.2 + - - +
412B ILE* 3.9 6.3 - - - +
414B PRO* 1.3 75.8 - - - +
416B LEU* 1.3 57.4 + - - +
418B LEU* 3.4 5.5 + - - +
419B VAL* 2.9 31.2 + - - +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TYR* 5.4 3.1 - - + -
384B VAL* 5.9 10.5 - - + +
385B VAL* 6.4 1.8 - - + -
412B ILE 2.9 19.7 + - - +
413B ARG* 3.7 6.7 - - - +
415B LEU* 1.3 76.8 - - - +
417B ARG* 1.3 55.4 + - - +
419B VAL* 3.4 3.9 + - - +
420B CYS* 3.0 33.1 + - - +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLN 4.7 4.7 - - - +
314B TYR* 4.1 31.9 - - + +
413B ARG 2.9 18.4 + - - +
414B PRO* 3.8 7.4 - - + +
416B LEU* 1.3 75.4 - - - +
418B LEU* 1.3 58.0 + - - +
420B CYS* 3.9 0.6 - - - -
421B LYS* 2.9 32.1 + - - +
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Residues in contact with LEU 418 (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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407B GLU* 5.8 7.0 - - + +
414B PRO 2.9 18.0 + - - +
415B LEU* 3.7 6.3 - - - +
417B ARG* 1.3 78.1 - - - +
419B VAL* 1.3 57.2 + - - +
421B LYS* 3.7 4.8 - - - +
422B LYS* 2.9 30.8 + - - +
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Residues in contact with VAL 419 (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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384B VAL* 6.0 6.1 - - + -
415B LEU 2.9 17.2 + - - +
416B LEU* 4.2 3.6 - - - +
418B LEU* 1.3 76.9 - - - +
420B CYS* 1.3 59.1 + - - +
422B LYS* 3.5 5.8 + - - +
423B PHE* 2.9 27.7 + - - +
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Residues in contact with CYS 420 (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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314B TYR* 4.8 15.0 - - + +
315B SER 4.9 2.2 - - - +
316B ILE* 5.4 8.6 - - + +
416B LEU 3.0 16.8 + - - +
417B ARG* 4.4 1.6 - - - +
419B VAL* 1.3 76.4 - - - +
421B LYS* 1.3 61.1 + - - +
423B PHE* 3.9 5.6 - - - +
424B PHE* 2.9 33.9 + - + +
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TYR 4.7 5.9 + - - +
315B SER* 4.6 15.0 - - - +
417B ARG 2.9 20.9 + - - +
418B LEU* 3.7 5.8 - - - +
420B CYS* 1.3 76.8 - - - +
422B LYS* 1.3 56.4 + - - +
425B GLY* 3.0 33.5 + - - +
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Residues in contact with LYS 422 (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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401B ILE* 5.6 10.8 - - + -
418B LEU 2.9 17.4 + - - +
419B VAL* 4.0 5.6 - - - +
421B LYS* 1.3 76.5 - - - +
423B PHE* 1.3 63.7 + - - +
425B GLY* 4.2 3.6 + - - -
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Residues in contact with PHE 423 (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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326B ILE* 5.3 7.6 - - - +
399B LEU* 6.3 3.6 - - + -
419B VAL 2.9 17.5 + - - +
420B CYS* 3.9 7.2 - - - +
421B LYS 3.3 0.4 - - - -
422B LYS* 1.3 80.4 - - - +
424B PHE* 1.3 63.3 + - - +
425B GLY* 3.4 0.9 + - - -
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Residues in contact with PHE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B SER 5.3 1.6 - - - +
316B ILE* 4.7 10.5 - - + -
317B CYS* 4.6 25.7 - - + +
326B ILE* 6.1 3.6 - - - +
420B CYS* 2.9 19.0 + - + +
421B LYS* 5.4 0.2 - - - -
423B PHE* 1.3 74.3 - - - +
425B GLY* 1.3 63.5 + - - +
426B GLU 3.2 12.2 + - - +
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Residues in contact with GLY 425 (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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152B GLN* 6.1 0.9 - - - +
315B SER 5.4 3.3 - - - +
421B LYS* 3.0 25.3 + - - +
422B LYS* 4.8 3.8 - - - -
423B PHE 3.3 3.5 - - - -
424B PHE* 1.3 73.9 - - - +
426B GLU* 1.3 60.4 + - - -
427B PHE 4.2 0.3 + - - -
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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