Contacts of the helix formed by residues 441 - 452 (chain A) in PDB entry 3VN4
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 THR 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ARG* 6.1 0.7 - - - -
439A GLU 5.5 0.9 - - - +
440A LYS* 1.3 77.6 - - - +
442A GLN* 1.3 65.2 + - - +
443A LEU* 3.7 4.7 + - - +
444A GLU* 2.9 50.1 + - - +
445A PHE* 3.0 13.0 + - - +
618A PRO* 4.2 22.9 - - + -
619A SER* 5.5 0.3 - - - -
622A GLU* 3.5 17.0 + - - +
2C BGC 4.9 0.2 + - - -
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Residues in contact with GLN 442 (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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398A ARG* 2.9 27.3 + - - +
401A GLY* 2.8 37.2 + - - -
441A THR* 1.3 70.8 - - - +
443A LEU* 1.3 60.7 + - - +
445A PHE* 3.4 8.9 + - - +
446A MET* 3.3 19.6 + - - +
505A GLY 4.1 0.3 - - - +
506A THR* 5.3 2.6 - - - +
507A ARG* 3.3 42.9 + - + +
621A LEU* 4.0 17.0 - - + +
622A GLU* 2.9 26.6 + - - +
623A ASP* 4.7 5.8 + - - +
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Residues in contact with LEU 443 (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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441A THR* 4.1 3.8 - - - +
442A GLN* 1.3 75.0 - - - +
444A GLU* 1.3 58.7 + - + +
446A MET* 3.4 4.6 + - + +
447A SER* 2.9 30.2 + - - +
472A ALA* 3.4 32.5 - - + -
474A VAL* 4.2 18.6 - - + -
618A PRO 5.1 1.8 - - - +
619A SER* 3.5 34.5 + - - +
621A LEU* 4.2 11.3 - - + +
622A GLU* 3.2 6.7 + - - +
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Residues in contact with GLU 444 (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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440A LYS* 3.4 29.9 - - + +
441A THR* 2.9 45.0 + - - +
443A LEU* 1.3 77.6 - - + +
445A PHE* 1.3 56.0 + - - +
447A SER* 3.6 7.3 - - - -
448A GLN* 2.6 45.9 + - + +
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Residues in contact with PHE 445 (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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398A ARG* 3.4 56.3 - - + +
441A THR 3.0 10.0 + - - +
442A GLN* 3.6 10.3 - - - +
443A LEU 3.4 0.2 - - - -
444A GLU* 1.3 75.1 - - - +
446A MET* 1.3 62.8 + - - +
448A GLN* 3.5 12.8 + - - +
449A GLN* 3.2 50.0 + - + +
452A ARG* 4.9 6.5 - - - -
503A LEU* 3.7 27.1 - - + -
506A THR* 3.3 27.6 - - + -
2C BGC 3.4 32.0 + - - +
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Residues in contact with MET 446 (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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442A GLN 3.3 8.8 + - - +
443A LEU* 3.6 9.6 - - - +
444A GLU 3.2 0.4 - - - -
445A PHE* 1.3 77.0 - - - +
447A SER* 1.3 65.5 + - - +
449A GLN* 3.1 14.9 + - - +
450A CYS* 3.0 21.5 + - - -
472A ALA* 3.9 25.1 - - + -
473A ALA 4.8 0.2 - - - -
474A VAL* 4.1 6.7 - - - -
482A LEU* 4.0 24.7 - - + -
502A PHE* 3.7 36.3 - - + -
506A THR* 3.7 14.4 - - + -
507A ARG 3.1 28.3 - - - +
508A CYS* 4.9 0.4 - - - -
522A CYS* 5.4 1.6 - - - -
621A LEU* 4.1 12.3 - - + -
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Residues in contact with SER 447 (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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443A LEU* 2.9 23.0 + - - +
444A GLU* 3.6 8.7 - - - -
446A MET* 1.3 75.0 - - - +
448A GLN* 1.3 53.8 - - - +
450A CYS* 2.7 11.1 + - - +
451A ALA* 2.7 37.7 + - - +
470A TRP 4.4 1.2 - - - +
471A GLY* 4.1 5.8 - - - -
472A ALA* 3.5 22.7 + - - +
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Residues in contact with GLN 448 (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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440A LYS* 3.2 31.5 - - - +
444A GLU* 2.6 28.7 + - + +
445A PHE* 3.5 11.8 - - - +
447A SER* 1.3 70.3 - - - +
449A GLN* 1.3 57.7 + - - +
451A ALA* 3.4 6.2 + - - +
452A ARG* 3.0 47.9 + - - +
2C BGC 2.6 50.5 + - - -
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Residues in contact with GLN 449 (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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445A PHE* 3.2 36.2 + - + +
446A MET* 3.1 8.8 + - - +
448A GLN* 1.3 79.0 - - - +
450A CYS* 1.3 61.9 + - - +
452A ARG* 3.6 37.9 - - - +
453A THR* 4.2 3.8 - - - +
485A HIS* 3.6 19.5 + - - +
501A SER 4.7 0.7 - - - +
502A PHE* 3.6 20.8 - - + -
503A LEU* 3.0 36.2 + - - +
506A THR* 3.0 29.9 + - - +
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Residues in contact with CYS 450 (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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446A MET 3.0 15.6 + - - +
447A SER 2.7 13.0 + - - +
449A GLN* 1.3 69.2 - - - +
451A ALA* 1.3 59.1 + - - +
452A ARG 3.0 5.1 + - - -
453A THR* 2.8 27.7 + - - -
470A TRP* 3.6 7.3 - - - +
471A GLY* 3.4 28.0 - - - +
472A ALA* 4.4 2.2 - - - -
485A HIS* 4.3 1.1 - - - -
486A MET 4.0 0.7 - - - -
487A CYS* 2.0 53.8 - - + -
502A PHE* 3.7 14.8 - - - -
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Residues in contact with ALA 451 (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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447A SER* 2.7 19.9 + - - +
448A GLN* 3.9 5.8 - - - +
450A CYS* 1.3 72.2 - - - +
452A ARG* 1.3 60.8 + - - +
453A THR 3.1 0.4 - - - -
454A ASP* 3.0 32.6 + - - +
469A HIS* 3.6 28.0 - - + -
470A TRP 3.8 6.0 + - - +
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Residues in contact with ARG 452 (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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445A PHE* 4.9 6.3 - - - -
448A GLN* 3.0 41.7 + - - +
449A GLN* 3.6 34.1 - - - +
450A CYS 3.0 0.6 + - - -
451A ALA* 1.3 77.7 - - - +
453A THR* 1.3 60.1 + - + +
454A ASP 3.4 0.7 + - - -
455A GLY 4.9 1.2 + - - -
503A LEU* 4.5 12.7 - - - +
2C BGC 6.0 0.6 - - - -
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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