Contacts of the helix formed by residues 3715 - 3731 (chain D) in PDB entry 6X34
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 ASP3715 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2119D ARG* 5.9 0.4 - - - +
3701D PHE* 6.0 0.4 - - + -
3713D ASP* 4.6 8.2 - - + +
3714D GLU* 1.3 82.5 - - - +
3716D TYR* 1.3 64.1 + - - +
3717D LEU* 3.1 16.6 - - + -
3718D TYR* 3.0 35.2 + - + +
3719D MET* 3.6 5.5 + - - +
3788D MET* 4.0 11.7 - - - +
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Residues in contact with TYR3716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2123D SER* 4.8 14.2 - - - -
2126D HIS* 6.2 4.5 - + - -
2127D ARG* 5.9 4.3 - - + -
3714D GLU* 3.5 15.4 - - + +
3715D ASP* 1.3 78.3 - - - +
3717D LEU* 1.3 77.5 + - + +
3719D MET* 3.7 7.2 + - - +
3720D ALA* 3.3 23.1 + - + +
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Residues in contact with LEU3717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119D ARG* 3.5 57.2 - - + +
2122D PHE* 5.6 4.9 - - + -
2123D SER* 5.3 12.6 - - - +
2126D HIS* 6.2 0.7 - - - -
3700D HIS* 4.5 10.1 - - + +
3701D PHE* 4.2 17.0 - - + -
3715D ASP* 3.1 20.8 - - + -
3716D TYR* 1.3 96.3 - - + +
3718D TYR* 1.3 71.9 + - - +
3720D ALA* 3.7 6.2 - - - +
3721D TYR* 3.5 34.7 + - + +
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Residues in contact with TYR3718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3701D PHE* 3.5 52.0 - + + +
3715D ASP* 3.0 21.1 + - + +
3717D LEU* 1.3 82.4 - - - +
3719D MET* 1.3 57.6 + - - +
3720D ALA 3.2 0.2 + - - -
3721D TYR* 3.5 1.4 + - + +
3722D ALA* 3.0 34.1 + - + +
3773D MET* 4.4 14.4 + - - +
3774D VAL* 5.3 3.5 - - - +
3777D MET* 3.8 25.7 - - + +
3788D MET* 3.7 25.8 - - + -
3791D SER* 6.5 0.4 - - - -
3792D THR* 3.4 33.7 - - + +
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Residues in contact with MET3719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3714D GLU 6.1 0.2 - - - +
3715D ASP 3.6 6.6 + - - +
3716D TYR* 3.7 7.8 + - - +
3717D LEU 3.5 0.2 - - - -
3718D TYR* 1.3 78.6 - - - +
3720D ALA* 1.3 64.0 + - - +
3722D ALA* 3.8 8.4 - - - +
3723D ASP* 3.6 19.2 + - - +
3787D ALA 6.1 0.7 - - - -
3788D MET* 5.7 7.1 - - + +
3791D SER* 4.0 22.2 - - - +
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Residues in contact with ALA3720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126D HIS* 3.4 36.2 - - + +
3716D TYR* 3.3 18.9 + - + +
3717D LEU* 3.7 9.4 - - - +
3718D TYR 3.1 1.0 - - - -
3719D MET* 1.3 79.8 - - - +
3721D TYR* 1.3 63.1 + - + +
3722D ALA 3.4 0.2 + - - -
3723D ASP* 3.7 2.6 + - - +
3724D ILE* 3.3 26.8 + - - +
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Residues in contact with TYR3721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2122D PHE* 2.3 50.4 + + + -
2123D SER* 4.9 1.3 - - - -
2125D LEU* 3.3 20.2 - - + +
2126D HIS* 3.3 30.0 + + + -
3673D LEU* 5.4 3.4 - - + -
3697D LEU* 4.3 23.3 - - + -
3701D PHE* 5.2 15.3 - + + -
3717D LEU* 3.5 24.9 + - + +
3718D TYR* 4.4 2.0 - - + +
3720D ALA* 1.3 80.0 - - + +
3722D ALA* 1.3 59.0 + - - +
3724D ILE* 3.8 15.9 - - + +
3725D MET* 2.9 43.1 + - + +
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Residues in contact with ALA3722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3718D TYR* 3.0 30.3 + - + +
3719D MET* 3.9 10.3 - - - +
3720D ALA 3.2 0.6 - - - -
3721D TYR* 1.3 78.3 - - - +
3723D ASP* 1.3 58.7 + - - +
3725D MET* 6.1 0.2 - - - -
3726D ALA* 3.0 32.1 + - - +
3791D SER* 4.3 26.9 - - - +
3792D THR* 5.8 1.1 - - + -
3795D LEU* 3.5 16.9 - - + +
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Residues in contact with ASP3723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3719D MET 3.6 12.6 + - - +
