Contacts of the helix formed by residues 399 - 412 (chain U) 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 ASP 399 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397U THR 4.1 0.8 + - - -
398U PHE* 1.3 77.0 - - - +
400U LYS* 1.3 66.4 + - - +
401U GLU* 4.1 9.9 - - + +
402U PHE* 3.2 15.7 + - + +
403U LEU* 3.1 22.1 + - - +
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Residues in contact with LYS 400 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373U SER 5.8 0.4 - - - -
374U SER* 4.4 24.8 - - - +
398U PHE 3.8 1.2 + - - -
399U ASP* 1.3 74.6 - - - +
401U GLU* 1.3 57.5 + - - +
403U LEU* 3.3 6.8 + - - +
404U LEU* 2.8 31.6 + - - +
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Residues in contact with GLU 401 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285U LEU* 5.9 6.2 - - + +
399U ASP* 3.2 5.4 - - + +
400U LYS* 1.3 78.8 - - - +
402U PHE* 1.3 58.1 + - - +
404U LEU* 4.0 5.7 - - - +
405U GLU* 3.0 31.0 + - - +
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Residues in contact with PHE 402 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281U VAL* 5.3 4.5 - - + +
285U LEU* 5.8 6.9 - - + +
398U PHE* 5.0 6.5 - - + -
399U ASP* 3.2 24.2 + - + +
400U LYS 3.2 0.2 - - - -
401U GLU* 1.3 76.1 - - - +
403U LEU* 1.3 58.9 + - - +
405U GLU* 3.3 3.9 + - - +
406U LEU* 2.8 33.1 + - - +
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Residues in contact with LEU 403 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374U SER* 4.9 4.9 - - - +
377U LEU* 3.9 28.1 - - + +
378U HIS* 4.8 9.0 - - + +
398U PHE* 5.3 7.5 - - + +
399U ASP 3.1 13.4 + - - +
400U LYS* 3.7 7.4 - - - +
402U PHE* 1.3 79.2 - - - +
404U LEU* 1.3 62.1 + - - +
406U LEU* 3.5 7.0 - - - +
407U LEU* 3.2 22.5 + - - +
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Residues in contact with LEU 404 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369U PHE* 5.6 12.0 - - + +
370U GLY* 5.7 7.4 - - - -
377U LEU* 5.1 3.3 - - - +
400U LYS 2.8 18.4 + - - +
401U GLU* 4.0 5.6 - - - +
403U LEU* 1.3 74.9 - - - +
405U GLU* 1.3 60.7 + - - +
407U LEU* 3.2 5.7 + - - +
408U VAL* 2.8 32.1 + - - +
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Residues in contact with GLU 405 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281U VAL* 5.2 12.7 - - + +
285U LEU* 6.1 4.3 - - + -
401U GLU 3.0 20.2 + - - +
402U PHE* 3.9 3.1 - - - +
404U LEU* 1.3 74.2 - - - +
406U LEU* 1.3 61.0 + - - +
408U VAL* 4.4 6.1 - - - -
409U SER* 2.9 36.5 + - - -
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Residues in contact with LEU 406 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278U HIS* 6.0 4.9 - - + -
281U VAL* 4.9 13.0 - - + +
381U ALA* 6.0 6.1 - - + -
402U PHE 2.8 18.1 + - - +
403U LEU* 3.5 9.9 - - - +
405U GLU* 1.3 80.2 - - - +
407U LEU* 1.3 61.0 + - - +
409U SER* 4.5 0.9 - - - -
410U ARG* 3.3 22.3 + - - +
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Residues in contact with LEU 407 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369U PHE* 5.5 11.2 - - + -
377U LEU* 6.1 3.4 - - + +
380U VAL* 6.3 3.4 - - + -
381U ALA* 6.2 4.3 - - + -
403U LEU 3.2 13.2 + - - +
404U LEU* 3.8 3.8 - - - +
406U LEU* 1.3 77.0 - - - +
408U VAL* 1.3 68.0 + - - +
410U ARG* 3.6 5.4 + - - +
411U HIS* 3.4 22.2 + - - +
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Residues in contact with VAL 408 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362U ARG* 5.5 7.0 - - + +
365U LEU* 4.6 23.1 - - + +
366U VAL* 5.5 5.2 - - + +
404U LEU* 2.8 20.3 + - + +
405U GLU* 4.2 5.2 - - - +
407U LEU* 1.3 73.8 - - - +
409U SER* 1.3 60.4 + - - +
411U HIS* 3.1 1.4 + - - -
412U GLU* 2.9 36.2 + - + +
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Residues in contact with SER 409 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281U VAL* 6.1 3.1 - - - -
405U GLU* 2.9 20.6 + - - -
406U LEU* 4.5 1.3 - - - -
408U VAL* 1.3 76.6 - - - +
410U ARG* 1.3 61.5 + - - +
411U HIS 3.5 0.3 + - - -
412U GLU* 4.1 10.0 + - - +
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Residues in contact with ARG 410 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333U ARG* 4.9 8.8 - - - +
406U LEU 3.3 18.6 + - - +
407U LEU* 3.8 5.8 - - - +
408U VAL 3.1 0.8 - - - -
409U SER* 1.3 81.4 - - - +
411U HIS* 1.3 57.6 + - + +
412U GLU 5.0 1.1 - - - +
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Residues in contact with HIS 411 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330U HIS* 5.4 6.1 - - - +
333U ARG* 5.4 11.2 - - + -
334U ILE* 5.6 11.4 - - + +
360U ASP* 3.7 17.0 - - - +
365U LEU* 5.9 5.2 - - + -
407U LEU 3.4 14.3 + - - +
408U VAL* 3.1 2.5 + - - +
410U ARG* 1.3 81.1 - - + +
412U GLU* 1.3 65.8 - - - +
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Residues in contact with GLU 412 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330U HIS* 5.9 2.9 - - - +
360U ASP 3.3 7.4 - - - -
361U THR 4.8 0.4 - - - -
362U ARG* 4.0 29.2 - - + +
365U LEU* 5.8 2.5 - - + -
408U VAL 2.9 17.6 + - - +
409U SER* 4.1 8.3 + - - +
410U ARG 3.8 1.3 - - - +
411U HIS* 1.3 81.4 - - - +
413U ARG* 1.3 71.6 + - - +
414U ARG* 3.5 4.3 + - - +
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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