Contacts of the helix formed by residues 405 - 416 (chain B) in PDB entry 3F7F
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 GLU 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A GLU* 2.3 46.8 - - - +
437A ASN* 3.7 4.9 + - - +
403B ASP* 3.4 16.3 - - - +
404B VAL* 1.3 85.8 - - + +
406B ARG* 1.3 60.7 + - - +
407B GLY 3.2 0.4 - - - -
408B PHE* 3.1 13.9 + - + +
409B CYS* 2.9 35.3 + - - -
437B ASN* 3.2 27.2 - - + +
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Residues in contact with ARG 406 (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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400B LYS* 3.5 48.2 - - - +
401B THR 3.6 22.9 - - - +
403B ASP* 3.4 27.1 + - + +
405B GLU* 1.3 79.2 - - - +
407B GLY* 1.3 56.3 + - - +
409B CYS* 3.3 21.9 + - - +
410B ASN* 2.9 59.5 + - - +
669B ARG 5.5 4.8 + - - -
670B GLN* 3.9 23.4 - - - +
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Residues in contact with GLY 407 (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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403B ASP 3.3 6.9 + - - -
404B VAL 3.3 9.6 + - - -
405B GLU 3.2 0.2 - - - -
406B ARG* 1.3 79.6 - - - +
408B PHE* 1.3 56.1 + - - +
410B ASN* 3.8 14.0 - - - +
411B LEU* 2.9 36.1 + - - +
443B LEU* 4.1 13.6 - - - +
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Residues in contact with PHE 408 (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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437A ASN* 6.1 3.6 - - - -
404B VAL* 3.2 8.4 + - + -
405B GLU* 3.1 20.8 + - + +
407B GLY* 1.3 77.9 - - - +
409B CYS* 1.3 60.7 + - - +
411B LEU* 3.4 5.4 + - + +
412B LYS* 2.9 38.6 + - + +
420B PHE* 3.6 26.2 - + - -
424B GLN* 3.3 27.6 - - - -
434B MET* 3.9 30.7 - - + -
442B TYR* 4.3 5.2 - + - -
443B LEU* 5.4 7.0 - - + -
446B LEU* 3.4 24.9 - - + -
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Residues in contact with CYS 409 (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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405B GLU* 2.9 18.6 + - - -
406B ARG* 3.7 26.9 - - - +
408B PHE* 1.3 74.9 - - - +
410B ASN* 1.3 61.9 + - - +
412B LYS* 4.4 5.4 - - - -
413B SER* 2.9 34.3 + - - -
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Residues in contact with ASN 410 (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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399B THR* 3.4 25.3 - - + +
400B LYS 2.9 28.1 + - - +
401B THR* 5.2 0.2 - - - +
406B ARG* 2.9 54.0 + - - +
407B GLY* 3.8 10.8 - - - +
409B CYS* 1.3 77.1 - - - +
411B LEU* 1.3 55.6 + - + +
413B SER* 3.7 3.8 - - - -
414B ARG* 2.8 37.2 + - - +
669B ARG 5.7 2.4 - - - +
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Residues in contact with LEU 411 (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 GLY 2.9 26.4 + - - +
408B PHE* 3.9 4.7 - - - +
410B ASN* 1.3 76.2 - - + +
412B LYS* 1.3 56.8 + - - +
414B ARG* 4.1 10.1 - - - +
415B TYR* 2.7 51.0 + - + +
420B PHE* 4.2 3.8 - - + -
443B LEU* 4.3 20.4 - - + -
446B LEU* 4.4 18.6 - - + -
447B GLU* 3.8 28.9 - - - +
450B LEU* 3.7 31.0 - - + -
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Residues in contact with LYS 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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16B GLU* 5.4 7.8 - - - +
408B PHE* 2.9 24.8 + - + +
409B CYS* 3.9 5.8 - - - +
411B LEU* 1.3 75.2 - - - +
413B SER* 1.3 58.9 + - - +
416B GLY* 3.0 30.8 + - - -
417B THR* 3.7 24.1 + - - +
420B PHE* 3.7 45.7 - - + -
421B GLU* 5.0 8.1 + - - -
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Residues in contact with SER 413 (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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13B GLN* 3.9 8.3 + - - +
409B CYS 2.9 20.0 + - - -
410B ASN* 3.7 3.4 - - - -
412B LYS* 1.3 79.5 - - - +
414B ARG* 1.3 62.9 + - - +
415B TYR 3.5 0.2 + - - -
416B GLY* 4.0 1.9 + - - -
668B TYR 4.7 0.3 + - - -
669B ARG* 2.8 29.8 + - - +
670B GLN 4.8 5.5 - - - -
671B ASP* 4.9 0.9 + - - -
672B LYS* 3.2 25.5 + - - +
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Residues in contact with ARG 414 (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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13B GLN* 3.7 10.2 + - - -
387B VAL* 3.5 28.7 + - + +
388B ASP* 3.2 27.3 + - - +
391B SER* 2.7 42.9 + - - -
410B ASN 2.8 21.9 + - - +
411B LEU* 3.1 11.6 + - - +
413B SER* 1.3 76.7 + - - +
415B TYR* 1.3 101.2 + - + +
447B GLU* 5.3 5.1 + - - -
451B ARG* 5.9 2.2 - - - +
669B ARG* 6.5 0.4 - - - -
672B LYS* 4.2 10.6 + - - +
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Residues in contact with TYR 415 (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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10B ASN* 5.2 6.4 + - - +
13B GLN* 4.4 5.2 + - - -
388B ASP* 5.6 0.2 - - - -
411B LEU* 2.7 37.0 + - + +
412B LYS 4.6 0.4 - - - +
414B ARG* 1.3 125.7 + - + +
416B GLY* 1.3 62.9 + - - +
419B ILE* 3.6 46.0 + - + +
420B PHE* 4.6 1.6 - - + +
447B GLU* 4.5 3.5 + - - -
450B LEU* 3.6 52.9 - - + +
451B ARG* 3.8 19.2 + - - +
454B LYS* 4.1 22.9 - - + -
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Residues in contact with GLY 416 (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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10B ASN* 6.1 1.6 - - - -
13B GLN* 4.5 25.1 - - - -
412B LYS 3.0 17.7 + - - -
413B SER 4.0 2.7 + - - -
414B ARG 3.7 1.2 - - - -
415B TYR* 1.3 80.8 - - - +
417B THR* 1.3 61.6 + - - -
418B GLN* 3.4 2.7 - - - -
419B ILE 3.3 1.9 + - - -
420B PHE* 2.9 26.5 + - - +
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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