Contacts of the helix formed by residues 406 - 418 (chain F) in PDB entry 6VVT
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 SER 406 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F LEU* 1.3 76.3 - - - +
407F GLU* 1.3 60.4 + - - +
408F ARG 3.4 4.2 + - - -
409F GLU* 3.3 20.6 + - - +
410F ALA* 2.5 35.6 + - - +
451F LYS* 6.2 0.4 - - - +
504F SO4 2.2 40.7 + - - -
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Residues in contact with GLU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F LEU 3.7 1.4 + - - -
406F SER* 1.3 77.5 + - - +
408F ARG* 1.3 62.3 + - - +
410F ALA* 3.5 5.3 + - - +
411F GLY* 3.2 15.9 + - - -
414F ARG* 5.3 1.0 + - - -
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Residues in contact with ARG 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F SER* 3.3 2.0 + - - -
407F GLU* 1.3 80.1 - - - +
409F GLU* 1.3 62.4 + - - +
411F GLY 3.2 0.5 + - - -
412F VAL* 3.0 27.0 + - + +
434F TYR* 3.1 46.0 + - + -
436F VAL* 5.4 7.1 - - - +
440F ARG* 4.6 3.8 - - - +
441F ILE* 6.5 0.4 - - - -
444F ILE* 3.9 19.8 - - - +
504F SO4 2.4 48.0 + - - +
1O G 5.1 2.2 - - - -
2O C 3.1 37.6 + - - -
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Residues in contact with GLU 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F LEU* 4.4 7.6 - - + -
406F SER* 3.0 35.8 + - - +
408F ARG* 1.3 79.3 - - - +
410F ALA* 1.3 62.7 + - - +
412F VAL* 3.4 8.2 + - - +
413F VAL* 3.1 27.0 + - - +
444F ILE* 3.9 11.2 - - + +
447F LYS* 3.9 7.4 - - - +
448F THR* 2.8 51.6 + - + +
451F LYS* 4.1 22.3 - - - +
504F SO4 3.8 14.6 + - - +
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Residues in contact with ALA 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F LEU* 3.5 37.6 - - + +
405F LEU* 4.1 11.6 - - + +
406F SER 2.5 20.3 + - - +
407F GLU* 3.8 6.3 - - - +
409F GLU* 1.3 73.3 - - - +
411F GLY* 1.3 62.0 + - - +
413F VAL* 3.2 5.9 + - - +
414F ARG* 3.0 36.3 + - - +
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Residues in contact with GLY 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407F GLU 3.2 8.5 + - - -
408F ARG 3.2 3.8 + - - -
410F ALA* 1.3 79.8 - - - +
412F VAL* 1.3 56.7 + - - +
414F ARG* 3.1 16.7 + - - +
415F LEU* 2.8 36.3 + - - +
434F TYR* 3.2 17.3 - - - -
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Residues in contact with VAL 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ARG* 3.0 29.0 + - + +
409F GLU* 3.7 8.7 - - - +
410F ALA 3.3 0.4 - - - -
411F GLY* 1.3 74.4 - - - +
413F VAL* 1.3 60.7 + - + +
415F LEU* 3.4 0.7 + - - +
416F ARG* 2.8 37.1 + - + +
430F ILE* 4.2 15.8 - - + +
434F TYR* 3.1 29.4 + - + -
441F ILE* 4.2 20.9 - - + -
444F ILE* 4.6 18.6 - - + -
445F GLU* 4.8 15.7 - - + -
448F THR* 5.5 0.2 - - + -
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Residues in contact with VAL 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811C LEU* 3.5 39.5 - - + -
402F LEU* 4.8 7.0 - - + -
405F LEU* 4.1 13.5 - - + -
409F GLU 3.1 17.3 - - - +
410F ALA* 3.2 6.7 + - - +
412F VAL* 1.3 75.9 - - + +
414F ARG* 1.3 64.9 + - - +
416F ARG* 4.5 4.3 - - - -
417F PHE* 3.2 30.0 + - + +
419F LEU* 4.6 1.5 - - + +
445F GLU* 6.1 3.6 - - + -
448F THR* 4.0 29.6 - - + +
449F MET* 5.6 1.1 - - - -
452F LEU* 4.7 6.7 - - + -
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Residues in contact with ARG 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F GLN* 3.6 23.2 + - - +
402F LEU* 3.1 42.8 - - + +
403F GLU* 4.9 4.4 + - - -
407F GLU 5.3 1.0 + - - -
410F ALA* 3.0 34.8 + - - +
411F GLY* 3.1 13.5 + - - +
413F VAL* 1.3 76.6 - - - +
415F LEU* 1.3 52.0 + - + +
418F GLY* 2.5 34.4 + - - -
419F LEU* 2.9 25.9 + - + -
420F THR* 4.1 28.3 - - + +
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Residues in contact with LEU 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411F GLY* 2.8 27.7 + - - +
412F VAL 4.0 2.0 - - - +
414F ARG* 1.3 73.9 - - + +
416F ARG* 1.3 64.8 + - - +
418F GLY* 3.2 9.1 + - - +
420F THR* 4.8 14.1 - - + -
421F ASP* 6.4 0.4 - - - -
424F PRO* 3.6 0.3 - - - +
425F ARG* 3.1 55.3 + - + +
430F ILE* 4.1 12.6 - - + -
433F VAL* 4.3 23.3 - - + -
434F TYR* 4.0 27.1 - - + +
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Residues in contact with ARG 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F VAL* 2.8 26.7 + - + +
413F VAL* 4.0 5.4 - - - +
414F ARG 3.3 0.2 - - - -
415F LEU* 1.3 73.7 - - - +
417F PHE* 1.3 71.9 + - + +
424F PRO* 3.4 17.2 - - - +
425F ARG 3.4 16.0 + - - +
426F THR* 3.6 0.2 - - - +
427F LEU* 3.5 28.0 - - - +
430F ILE* 3.4 19.7 - - + +
441F ILE* 5.9 0.7 - - + -
445F GLU* 3.6 35.6 + - + +
20P G 2.6 47.1 + - - -
21P T 5.0 2.6 + - - -
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Residues in contact with PHE 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807C PRO* 3.2 19.6 - - - +
810C ARG* 3.8 34.8 - - + +
811C LEU* 3.6 28.3 - - + -
814C ALA* 3.6 26.2 - - + -
413F VAL* 3.2 29.0 + - + +
415F LEU 3.2 0.2 - - - -
416F ARG* 1.3 89.7 - - + +
418F GLY* 1.3 62.5 + - - +
419F LEU* 4.3 15.3 - - + -
422F GLY 5.4 0.3 - - - -
424F PRO* 3.9 16.5 - - - +
445F GLU* 4.5 14.6 - - + -
449F MET* 4.7 6.7 - - - -
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Residues in contact with GLY 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807C PRO* 3.8 4.6 - - - +
414F ARG 2.5 15.2 + - - -
415F LEU* 3.2 7.4 + - - -
417F PHE* 1.3 75.8 - - - +
419F LEU* 1.3 57.3 + - - +
420F THR* 3.2 4.0 - - - -
421F ASP 4.8 1.6 - - - -
422F GLY* 2.7 32.7 + - - -
423F GLN 3.6 28.0 - - - -
424F PRO* 3.9 0.2 - - - +
425F ARG* 5.6 0.4 - - - -
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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