3720D ALA 4.3 3.1 - - - +
3721D TYR 3.4 0.2 - - - -
3722D ALA* 1.3 79.1 - - - +
3724D ILE* 1.3 62.8 + - + +
3726D ALA* 4.4 3.3 - - - +
3727D LYS* 3.2 26.7 + - - +
3794D LYS* 6.2 3.1 - - - -
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Residues in contact with ILE3724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126D HIS* 3.8 23.8 - - + +
3665D PHE* 3.6 30.3 - - + -
3666D GLU* 3.2 41.9 - - + +
3669D MET* 4.4 14.8 - - + -
3670D ILE* 4.8 6.7 - - + -
3720D ALA 3.3 20.2 + - - +
3721D TYR* 3.5 16.7 + - + +
3722D ALA 3.3 0.4 - - - -
3723D ASP* 1.3 81.0 - - + +
3725D MET* 1.3 59.9 + - - +
3728D SER* 3.0 17.2 + - - -
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Residues in contact with MET3725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3670D ILE* 4.4 19.1 - - + -
3694D LEU* 5.8 5.8 - - + -
3697D LEU* 5.1 20.6 - - + -
3698D VAL* 6.1 1.1 - - - +
3701D PHE* 6.3 2.7 - - + -
3721D TYR* 2.9 28.1 + - + +
3724D ILE* 1.3 77.1 - - - +
3726D ALA* 1.3 61.4 + - - +
3728D SER* 2.7 18.4 + - - +
3729D CYS* 3.5 11.6 + - - +
3765D LEU* 3.6 42.3 - - + +
3770D ALA* 5.2 7.0 - - - -
3795D LEU* 3.8 20.6 - - + -
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Residues in contact with ALA3726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3722D ALA 3.0 18.9 + - - +
3723D ASP* 4.4 3.8 - - - +
3725D MET* 1.3 74.5 - - - +
3727D LYS* 1.3 65.1 + - - +
3729D CYS* 3.4 0.7 + - - -
3730D HIS* 3.3 13.9 + - - +
3765D LEU* 6.0 0.2 - - - -
3794D LYS* 4.2 15.5 - - + +
3795D LEU* 3.8 32.3 - - + +
3798D SER* 3.2 24.8 + - - -
3799D ILE* 6.5 0.4 - - - -
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Residues in contact with LYS3727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3666D GLU* 3.9 16.4 - - + -
3723D ASP 3.2 20.4 + - - +
3725D MET 3.4 0.2 - - - -
3726D ALA* 1.3 78.2 - - - +
3728D SER* 1.3 57.2 + - - +
3730D HIS* 4.8 2.9 - - - +
3731D LEU* 2.9 35.9 + - + +
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Residues in contact with SER3728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3666D GLU* 3.2 30.7 - - - +
3667D ASP* 4.5 7.9 - - - +
3670D ILE* 3.6 16.7 - - - +
3724D ILE 3.0 9.4 + - - -
3725D MET* 2.7 26.3 + - - +
3727D LYS* 1.3 79.3 - - - +
3729D CYS* 1.3 60.2 + - - +
3731D LEU 3.8 12.8 - - - -
3761D GLN* 3.5 16.0 - - - +
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Residues in contact with CYS3729 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3725D MET 3.5 8.3 + - - +
3726D ALA* 3.4 3.3 + - - +
3727D LYS 3.3 0.6 - - - -
3728D SER* 1.3 82.3 + - - +
3730D HIS* 1.3 61.4 + - - +
3731D LEU 4.9 0.3 - - - +
3758D LEU* 4.6 13.1 - - - +
3761D GLN* 3.4 28.1 - - - +
3762D GLN* 4.0 24.9 - - - -
3765D LEU* 4.7 4.3 - - + -
3798D SER* 3.2 35.2 - - - +
3799D ILE* 3.9 20.4 - - + -
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Residues in contact with HIS3730 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3726D ALA 3.3 13.3 + - - +
3727D LYS* 4.4 2.9 - - - +
3729D CYS* 1.3 82.9 - - - +
3731D LEU* 1.3 62.9 + - + +
3758D LEU* 5.2 11.7 - - - +
3798D SER* 4.2 12.8 - - - +
3801D ASN* 5.0 14.4 - - - +
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Residues in contact with LEU3731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3667D ASP* 6.0 3.8 - - - -
3727D LYS* 2.9 22.4 + - + +
3728D SER* 3.8 13.4 - - - +
3729D CYS 4.9 0.7 - - - +
3730D HIS* 1.3 81.0 - - + +
3761D GLN* 5.2 5.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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