Contacts of the helix formed by residues 405 - 416 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A ASP* 3.4 16.3 - - - +
404A VAL* 1.3 85.6 - - + +
406A ARG* 1.3 60.8 + - - +
407A GLY 3.2 0.4 - - - -
408A PHE* 3.1 13.8 + - + +
409A CYS* 2.9 35.0 + - - -
437A ASN* 3.1 26.9 + - - +
405B GLU* 2.3 46.6 - - - +
437B ASN* 3.5 5.9 + - - +
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LYS* 3.5 47.2 - - - +
401A THR 3.6 22.9 - - - +
403A ASP* 3.4 27.3 + - + +
405A GLU* 1.3 79.0 - - - +
407A GLY* 1.3 56.3 + - - +
409A CYS* 3.3 22.1 + - - +
410A ASN* 2.9 59.2 + - - +
669A ARG 5.5 4.4 + - - -
670A GLN* 3.8 23.6 - - - +
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ASP 3.4 6.9 + - - -
404A VAL 3.3 9.6 + - - -
405A GLU 3.2 0.2 - - - -
406A ARG* 1.3 80.3 - - - +
408A PHE* 1.3 55.4 + - - +
410A ASN* 3.8 14.2 - - - +
411A LEU* 2.9 36.3 + - - +
443A LEU* 4.1 13.6 - - - +
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Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A VAL* 3.2 8.6 + - + -
405A GLU* 3.1 20.8 + - + +
407A GLY* 1.3 78.2 - - - +
409A CYS* 1.3 60.6 + - - +
411A LEU* 3.4 5.3 + - + +
412A LYS* 2.9 38.3 + - + +
420A PHE* 3.6 26.4 - + - -
424A GLN* 3.3 27.4 - - - -
434A MET* 4.0 31.2 - - + -
442A TYR* 4.3 5.2 - + - -
443A LEU* 5.4 7.0 - - + -
446A LEU* 3.4 24.9 - - + -
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Residues in contact with CYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLU* 2.9 18.8 + - - -
406A ARG* 3.7 26.7 - - - +
408A PHE* 1.3 73.9 - - - +
410A ASN* 1.3 61.6 + - - +
412A LYS* 4.4 5.4 - - - -
413A SER* 2.9 34.7 + - - -
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A THR* 3.4 24.6 - - + +
400A LYS 2.9 28.3 + - - +
401A THR* 5.2 0.2 - - - +
406A ARG* 2.9 54.2 + - - +
407A GLY* 3.8 11.0 - - - +
409A CYS* 1.3 76.5 - - - +
411A LEU* 1.3 55.4 + - + +
413A SER* 3.7 3.8 - - - -
414A ARG* 2.8 37.2 + - - +
669A ARG* 5.7 2.7 - - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A GLY 2.9 27.3 + - - +
408A PHE* 3.9 5.8 - - - +
410A ASN* 1.3 75.5 - - + +
412A LYS* 1.3 58.3 + - - +
414A ARG* 4.1 9.6 - - - +
415A TYR* 2.7 50.9 + - + +
420A PHE* 4.2 4.3 - - + -
443A LEU* 4.3 20.6 - - + -
446A LEU* 4.5 17.3 - - + -
447A GLU* 3.8 28.5 - - - +
450A LEU* 3.7 30.3 - - + -
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Residues in contact with LYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 5.4 7.6 - - - +
408A PHE* 2.9 25.2 + - + +
409A CYS* 3.9 5.8 - - - +
411A LEU* 1.3 75.4 - - - +
413A SER* 1.3 58.7 + - - +
416A GLY* 3.0 30.3 + - - -
417A THR* 3.7 23.5 + - - +
420A PHE* 3.7 45.5 - - + -
421A GLU* 5.0 8.3 + - - +
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN* 3.9 8.3 + - - -
409A CYS 2.9 19.8 + - - -
410A ASN* 3.7 3.1 - - - -
412A LYS* 1.3 79.1 - - - +
414A ARG* 1.3 62.5 + - - +
415A TYR 3.5 0.2 + - - -
416A GLY* 4.0 1.9 + - - -
668A TYR 4.7 0.3 + - - -
669A ARG* 2.8 32.4 + - - +
670A GLN 4.7 5.9 - - - -
671A ASP* 4.8 1.7 + - - -
672A LYS* 3.2 22.2 + - - +
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN* 3.7 10.2 + - - -
387A VAL* 3.5 29.0 + - + +
388A ASP* 3.2 27.3 + - - +
391A SER* 2.7 42.7 + - - -
410A ASN 2.8 22.8 + - - +
411A LEU* 3.1 11.3 + - - +
413A SER* 1.3 76.7 + - - +
415A TYR* 1.3 101.6 + - + +
447A GLU* 5.3 4.8 + - - -
451A ARG* 6.0 2.2 - - - +
669A ARG* 6.5 0.9 - - - -
672A LYS* 4.1 10.6 + - - +
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Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 5.3 6.2 + - - +
13A GLN* 4.3 5.5 + - - -
388A ASP* 5.5 0.2 - - - -
411A LEU* 2.7 37.5 + - + +
412A LYS 4.6 0.4 - - - +
414A ARG* 1.3 126.3 + - + +
416A GLY* 1.3 65.9 + - - +
419A ILE* 3.6 43.2 + - + +
420A PHE* 4.6 1.6 - - + +
447A GLU* 4.5 3.8 + - - -
450A LEU* 3.7 53.6 - - + +
451A ARG* 3.8 19.5 + - - +
454A LYS* 4.1 22.4 - - + -
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Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 6.1 1.3 - - - -
13A GLN* 4.4 25.1 - - - -
412A LYS 3.0 17.6 + - - -
413A SER 4.0 2.7 + - - -
414A ARG 3.7 1.2 - - - -
415A TYR* 1.3 80.6 - - - +
417A THR* 1.3 61.6 + - - -
418A GLN* 3.4 2.5 - - - -
419A ILE 3.4 1.7 + - - -
420A PHE* 3.0 26.7 + - - +
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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